diff --git a/README b/README index 34a28f1..0034999 100644 --- a/README +++ b/README @@ -1,14 +1,23 @@ GTfold: A Scalable Multicore Code for RNA Secondary Structure Prediction -(C) 2007-2010, David A. Bader - Amrita Mathuriya +(C) 2007-2011, David A. Bader College of Computing, Georgia Institute of Technology Christine E. Heitsch School of Mathematics, Georgia Institute of Technology Stephen C. Harvey School of Biology, Georgia Institute of Technology - Sainath Mallidi - College of Computing, Georgia Institute of Technology + And various contributing authors + +This program is free software: you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation, either version 3 of the License, or +(at your option) any later version. +This program is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +GNU General Public License for more details. +You should have received a copy of the GNU General Public License +along with this program. If not, see . The prediction of the correct secondary structures of large RNAs is one of the unsolved challenges of computational molecular biology. @@ -28,8 +37,11 @@ DBI-04-20513. Additionally, the research of Christine E. Heitsch, Ph.D., is supported in part by a Career Award at the Scientific Interface (CASI) from the Burroughs Wellcome Fund (BWF). -Additional contributors to GTfold's implementation include Georgia -Tech visiting students Gregory Nou, Sonny Hernandez, and Manoj Soni. +Additional contributors to GTfold's implementation include +Georgia Tech graduate students Sainath Mallidi, Amrita Mathuriya, +and Prashant Gaurav, undergraduates Joshua Anderson and Andrew Ash +and visiting students Gregory Nou, Sonny Hernandez, Manoj Soni, +and Zsuzsanna Sukosd. INSTALLATION - Please execute the following commands @@ -110,4 +122,18 @@ Version History: 1.16 20 May 2010 Fixed another nasty bug with prohibited constraints handling. Earlier not used to update the WM array if a base pair is prohibited which is causing GTfold to trace partial structure. Some documentation added. - +2.0 11 July 2011 + Optimized the code to enable faster multiloop calculations + Added -d, --dangle to allow treatment of dangling end energies based on user input + Added -m --mismatch to enable terminal mismatch calculations + Added -o, --output, , -w --workdir options to allow to write output files/directories with desired name + Added -p --paramdir to allow user to provide custom parameters + Added -t, --threads to limit number of threads used + Added -v, --verbose to print loop-by-loop energy decomposition and confirm that constraints are satisfied + Added --prefilter to prohibit any basepair which does not have appropriate neighboring nucleotides + such that it could be part of a helix of length INT + Added --rnafold to run GTfold in RNAfold default mode (ViennaPackage version 1.8.5) + Added --unafold to run GTfold in UNAfold default mode (version 3.8) + Added --subopt NUM (Beta only) to produce all suboptimal structures whose energies are within NUM of the MFE + Added --bpp (Beta only) which outputs basepair probabilities based on the partition function + Added --useShape (Beta only) which allows the user to incorporate SHAPE-type data diff --git a/gtfold-mfe/AUTHORS b/gtfold-mfe/AUTHORS index 0f01d3b..0e9ed76 100644 --- a/gtfold-mfe/AUTHORS +++ b/gtfold-mfe/AUTHORS @@ -4,4 +4,5 @@ Amrita Mathuriya August 2007 - January 2009 Sainath Mallidi August 2009 - December 2010 Josh Anderson August 2010 - May 2011 Andrew Ash August 2010 - May 2011 +Zsuzsanna Sukosd February 2011 - June 2011 Prashant Gaurav August 2010 - diff --git a/gtfold-mfe/INSTALL b/gtfold-mfe/INSTALL index 54caf7c..7d1c323 100644 --- a/gtfold-mfe/INSTALL +++ b/gtfold-mfe/INSTALL @@ -1,13 +1,25 @@ -Copyright (C) 1994, 1995, 1996, 1999, 2000, 2001, 2002 Free Software -Foundation, Inc. +Installation Instructions +************************* - This file is free documentation; the Free Software Foundation gives -unlimited permission to copy, distribute and modify it. +Copyright (C) 1994, 1995, 1996, 1999, 2000, 2001, 2002, 2004, 2005, +2006, 2007, 2008, 2009 Free Software Foundation, Inc. + + Copying and distribution of this file, with or without modification, +are permitted in any medium without royalty provided the copyright +notice and this notice are preserved. This file is offered as-is, +without warranty of any kind. Basic Installation ================== - These are generic installation instructions. + Briefly, the shell commands `./configure; make; make install' should +configure, build, and install this package. The following +more-detailed instructions are generic; see the `README' file for +instructions specific to this package. Some packages provide this +`INSTALL' file but do not implement all of the features documented +below. The lack of an optional feature in a given package is not +necessarily a bug. More recommendations for GNU packages can be found +in *note Makefile Conventions: (standards)Makefile Conventions. The `configure' shell script attempts to guess correct values for various system-dependent variables used during compilation. It uses @@ -20,9 +32,9 @@ debugging `configure'). It can also use an optional file (typically called `config.cache' and enabled with `--cache-file=config.cache' or simply `-C') that saves -the results of its tests to speed up reconfiguring. (Caching is +the results of its tests to speed up reconfiguring. Caching is disabled by default to prevent problems with accidental use of stale -cache files.) +cache files. If you need to do unusual things to compile the package, please try to figure out how `configure' could check whether to do them, and mail @@ -32,30 +44,37 @@ some point `config.cache' contains results you don't want to keep, you may remove or edit it. The file `configure.ac' (or `configure.in') is used to create -`configure' by a program called `autoconf'. You only need -`configure.ac' if you want to change it or regenerate `configure' using -a newer version of `autoconf'. +`configure' by a program called `autoconf'. You need `configure.ac' if +you want to change it or regenerate `configure' using a newer version +of `autoconf'. -The simplest way to compile this package is: + The simplest way to compile this package is: 1. `cd' to the directory containing the package's source code and type - `./configure' to configure the package for your system. If you're - using `csh' on an old version of System V, you might need to type - `sh ./configure' instead to prevent `csh' from trying to execute - `configure' itself. + `./configure' to configure the package for your system. - Running `configure' takes awhile. While running, it prints some - messages telling which features it is checking for. + Running `configure' might take a while. While running, it prints + some messages telling which features it is checking for. 2. Type `make' to compile the package. 3. Optionally, type `make check' to run any self-tests that come with - the package. + the package, generally using the just-built uninstalled binaries. 4. Type `make install' to install the programs and any data files and - documentation. - - 5. You can remove the program binaries and object files from the + documentation. When installing into a prefix owned by root, it is + recommended that the package be configured and built as a regular + user, and only the `make install' phase executed with root + privileges. + + 5. Optionally, type `make installcheck' to repeat any self-tests, but + this time using the binaries in their final installed location. + This target does not install anything. Running this target as a + regular user, particularly if the prior `make install' required + root privileges, verifies that the installation completed + correctly. + + 6. You can remove the program binaries and object files from the source code directory by typing `make clean'. To also remove the files that `configure' created (so you can compile the package for a different kind of computer), type `make distclean'. There is @@ -64,6 +83,16 @@ The simplest way to compile this package is: all sorts of other programs in order to regenerate files that came with the distribution. + 7. Often, you can also type `make uninstall' to remove the installed + files again. In practice, not all packages have tested that + uninstallation works correctly, even though it is required by the + GNU Coding Standards. + + 8. Some packages, particularly those that use Automake, provide `make + distcheck', which can by used by developers to test that all other + targets like `make install' and `make uninstall' work correctly. + This target is generally not run by end users. + Compilers and Options ===================== @@ -75,7 +104,7 @@ for details on some of the pertinent environment variables. by setting variables in the command line or in the environment. Here is an example: - ./configure CC=c89 CFLAGS=-O2 LIBS=-lposix + ./configure CC=c99 CFLAGS=-g LIBS=-lposix *Note Defining Variables::, for more details. @@ -84,44 +113,89 @@ Compiling For Multiple Architectures You can compile the package for more than one kind of computer at the same time, by placing the object files for each architecture in their -own directory. To do this, you must use a version of `make' that -supports the `VPATH' variable, such as GNU `make'. `cd' to the +own directory. To do this, you can use GNU `make'. `cd' to the directory where you want the object files and executables to go and run the `configure' script. `configure' automatically checks for the -source code in the directory that `configure' is in and in `..'. +source code in the directory that `configure' is in and in `..'. This +is known as a "VPATH" build. - If you have to use a `make' that does not support the `VPATH' -variable, you have to compile the package for one architecture at a -time in the source code directory. After you have installed the -package for one architecture, use `make distclean' before reconfiguring -for another architecture. + With a non-GNU `make', it is safer to compile the package for one +architecture at a time in the source code directory. After you have +installed the package for one architecture, use `make distclean' before +reconfiguring for another architecture. + + On MacOS X 10.5 and later systems, you can create libraries and +executables that work on multiple system types--known as "fat" or +"universal" binaries--by specifying multiple `-arch' options to the +compiler but only a single `-arch' option to the preprocessor. Like +this: + + ./configure CC="gcc -arch i386 -arch x86_64 -arch ppc -arch ppc64" \ + CXX="g++ -arch i386 -arch x86_64 -arch ppc -arch ppc64" \ + CPP="gcc -E" CXXCPP="g++ -E" + + This is not guaranteed to produce working output in all cases, you +may have to build one architecture at a time and combine the results +using the `lipo' tool if you have problems. Installation Names ================== - By default, `make install' will install the package's files in -`/usr/local/bin', `/usr/local/man', etc. You can specify an -installation prefix other than `/usr/local' by giving `configure' the -option `--prefix=PATH'. + By default, `make install' installs the package's commands under +`/usr/local/bin', include files under `/usr/local/include', etc. You +can specify an installation prefix other than `/usr/local' by giving +`configure' the option `--prefix=PREFIX', where PREFIX must be an +absolute file name. You can specify separate installation prefixes for architecture-specific files and architecture-independent files. If you -give `configure' the option `--exec-prefix=PATH', the package will use -PATH as the prefix for installing programs and libraries. -Documentation and other data files will still use the regular prefix. +pass the option `--exec-prefix=PREFIX' to `configure', the package uses +PREFIX as the prefix for installing programs and libraries. +Documentation and other data files still use the regular prefix. In addition, if you use an unusual directory layout you can give -options like `--bindir=PATH' to specify different values for particular +options like `--bindir=DIR' to specify different values for particular kinds of files. Run `configure --help' for a list of the directories -you can set and what kinds of files go in them. +you can set and what kinds of files go in them. In general, the +default for these options is expressed in terms of `${prefix}', so that +specifying just `--prefix' will affect all of the other directory +specifications that were not explicitly provided. + + The most portable way to affect installation locations is to pass the +correct locations to `configure'; however, many packages provide one or +both of the following shortcuts of passing variable assignments to the +`make install' command line to change installation locations without +having to reconfigure or recompile. + + The first method involves providing an override variable for each +affected directory. For example, `make install +prefix=/alternate/directory' will choose an alternate location for all +directory configuration variables that were expressed in terms of +`${prefix}'. Any directories that were specified during `configure', +but not in terms of `${prefix}', must each be overridden at install +time for the entire installation to be relocated. The approach of +makefile variable overrides for each directory variable is required by +the GNU Coding Standards, and ideally causes no recompilation. +However, some platforms have known limitations with the semantics of +shared libraries that end up requiring recompilation when using this +method, particularly noticeable in packages that use GNU Libtool. + + The second method involves providing the `DESTDIR' variable. For +example, `make install DESTDIR=/alternate/directory' will prepend +`/alternate/directory' before all installation names. The approach of +`DESTDIR' overrides is not required by the GNU Coding Standards, and +does not work on platforms that have drive letters. On the other hand, +it does better at avoiding recompilation issues, and works well even +when some directory options were not specified in terms of `${prefix}' +at `configure' time. + +Optional Features +================= If the package supports it, you can cause programs to be installed with an extra prefix or suffix on their names by giving `configure' the option `--program-prefix=PREFIX' or `--program-suffix=SUFFIX'. -Optional Features -================= - Some packages pay attention to `--enable-FEATURE' options to `configure', where FEATURE indicates an optional part of the package. They may also pay attention to `--with-PACKAGE' options, where PACKAGE @@ -134,6 +208,45 @@ find the X include and library files automatically, but if it doesn't, you can use the `configure' options `--x-includes=DIR' and `--x-libraries=DIR' to specify their locations. + Some packages offer the ability to configure how verbose the +execution of `make' will be. For these packages, running `./configure +--enable-silent-rules' sets the default to minimal output, which can be +overridden with `make V=1'; while running `./configure +--disable-silent-rules' sets the default to verbose, which can be +overridden with `make V=0'. + +Particular systems +================== + + On HP-UX, the default C compiler is not ANSI C compatible. If GNU +CC is not installed, it is recommended to use the following options in +order to use an ANSI C compiler: + + ./configure CC="cc -Ae -D_XOPEN_SOURCE=500" + +and if that doesn't work, install pre-built binaries of GCC for HP-UX. + + On OSF/1 a.k.a. Tru64, some versions of the default C compiler cannot +parse its `' header file. The option `-nodtk' can be used as +a workaround. If GNU CC is not installed, it is therefore recommended +to try + + ./configure CC="cc" + +and if that doesn't work, try + + ./configure CC="cc -nodtk" + + On Solaris, don't put `/usr/ucb' early in your `PATH'. This +directory contains several dysfunctional programs; working variants of +these programs are available in `/usr/bin'. So, if you need `/usr/ucb' +in your `PATH', put it _after_ `/usr/bin'. + + On Haiku, software installed for all users goes in `/boot/common', +not `/usr/local'. It is recommended to use the following options: + + ./configure --prefix=/boot/common + Specifying the System Type ========================== @@ -149,14 +262,15 @@ type, such as `sun4', or a canonical name which has the form: where SYSTEM can have one of these forms: - OS KERNEL-OS + OS + KERNEL-OS See the file `config.sub' for the possible values of each field. If `config.sub' isn't included in this package, then this package doesn't need to know the machine type. If you are _building_ compiler tools for cross-compiling, you should -use the `--target=TYPE' option to select the type of system they will +use the option `--target=TYPE' to select the type of system they will produce code for. If you want to _use_ a cross compiler, that generates code for a @@ -186,9 +300,14 @@ them in the `configure' command line, using `VAR=value'. For example: ./configure CC=/usr/local2/bin/gcc -will cause the specified gcc to be used as the C compiler (unless it is +causes the specified `gcc' to be used as the C compiler (unless it is overridden in the site shell script). +Unfortunately, this technique does not work for `CONFIG_SHELL' due to +an Autoconf bug. Until the bug is fixed you can use this workaround: + + CONFIG_SHELL=/bin/bash /bin/bash ./configure CONFIG_SHELL=/bin/bash + `configure' Invocation ====================== @@ -197,7 +316,14 @@ operates. `--help' `-h' - Print a summary of the options to `configure', and exit. + Print a summary of all of the options to `configure', and exit. + +`--help=short' +`--help=recursive' + Print a summary of the options unique to this package's + `configure', and exit. The `short' variant lists options used + only in the top level, while the `recursive' variant lists options + also present in any nested packages. `--version' `-V' @@ -224,6 +350,16 @@ operates. Look for the package's source code in directory DIR. Usually `configure' can determine that directory automatically. +`--prefix=DIR' + Use DIR as the installation prefix. *note Installation Names:: + for more details, including other options available for fine-tuning + the installation locations. + +`--no-create' +`-n' + Run the configure checks, but stop before creating any output + files. + `configure' also accepts some other, not widely useful, options. Run `configure --help' for more details. diff --git a/gtfold-mfe/Makefile.in b/gtfold-mfe/Makefile.in index 61df044..5f77d42 100644 --- a/gtfold-mfe/Makefile.in +++ b/gtfold-mfe/Makefile.in @@ -1,4 +1,4 @@ -# Makefile.in generated by automake 1.11.1 from Makefile.am. +# Makefile.in generated by automake 1.11 from Makefile.am. # @configure_input@ # Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, @@ -39,7 +39,7 @@ subdir = . DIST_COMMON = README $(am__configure_deps) $(include_HEADERS) \ $(srcdir)/Makefile.am $(srcdir)/Makefile.in \ $(srcdir)/gtfold_config.h.in $(top_srcdir)/configure AUTHORS \ - COPYING ChangeLog INSTALL NEWS TODO config.guess config.sub \ + COPYING ChangeLog INSTALL config.guess config.sub \ depcomp install-sh missing ACLOCAL_M4 = $(top_srcdir)/aclocal.m4 am__aclocal_m4_deps = $(top_srcdir)/configure.in @@ -167,7 +167,6 @@ PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@ PACKAGE_NAME = @PACKAGE_NAME@ PACKAGE_STRING = @PACKAGE_STRING@ PACKAGE_TARNAME = @PACKAGE_TARNAME@ -PACKAGE_URL = @PACKAGE_URL@ PACKAGE_VERSION = @PACKAGE_VERSION@ PATH_SEPARATOR = @PATH_SEPARATOR@ SET_MAKE = @SET_MAKE@ @@ -320,7 +319,7 @@ uninstall-includeHEADERS: # (which will cause the Makefiles to be regenerated when you run `make'); # (2) otherwise, pass the desired values on the `make' command line. $(RECURSIVE_TARGETS): - @fail= failcom='exit 1'; \ + @failcom='exit 1'; \ for f in x $$MAKEFLAGS; do \ case $$f in \ *=* | --[!k]*);; \ @@ -345,7 +344,7 @@ $(RECURSIVE_TARGETS): fi; test -z "$$fail" $(RECURSIVE_CLEAN_TARGETS): - @fail= failcom='exit 1'; \ + @failcom='exit 1'; \ for f in x $$MAKEFLAGS; do \ case $$f in \ *=* | --[!k]*);; \ @@ -509,8 +508,7 @@ distdir: $(DISTFILES) fi; \ done -test -n "$(am__skip_mode_fix)" \ - || find "$(distdir)" -type d ! -perm -755 \ - -exec chmod u+rwx,go+rx {} \; -o \ + || find "$(distdir)" -type d ! -perm -777 -exec chmod a+rwx {} \; -o \ ! -type d ! -perm -444 -links 1 -exec chmod a+r {} \; -o \ ! -type d ! -perm -400 -exec chmod a+r {} \; -o \ ! -type d ! -perm -444 -exec $(install_sh) -c -m a+r {} {} \; \ @@ -554,17 +552,17 @@ dist dist-all: distdir distcheck: dist case '$(DIST_ARCHIVES)' in \ *.tar.gz*) \ - GZIP=$(GZIP_ENV) gzip -dc $(distdir).tar.gz | $(am__untar) ;;\ + GZIP=$(GZIP_ENV) gunzip -c $(distdir).tar.gz | $(am__untar) ;;\ *.tar.bz2*) \ - bzip2 -dc $(distdir).tar.bz2 | $(am__untar) ;;\ + bunzip2 -c $(distdir).tar.bz2 | $(am__untar) ;;\ *.tar.lzma*) \ - lzma -dc $(distdir).tar.lzma | $(am__untar) ;;\ + unlzma -c $(distdir).tar.lzma | $(am__untar) ;;\ *.tar.xz*) \ xz -dc $(distdir).tar.xz | $(am__untar) ;;\ *.tar.Z*) \ uncompress -c $(distdir).tar.Z | $(am__untar) ;;\ *.shar.gz*) \ - GZIP=$(GZIP_ENV) gzip -dc $(distdir).shar.gz | unshar ;;\ + GZIP=$(GZIP_ENV) gunzip -c $(distdir).shar.gz | unshar ;;\ *.zip*) \ unzip $(distdir).zip ;;\ esac diff --git a/gtfold-mfe/README b/gtfold-mfe/README index 34a28f1..0034999 100644 --- a/gtfold-mfe/README +++ b/gtfold-mfe/README @@ -1,14 +1,23 @@ GTfold: A Scalable Multicore Code for RNA Secondary Structure Prediction -(C) 2007-2010, David A. Bader - Amrita Mathuriya +(C) 2007-2011, David A. Bader College of Computing, Georgia Institute of Technology Christine E. Heitsch School of Mathematics, Georgia Institute of Technology Stephen C. Harvey School of Biology, Georgia Institute of Technology - Sainath Mallidi - College of Computing, Georgia Institute of Technology + And various contributing authors + +This program is free software: you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation, either version 3 of the License, or +(at your option) any later version. +This program is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +GNU General Public License for more details. +You should have received a copy of the GNU General Public License +along with this program. If not, see . The prediction of the correct secondary structures of large RNAs is one of the unsolved challenges of computational molecular biology. @@ -28,8 +37,11 @@ DBI-04-20513. Additionally, the research of Christine E. Heitsch, Ph.D., is supported in part by a Career Award at the Scientific Interface (CASI) from the Burroughs Wellcome Fund (BWF). -Additional contributors to GTfold's implementation include Georgia -Tech visiting students Gregory Nou, Sonny Hernandez, and Manoj Soni. +Additional contributors to GTfold's implementation include +Georgia Tech graduate students Sainath Mallidi, Amrita Mathuriya, +and Prashant Gaurav, undergraduates Joshua Anderson and Andrew Ash +and visiting students Gregory Nou, Sonny Hernandez, Manoj Soni, +and Zsuzsanna Sukosd. INSTALLATION - Please execute the following commands @@ -110,4 +122,18 @@ Version History: 1.16 20 May 2010 Fixed another nasty bug with prohibited constraints handling. Earlier not used to update the WM array if a base pair is prohibited which is causing GTfold to trace partial structure. Some documentation added. - +2.0 11 July 2011 + Optimized the code to enable faster multiloop calculations + Added -d, --dangle to allow treatment of dangling end energies based on user input + Added -m --mismatch to enable terminal mismatch calculations + Added -o, --output, , -w --workdir options to allow to write output files/directories with desired name + Added -p --paramdir to allow user to provide custom parameters + Added -t, --threads to limit number of threads used + Added -v, --verbose to print loop-by-loop energy decomposition and confirm that constraints are satisfied + Added --prefilter to prohibit any basepair which does not have appropriate neighboring nucleotides + such that it could be part of a helix of length INT + Added --rnafold to run GTfold in RNAfold default mode (ViennaPackage version 1.8.5) + Added --unafold to run GTfold in UNAfold default mode (version 3.8) + Added --subopt NUM (Beta only) to produce all suboptimal structures whose energies are within NUM of the MFE + Added --bpp (Beta only) which outputs basepair probabilities based on the partition function + Added --useShape (Beta only) which allows the user to incorporate SHAPE-type data diff --git a/gtfold-mfe/TODO b/gtfold-mfe/TODO deleted file mode 100644 index 366385a..0000000 --- a/gtfold-mfe/TODO +++ /dev/null @@ -1,7 +0,0 @@ -Make single-letter options work - -Partition Function -================== - - - fast inner loops optimization - - factor in dangling energies diff --git a/gtfold-mfe/aclocal.m4 b/gtfold-mfe/aclocal.m4 index f5a02ce..eba341b 100644 --- a/gtfold-mfe/aclocal.m4 +++ b/gtfold-mfe/aclocal.m4 @@ -406,18 +406,6 @@ AC_DEFUN([AM_OUTPUT_DEPENDENCY_COMMANDS], [AMDEP_TRUE="$AMDEP_TRUE" ac_aux_dir="$ac_aux_dir"]) ]) -# Copyright (C) 1996, 1997, 2000, 2001, 2003, 2005 -# Free Software Foundation, Inc. -# -# This file is free software; the Free Software Foundation -# gives unlimited permission to copy and/or distribute it, -# with or without modifications, as long as this notice is preserved. - -# serial 8 - -# AM_CONFIG_HEADER is obsolete. It has been replaced by AC_CONFIG_HEADERS. -AU_DEFUN([AM_CONFIG_HEADER], [AC_CONFIG_HEADERS($@)]) - # Do all the work for Automake. -*- Autoconf -*- # Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004, diff --git a/gtfold-mfe/config.guess b/gtfold-mfe/config.guess old mode 100644 new mode 100755 index ca2a03c..c2246a4 --- a/gtfold-mfe/config.guess +++ b/gtfold-mfe/config.guess @@ -1,10 +1,10 @@ #! /bin/sh # Attempt to guess a canonical system name. # Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, -# 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008 +# 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010 # Free Software Foundation, Inc. -timestamp='2008-01-08' +timestamp='2009-12-30' # This file is free software; you can redistribute it and/or modify it # under the terms of the GNU General Public License as published by @@ -27,16 +27,16 @@ timestamp='2008-01-08' # the same distribution terms that you use for the rest of that program. -# Originally written by Per Bothner . -# Please send patches to . Submit a context -# diff and a properly formatted ChangeLog entry. +# Originally written by Per Bothner. Please send patches (context +# diff format) to and include a ChangeLog +# entry. # # This script attempts to guess a canonical system name similar to # config.sub. If it succeeds, it prints the system name on stdout, and # exits with 0. Otherwise, it exits with 1. # -# The plan is that this can be called by configure scripts if you -# don't specify an explicit build system type. +# You can get the latest version of this script from: +# http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.guess;hb=HEAD me=`echo "$0" | sed -e 's,.*/,,'` @@ -56,8 +56,9 @@ version="\ GNU config.guess ($timestamp) Originally written by Per Bothner. -Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, -2002, 2003, 2004, 2005, 2006, 2007, 2008 Free Software Foundation, Inc. +Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, +2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010 Free +Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE." @@ -170,7 +171,7 @@ case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in arm*|i386|m68k|ns32k|sh3*|sparc|vax) eval $set_cc_for_build if echo __ELF__ | $CC_FOR_BUILD -E - 2>/dev/null \ - | grep __ELF__ >/dev/null + | grep -q __ELF__ then # Once all utilities can be ECOFF (netbsdecoff) or a.out (netbsdaout). # Return netbsd for either. FIX? @@ -324,14 +325,33 @@ case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in case `/usr/bin/uname -p` in sparc) echo sparc-icl-nx7; exit ;; esac ;; + s390x:SunOS:*:*) + echo ${UNAME_MACHINE}-ibm-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` + exit ;; sun4H:SunOS:5.*:*) echo sparc-hal-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` exit ;; sun4*:SunOS:5.*:* | tadpole*:SunOS:5.*:*) echo sparc-sun-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` exit ;; + i86pc:AuroraUX:5.*:* | i86xen:AuroraUX:5.*:*) + echo i386-pc-auroraux${UNAME_RELEASE} + exit ;; i86pc:SunOS:5.*:* | i86xen:SunOS:5.*:*) - echo i386-pc-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` + eval $set_cc_for_build + SUN_ARCH="i386" + # If there is a compiler, see if it is configured for 64-bit objects. + # Note that the Sun cc does not turn __LP64__ into 1 like gcc does. + # This test works for both compilers. + if [ "$CC_FOR_BUILD" != 'no_compiler_found' ]; then + if (echo '#ifdef __amd64'; echo IS_64BIT_ARCH; echo '#endif') | \ + (CCOPTS= $CC_FOR_BUILD -E - 2>/dev/null) | \ + grep IS_64BIT_ARCH >/dev/null + then + SUN_ARCH="x86_64" + fi + fi + echo ${SUN_ARCH}-pc-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` exit ;; sun4*:SunOS:6*:*) # According to config.sub, this is the proper way to canonicalize @@ -640,7 +660,7 @@ EOF # => hppa64-hp-hpux11.23 if echo __LP64__ | (CCOPTS= $CC_FOR_BUILD -E - 2>/dev/null) | - grep __LP64__ >/dev/null + grep -q __LP64__ then HP_ARCH="hppa2.0w" else @@ -791,12 +811,12 @@ EOF i*:PW*:*) echo ${UNAME_MACHINE}-pc-pw32 exit ;; - *:Interix*:[3456]*) + *:Interix*:*) case ${UNAME_MACHINE} in x86) echo i586-pc-interix${UNAME_RELEASE} exit ;; - EM64T | authenticamd) + authenticamd | genuineintel | EM64T) echo x86_64-unknown-interix${UNAME_RELEASE} exit ;; IA64) @@ -806,6 +826,9 @@ EOF [345]86:Windows_95:* | [345]86:Windows_98:* | [345]86:Windows_NT:*) echo i${UNAME_MACHINE}-pc-mks exit ;; + 8664:Windows_NT:*) + echo x86_64-pc-mks + exit ;; i*:Windows_NT*:* | Pentium*:Windows_NT*:*) # How do we know it's Interix rather than the generic POSIX subsystem? # It also conflicts with pre-2.0 versions of AT&T UWIN. Should we @@ -835,6 +858,20 @@ EOF i*86:Minix:*:*) echo ${UNAME_MACHINE}-pc-minix exit ;; + alpha:Linux:*:*) + case `sed -n '/^cpu model/s/^.*: \(.*\)/\1/p' < /proc/cpuinfo` in + EV5) UNAME_MACHINE=alphaev5 ;; + EV56) UNAME_MACHINE=alphaev56 ;; + PCA56) UNAME_MACHINE=alphapca56 ;; + PCA57) UNAME_MACHINE=alphapca56 ;; + EV6) UNAME_MACHINE=alphaev6 ;; + EV67) UNAME_MACHINE=alphaev67 ;; + EV68*) UNAME_MACHINE=alphaev68 ;; + esac + objdump --private-headers /bin/sh | grep -q ld.so.1 + if test "$?" = 0 ; then LIBC="libc1" ; else LIBC="" ; fi + echo ${UNAME_MACHINE}-unknown-linux-gnu${LIBC} + exit ;; arm*:Linux:*:*) eval $set_cc_for_build if echo __ARM_EABI__ | $CC_FOR_BUILD -E - 2>/dev/null \ @@ -857,6 +894,17 @@ EOF frv:Linux:*:*) echo frv-unknown-linux-gnu exit ;; + i*86:Linux:*:*) + LIBC=gnu + eval $set_cc_for_build + sed 's/^ //' << EOF >$dummy.c + #ifdef __dietlibc__ + LIBC=dietlibc + #endif +EOF + eval `$CC_FOR_BUILD -E $dummy.c 2>/dev/null | grep '^LIBC'` + echo "${UNAME_MACHINE}-pc-linux-${LIBC}" + exit ;; ia64:Linux:*:*) echo ${UNAME_MACHINE}-unknown-linux-gnu exit ;; @@ -866,74 +914,33 @@ EOF m68*:Linux:*:*) echo ${UNAME_MACHINE}-unknown-linux-gnu exit ;; - mips:Linux:*:*) - eval $set_cc_for_build - sed 's/^ //' << EOF >$dummy.c - #undef CPU - #undef mips - #undef mipsel - #if defined(__MIPSEL__) || defined(__MIPSEL) || defined(_MIPSEL) || defined(MIPSEL) - CPU=mipsel - #else - #if defined(__MIPSEB__) || defined(__MIPSEB) || defined(_MIPSEB) || defined(MIPSEB) - CPU=mips - #else - CPU= - #endif - #endif -EOF - eval "`$CC_FOR_BUILD -E $dummy.c 2>/dev/null | sed -n ' - /^CPU/{ - s: ::g - p - }'`" - test x"${CPU}" != x && { echo "${CPU}-unknown-linux-gnu"; exit; } - ;; - mips64:Linux:*:*) + mips:Linux:*:* | mips64:Linux:*:*) eval $set_cc_for_build sed 's/^ //' << EOF >$dummy.c #undef CPU - #undef mips64 - #undef mips64el + #undef ${UNAME_MACHINE} + #undef ${UNAME_MACHINE}el #if defined(__MIPSEL__) || defined(__MIPSEL) || defined(_MIPSEL) || defined(MIPSEL) - CPU=mips64el + CPU=${UNAME_MACHINE}el #else #if defined(__MIPSEB__) || defined(__MIPSEB) || defined(_MIPSEB) || defined(MIPSEB) - CPU=mips64 + CPU=${UNAME_MACHINE} #else CPU= #endif #endif EOF - eval "`$CC_FOR_BUILD -E $dummy.c 2>/dev/null | sed -n ' - /^CPU/{ - s: ::g - p - }'`" + eval `$CC_FOR_BUILD -E $dummy.c 2>/dev/null | grep '^CPU'` test x"${CPU}" != x && { echo "${CPU}-unknown-linux-gnu"; exit; } ;; or32:Linux:*:*) echo or32-unknown-linux-gnu exit ;; - ppc:Linux:*:*) - echo powerpc-unknown-linux-gnu - exit ;; - ppc64:Linux:*:*) - echo powerpc64-unknown-linux-gnu + padre:Linux:*:*) + echo sparc-unknown-linux-gnu exit ;; - alpha:Linux:*:*) - case `sed -n '/^cpu model/s/^.*: \(.*\)/\1/p' < /proc/cpuinfo` in - EV5) UNAME_MACHINE=alphaev5 ;; - EV56) UNAME_MACHINE=alphaev56 ;; - PCA56) UNAME_MACHINE=alphapca56 ;; - PCA57) UNAME_MACHINE=alphapca56 ;; - EV6) UNAME_MACHINE=alphaev6 ;; - EV67) UNAME_MACHINE=alphaev67 ;; - EV68*) UNAME_MACHINE=alphaev68 ;; - esac - objdump --private-headers /bin/sh | grep ld.so.1 >/dev/null - if test "$?" = 0 ; then LIBC="libc1" ; else LIBC="" ; fi - echo ${UNAME_MACHINE}-unknown-linux-gnu${LIBC} + parisc64:Linux:*:* | hppa64:Linux:*:*) + echo hppa64-unknown-linux-gnu exit ;; parisc:Linux:*:* | hppa:Linux:*:*) # Look for CPU level @@ -943,8 +950,11 @@ EOF *) echo hppa-unknown-linux-gnu ;; esac exit ;; - parisc64:Linux:*:* | hppa64:Linux:*:*) - echo hppa64-unknown-linux-gnu + ppc64:Linux:*:*) + echo powerpc64-unknown-linux-gnu + exit ;; + ppc:Linux:*:*) + echo powerpc-unknown-linux-gnu exit ;; s390:Linux:*:* | s390x:Linux:*:*) echo ${UNAME_MACHINE}-ibm-linux @@ -967,69 +977,6 @@ EOF xtensa*:Linux:*:*) echo ${UNAME_MACHINE}-unknown-linux-gnu exit ;; - i*86:Linux:*:*) - # The BFD linker knows what the default object file format is, so - # first see if it will tell us. cd to the root directory to prevent - # problems with other programs or directories called `ld' in the path. - # Set LC_ALL=C to ensure ld outputs messages in English. - ld_supported_targets=`cd /; LC_ALL=C ld --help 2>&1 \ - | sed -ne '/supported targets:/!d - s/[ ][ ]*/ /g - s/.*supported targets: *// - s/ .*// - p'` - case "$ld_supported_targets" in - elf32-i386) - TENTATIVE="${UNAME_MACHINE}-pc-linux-gnu" - ;; - a.out-i386-linux) - echo "${UNAME_MACHINE}-pc-linux-gnuaout" - exit ;; - coff-i386) - echo "${UNAME_MACHINE}-pc-linux-gnucoff" - exit ;; - "") - # Either a pre-BFD a.out linker (linux-gnuoldld) or - # one that does not give us useful --help. - echo "${UNAME_MACHINE}-pc-linux-gnuoldld" - exit ;; - esac - # Determine whether the default compiler is a.out or elf - eval $set_cc_for_build - sed 's/^ //' << EOF >$dummy.c - #include - #ifdef __ELF__ - # ifdef __GLIBC__ - # if __GLIBC__ >= 2 - LIBC=gnu - # else - LIBC=gnulibc1 - # endif - # else - LIBC=gnulibc1 - # endif - #else - #if defined(__INTEL_COMPILER) || defined(__PGI) || defined(__SUNPRO_C) || defined(__SUNPRO_CC) - LIBC=gnu - #else - LIBC=gnuaout - #endif - #endif - #ifdef __dietlibc__ - LIBC=dietlibc - #endif -EOF - eval "`$CC_FOR_BUILD -E $dummy.c 2>/dev/null | sed -n ' - /^LIBC/{ - s: ::g - p - }'`" - test x"${LIBC}" != x && { - echo "${UNAME_MACHINE}-pc-linux-${LIBC}" - exit - } - test x"${TENTATIVE}" != x && { echo "${TENTATIVE}"; exit; } - ;; i*86:DYNIX/ptx:4*:*) # ptx 4.0 does uname -s correctly, with DYNIX/ptx in there. # earlier versions are messed up and put the nodename in both @@ -1058,7 +1005,7 @@ EOF i*86:syllable:*:*) echo ${UNAME_MACHINE}-pc-syllable exit ;; - i*86:LynxOS:2.*:* | i*86:LynxOS:3.[01]*:* | i*86:LynxOS:4.0*:*) + i*86:LynxOS:2.*:* | i*86:LynxOS:3.[01]*:* | i*86:LynxOS:4.[02]*:*) echo i386-unknown-lynxos${UNAME_RELEASE} exit ;; i*86:*DOS:*:*) @@ -1102,8 +1049,11 @@ EOF pc:*:*:*) # Left here for compatibility: # uname -m prints for DJGPP always 'pc', but it prints nothing about - # the processor, so we play safe by assuming i386. - echo i386-pc-msdosdjgpp + # the processor, so we play safe by assuming i586. + # Note: whatever this is, it MUST be the same as what config.sub + # prints for the "djgpp" host, or else GDB configury will decide that + # this is a cross-build. + echo i586-pc-msdosdjgpp exit ;; Intel:Mach:3*:*) echo i386-pc-mach3 @@ -1141,6 +1091,16 @@ EOF 3[34]??:*:4.0:* | 3[34]??,*:*:4.0:*) /bin/uname -p 2>/dev/null | grep 86 >/dev/null \ && { echo i486-ncr-sysv4; exit; } ;; + NCR*:*:4.2:* | MPRAS*:*:4.2:*) + OS_REL='.3' + test -r /etc/.relid \ + && OS_REL=.`sed -n 's/[^ ]* [^ ]* \([0-9][0-9]\).*/\1/p' < /etc/.relid` + /bin/uname -p 2>/dev/null | grep 86 >/dev/null \ + && { echo i486-ncr-sysv4.3${OS_REL}; exit; } + /bin/uname -p 2>/dev/null | /bin/grep entium >/dev/null \ + && { echo i586-ncr-sysv4.3${OS_REL}; exit; } + /bin/uname -p 2>/dev/null | /bin/grep pteron >/dev/null \ + && { echo i586-ncr-sysv4.3${OS_REL}; exit; } ;; m68*:LynxOS:2.*:* | m68*:LynxOS:3.0*:*) echo m68k-unknown-lynxos${UNAME_RELEASE} exit ;; @@ -1153,7 +1113,7 @@ EOF rs6000:LynxOS:2.*:*) echo rs6000-unknown-lynxos${UNAME_RELEASE} exit ;; - PowerPC:LynxOS:2.*:* | PowerPC:LynxOS:3.[01]*:* | PowerPC:LynxOS:4.0*:*) + PowerPC:LynxOS:2.*:* | PowerPC:LynxOS:3.[01]*:* | PowerPC:LynxOS:4.[02]*:*) echo powerpc-unknown-lynxos${UNAME_RELEASE} exit ;; SM[BE]S:UNIX_SV:*:*) @@ -1216,6 +1176,9 @@ EOF BePC:BeOS:*:*) # BeOS running on Intel PC compatible. echo i586-pc-beos exit ;; + BePC:Haiku:*:*) # Haiku running on Intel PC compatible. + echo i586-pc-haiku + exit ;; SX-4:SUPER-UX:*:*) echo sx4-nec-superux${UNAME_RELEASE} exit ;; @@ -1243,6 +1206,16 @@ EOF *:Darwin:*:*) UNAME_PROCESSOR=`uname -p` || UNAME_PROCESSOR=unknown case $UNAME_PROCESSOR in + i386) + eval $set_cc_for_build + if [ "$CC_FOR_BUILD" != 'no_compiler_found' ]; then + if (echo '#ifdef __LP64__'; echo IS_64BIT_ARCH; echo '#endif') | \ + (CCOPTS= $CC_FOR_BUILD -E - 2>/dev/null) | \ + grep IS_64BIT_ARCH >/dev/null + then + UNAME_PROCESSOR="x86_64" + fi + fi ;; unknown) UNAME_PROCESSOR=powerpc ;; esac echo ${UNAME_PROCESSOR}-apple-darwin${UNAME_RELEASE} @@ -1324,6 +1297,9 @@ EOF i*86:rdos:*:*) echo ${UNAME_MACHINE}-pc-rdos exit ;; + i*86:AROS:*:*) + echo ${UNAME_MACHINE}-pc-aros + exit ;; esac #echo '(No uname command or uname output not recognized.)' 1>&2 @@ -1484,9 +1460,9 @@ This script, last modified $timestamp, has failed to recognize the operating system you are using. It is advised that you download the most up to date version of the config scripts from - http://savannah.gnu.org/cgi-bin/viewcvs/*checkout*/config/config/config.guess + http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.guess;hb=HEAD and - http://savannah.gnu.org/cgi-bin/viewcvs/*checkout*/config/config/config.sub + http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.sub;hb=HEAD If the version you run ($0) is already up to date, please send the following data and any information you think might be diff --git a/gtfold-mfe/config.sub b/gtfold-mfe/config.sub old mode 100644 new mode 100755 index 6759825..c2d1257 --- a/gtfold-mfe/config.sub +++ b/gtfold-mfe/config.sub @@ -1,10 +1,10 @@ #! /bin/sh # Configuration validation subroutine script. # Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, -# 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008 +# 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010 # Free Software Foundation, Inc. -timestamp='2008-01-16' +timestamp='2010-01-22' # This file is (in principle) common to ALL GNU software. # The presence of a machine in this file suggests that SOME GNU software @@ -32,13 +32,16 @@ timestamp='2008-01-16' # Please send patches to . Submit a context -# diff and a properly formatted ChangeLog entry. +# diff and a properly formatted GNU ChangeLog entry. # # Configuration subroutine to validate and canonicalize a configuration type. # Supply the specified configuration type as an argument. # If it is invalid, we print an error message on stderr and exit with code 1. # Otherwise, we print the canonical config type on stdout and succeed. +# You can get the latest version of this script from: +# http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.sub;hb=HEAD + # This file is supposed to be the same for all GNU packages # and recognize all the CPU types, system types and aliases # that are meaningful with *any* GNU software. @@ -72,8 +75,9 @@ Report bugs and patches to ." version="\ GNU config.sub ($timestamp) -Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, -2002, 2003, 2004, 2005, 2006, 2007, 2008 Free Software Foundation, Inc. +Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, +2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010 Free +Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE." @@ -122,6 +126,7 @@ maybe_os=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\2/'` case $maybe_os in nto-qnx* | linux-gnu* | linux-dietlibc | linux-newlib* | linux-uclibc* | \ uclinux-uclibc* | uclinux-gnu* | kfreebsd*-gnu* | knetbsd*-gnu* | netbsd*-gnu* | \ + kopensolaris*-gnu* | \ storm-chaos* | os2-emx* | rtmk-nova*) os=-$maybe_os basic_machine=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\1/'` @@ -148,10 +153,13 @@ case $os in -convergent* | -ncr* | -news | -32* | -3600* | -3100* | -hitachi* |\ -c[123]* | -convex* | -sun | -crds | -omron* | -dg | -ultra | -tti* | \ -harris | -dolphin | -highlevel | -gould | -cbm | -ns | -masscomp | \ - -apple | -axis | -knuth | -cray) + -apple | -axis | -knuth | -cray | -microblaze) os= basic_machine=$1 ;; + -bluegene*) + os=-cnk + ;; -sim | -cisco | -oki | -wec | -winbond) os= basic_machine=$1 @@ -249,13 +257,16 @@ case $basic_machine in | h8300 | h8500 | hppa | hppa1.[01] | hppa2.0 | hppa2.0[nw] | hppa64 \ | i370 | i860 | i960 | ia64 \ | ip2k | iq2000 \ + | lm32 \ | m32c | m32r | m32rle | m68000 | m68k | m88k \ - | maxq | mb | microblaze | mcore | mep \ + | maxq | mb | microblaze | mcore | mep | metag \ | mips | mipsbe | mipseb | mipsel | mipsle \ | mips16 \ | mips64 | mips64el \ - | mips64vr | mips64vrel \ + | mips64octeon | mips64octeonel \ | mips64orion | mips64orionel \ + | mips64r5900 | mips64r5900el \ + | mips64vr | mips64vrel \ | mips64vr4100 | mips64vr4100el \ | mips64vr4300 | mips64vr4300el \ | mips64vr5000 | mips64vr5000el \ @@ -268,6 +279,7 @@ case $basic_machine in | mipsisa64sr71k | mipsisa64sr71kel \ | mipstx39 | mipstx39el \ | mn10200 | mn10300 \ + | moxie \ | mt \ | msp430 \ | nios | nios2 \ @@ -276,20 +288,22 @@ case $basic_machine in | pdp10 | pdp11 | pj | pjl \ | powerpc | powerpc64 | powerpc64le | powerpcle | ppcbe \ | pyramid \ + | rx \ | score \ - | sh | sh[1234] | sh[24]a | sh[23]e | sh[34]eb | sheb | shbe | shle | sh[1234]le | sh3ele \ + | sh | sh[1234] | sh[24]a | sh[24]aeb | sh[23]e | sh[34]eb | sheb | shbe | shle | sh[1234]le | sh3ele \ | sh64 | sh64le \ | sparc | sparc64 | sparc64b | sparc64v | sparc86x | sparclet | sparclite \ | sparcv8 | sparcv9 | sparcv9b | sparcv9v \ | spu | strongarm \ | tahoe | thumb | tic4x | tic80 | tron \ + | ubicom32 \ | v850 | v850e \ | we32k \ | x86 | xc16x | xscale | xscalee[bl] | xstormy16 | xtensa \ - | z8k) + | z8k | z80) basic_machine=$basic_machine-unknown ;; - m6811 | m68hc11 | m6812 | m68hc12) + m6811 | m68hc11 | m6812 | m68hc12 | picochip) # Motorola 68HC11/12. basic_machine=$basic_machine-unknown os=-none @@ -329,14 +343,17 @@ case $basic_machine in | hppa-* | hppa1.[01]-* | hppa2.0-* | hppa2.0[nw]-* | hppa64-* \ | i*86-* | i860-* | i960-* | ia64-* \ | ip2k-* | iq2000-* \ + | lm32-* \ | m32c-* | m32r-* | m32rle-* \ | m68000-* | m680[012346]0-* | m68360-* | m683?2-* | m68k-* \ - | m88110-* | m88k-* | maxq-* | mcore-* \ + | m88110-* | m88k-* | maxq-* | mcore-* | metag-* | microblaze-* \ | mips-* | mipsbe-* | mipseb-* | mipsel-* | mipsle-* \ | mips16-* \ | mips64-* | mips64el-* \ - | mips64vr-* | mips64vrel-* \ + | mips64octeon-* | mips64octeonel-* \ | mips64orion-* | mips64orionel-* \ + | mips64r5900-* | mips64r5900el-* \ + | mips64vr-* | mips64vrel-* \ | mips64vr4100-* | mips64vr4100el-* \ | mips64vr4300-* | mips64vr4300el-* \ | mips64vr5000-* | mips64vr5000el-* \ @@ -357,21 +374,23 @@ case $basic_machine in | pdp10-* | pdp11-* | pj-* | pjl-* | pn-* | power-* \ | powerpc-* | powerpc64-* | powerpc64le-* | powerpcle-* | ppcbe-* \ | pyramid-* \ - | romp-* | rs6000-* \ - | sh-* | sh[1234]-* | sh[24]a-* | sh[23]e-* | sh[34]eb-* | sheb-* | shbe-* \ + | romp-* | rs6000-* | rx-* \ + | sh-* | sh[1234]-* | sh[24]a-* | sh[24]aeb-* | sh[23]e-* | sh[34]eb-* | sheb-* | shbe-* \ | shle-* | sh[1234]le-* | sh3ele-* | sh64-* | sh64le-* \ | sparc-* | sparc64-* | sparc64b-* | sparc64v-* | sparc86x-* | sparclet-* \ | sparclite-* \ | sparcv8-* | sparcv9-* | sparcv9b-* | sparcv9v-* | strongarm-* | sv1-* | sx?-* \ | tahoe-* | thumb-* \ | tic30-* | tic4x-* | tic54x-* | tic55x-* | tic6x-* | tic80-* \ + | tile-* | tilegx-* \ | tron-* \ + | ubicom32-* \ | v850-* | v850e-* | vax-* \ | we32k-* \ | x86-* | x86_64-* | xc16x-* | xps100-* | xscale-* | xscalee[bl]-* \ | xstormy16-* | xtensa*-* \ | ymp-* \ - | z8k-*) + | z8k-* | z80-*) ;; # Recognize the basic CPU types without company name, with glob match. xtensa*) @@ -439,6 +458,10 @@ case $basic_machine in basic_machine=m68k-apollo os=-bsd ;; + aros) + basic_machine=i386-pc + os=-aros + ;; aux) basic_machine=m68k-apple os=-aux @@ -455,10 +478,18 @@ case $basic_machine in basic_machine=bfin-`echo $basic_machine | sed 's/^[^-]*-//'` os=-linux ;; + bluegene*) + basic_machine=powerpc-ibm + os=-cnk + ;; c90) basic_machine=c90-cray os=-unicos ;; + cegcc) + basic_machine=arm-unknown + os=-cegcc + ;; convex-c1) basic_machine=c1-convex os=-bsd @@ -526,6 +557,10 @@ case $basic_machine in basic_machine=m88k-motorola os=-sysv3 ;; + dicos) + basic_machine=i686-pc + os=-dicos + ;; djgpp) basic_machine=i586-pc os=-msdosdjgpp @@ -699,6 +734,9 @@ case $basic_machine in basic_machine=ns32k-utek os=-sysv ;; + microblaze) + basic_machine=microblaze-xilinx + ;; mingw32) basic_machine=i386-pc os=-mingw32 @@ -1049,6 +1087,11 @@ case $basic_machine in basic_machine=tic6x-unknown os=-coff ;; + # This must be matched before tile*. + tilegx*) + basic_machine=tilegx-unknown + os=-linux-gnu + ;; tile*) basic_machine=tile-unknown os=-linux-gnu @@ -1128,6 +1171,10 @@ case $basic_machine in basic_machine=z8k-unknown os=-sim ;; + z80-*-coff) + basic_machine=z80-unknown + os=-sim + ;; none) basic_machine=none-none os=-none @@ -1166,7 +1213,7 @@ case $basic_machine in we32k) basic_machine=we32k-att ;; - sh[1234] | sh[24]a | sh[34]eb | sh[1234]le | sh[23]ele) + sh[1234] | sh[24]a | sh[24]aeb | sh[34]eb | sh[1234]le | sh[23]ele) basic_machine=sh-unknown ;; sparc | sparcv8 | sparcv9 | sparcv9b | sparcv9v) @@ -1216,6 +1263,9 @@ case $os in # First match some system type aliases # that might get confused with valid system types. # -solaris* is a basic system type, with this one exception. + -auroraux) + os=-auroraux + ;; -solaris1 | -solaris1.*) os=`echo $os | sed -e 's|solaris1|sunos4|'` ;; @@ -1236,10 +1286,11 @@ case $os in # Each alternative MUST END IN A *, to match a version number. # -sysv* is not here because it comes later, after sysvr4. -gnu* | -bsd* | -mach* | -minix* | -genix* | -ultrix* | -irix* \ - | -*vms* | -sco* | -esix* | -isc* | -aix* | -sunos | -sunos[34]*\ - | -hpux* | -unos* | -osf* | -luna* | -dgux* | -solaris* | -sym* \ + | -*vms* | -sco* | -esix* | -isc* | -aix* | -cnk* | -sunos | -sunos[34]*\ + | -hpux* | -unos* | -osf* | -luna* | -dgux* | -auroraux* | -solaris* \ + | -sym* | -kopensolaris* \ | -amigaos* | -amigados* | -msdos* | -newsos* | -unicos* | -aof* \ - | -aos* \ + | -aos* | -aros* \ | -nindy* | -vxsim* | -vxworks* | -ebmon* | -hms* | -mvs* \ | -clix* | -riscos* | -uniplus* | -iris* | -rtu* | -xenix* \ | -hiux* | -386bsd* | -knetbsd* | -mirbsd* | -netbsd* \ @@ -1248,7 +1299,7 @@ case $os in | -bosx* | -nextstep* | -cxux* | -aout* | -elf* | -oabi* \ | -ptx* | -coff* | -ecoff* | -winnt* | -domain* | -vsta* \ | -udi* | -eabi* | -lites* | -ieee* | -go32* | -aux* \ - | -chorusos* | -chorusrdb* \ + | -chorusos* | -chorusrdb* | -cegcc* \ | -cygwin* | -pe* | -psos* | -moss* | -proelf* | -rtems* \ | -mingw32* | -linux-gnu* | -linux-newlib* | -linux-uclibc* \ | -uxpv* | -beos* | -mpeix* | -udk* \ @@ -1258,7 +1309,7 @@ case $os in | -os2* | -vos* | -palmos* | -uclinux* | -nucleus* \ | -morphos* | -superux* | -rtmk* | -rtmk-nova* | -windiss* \ | -powermax* | -dnix* | -nx6 | -nx7 | -sei* | -dragonfly* \ - | -skyos* | -haiku* | -rdos* | -toppers* | -drops*) + | -skyos* | -haiku* | -rdos* | -toppers* | -drops* | -es*) # Remember, each alternative MUST END IN *, to match a version number. ;; -qnx*) @@ -1388,6 +1439,11 @@ case $os in -zvmoe) os=-zvmoe ;; + -dicos*) + os=-dicos + ;; + -nacl*) + ;; -none) ;; *) @@ -1585,7 +1641,7 @@ case $basic_machine in -sunos*) vendor=sun ;; - -aix*) + -cnk*|-aix*) vendor=ibm ;; -beos*) diff --git a/gtfold-mfe/configure b/gtfold-mfe/configure index c5acafe..e4e3fd1 100755 --- a/gtfold-mfe/configure +++ b/gtfold-mfe/configure @@ -1,22 +1,18 @@ #! /bin/sh # Guess values for system-dependent variables and create Makefiles. -# Generated by GNU Autoconf 2.67 for gtfold 1.18. -# +# Generated by GNU Autoconf 2.63 for gtfold 2.0. # # Copyright (C) 1992, 1993, 1994, 1995, 1996, 1998, 1999, 2000, 2001, -# 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010 Free Software -# Foundation, Inc. -# -# +# 2002, 2003, 2004, 2005, 2006, 2007, 2008 Free Software Foundation, Inc. # This configure script is free software; the Free Software Foundation # gives unlimited permission to copy, distribute and modify it. -## -------------------- ## -## M4sh Initialization. ## -## -------------------- ## +## --------------------- ## +## M4sh Initialization. ## +## --------------------- ## # Be more Bourne compatible DUALCASE=1; export DUALCASE # for MKS sh -if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then : +if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then emulate sh NULLCMD=: # Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which @@ -24,15 +20,23 @@ if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then : alias -g '${1+"$@"}'='"$@"' setopt NO_GLOB_SUBST else - case `(set -o) 2>/dev/null` in #( - *posix*) : - set -o posix ;; #( - *) : - ;; + case `(set -o) 2>/dev/null` in + *posix*) set -o posix ;; esac + fi + + +# PATH needs CR +# Avoid depending upon Character Ranges. +as_cr_letters='abcdefghijklmnopqrstuvwxyz' +as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ' +as_cr_Letters=$as_cr_letters$as_cr_LETTERS +as_cr_digits='0123456789' +as_cr_alnum=$as_cr_Letters$as_cr_digits + as_nl=' ' export as_nl @@ -40,13 +44,7 @@ export as_nl as_echo='\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\' as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo$as_echo -# Prefer a ksh shell builtin over an external printf program on Solaris, -# but without wasting forks for bash or zsh. -if test -z "$BASH_VERSION$ZSH_VERSION" \ - && (test "X`print -r -- $as_echo`" = "X$as_echo") 2>/dev/null; then - as_echo='print -r --' - as_echo_n='print -rn --' -elif (test "X`printf %s $as_echo`" = "X$as_echo") 2>/dev/null; then +if (test "X`printf %s $as_echo`" = "X$as_echo") 2>/dev/null; then as_echo='printf %s\n' as_echo_n='printf %s' else @@ -57,7 +55,7 @@ else as_echo_body='eval expr "X$1" : "X\\(.*\\)"' as_echo_n_body='eval arg=$1; - case $arg in #( + case $arg in *"$as_nl"*) expr "X$arg" : "X\\(.*\\)$as_nl"; arg=`expr "X$arg" : ".*$as_nl\\(.*\\)"`;; @@ -80,6 +78,13 @@ if test "${PATH_SEPARATOR+set}" != set; then } fi +# Support unset when possible. +if ( (MAIL=60; unset MAIL) || exit) >/dev/null 2>&1; then + as_unset=unset +else + as_unset=false +fi + # IFS # We need space, tab and new line, in precisely that order. Quoting is @@ -89,15 +94,15 @@ fi IFS=" "" $as_nl" # Find who we are. Look in the path if we contain no directory separator. -case $0 in #(( +case $0 in *[\\/]* ) as_myself=$0 ;; *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break - done + test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break +done IFS=$as_save_IFS ;; @@ -109,16 +114,12 @@ if test "x$as_myself" = x; then fi if test ! -f "$as_myself"; then $as_echo "$as_myself: error: cannot find myself; rerun with an absolute file name" >&2 - exit 1 + { (exit 1); exit 1; } fi -# Unset variables that we do not need and which cause bugs (e.g. in -# pre-3.0 UWIN ksh). But do not cause bugs in bash 2.01; the "|| exit 1" -# suppresses any "Segmentation fault" message there. '((' could -# trigger a bug in pdksh 5.2.14. -for as_var in BASH_ENV ENV MAIL MAILPATH -do eval test x\${$as_var+set} = xset \ - && ( (unset $as_var) || exit 1) >/dev/null 2>&1 && unset $as_var || : +# Work around bugs in pre-3.0 UWIN ksh. +for as_var in ENV MAIL MAILPATH +do ($as_unset $as_var) >/dev/null 2>&1 && $as_unset $as_var done PS1='$ ' PS2='> ' @@ -130,299 +131,330 @@ export LC_ALL LANGUAGE=C export LANGUAGE +# Required to use basename. +if expr a : '\(a\)' >/dev/null 2>&1 && + test "X`expr 00001 : '.*\(...\)'`" = X001; then + as_expr=expr +else + as_expr=false +fi + +if (basename -- /) >/dev/null 2>&1 && test "X`basename -- / 2>&1`" = "X/"; then + as_basename=basename +else + as_basename=false +fi + + +# Name of the executable. +as_me=`$as_basename -- "$0" || +$as_expr X/"$0" : '.*/\([^/][^/]*\)/*$' \| \ + X"$0" : 'X\(//\)$' \| \ + X"$0" : 'X\(/\)' \| . 2>/dev/null || +$as_echo X/"$0" | + sed '/^.*\/\([^/][^/]*\)\/*$/{ + s//\1/ + q + } + /^X\/\(\/\/\)$/{ + s//\1/ + q + } + /^X\/\(\/\).*/{ + s//\1/ + q + } + s/.*/./; q'` + # CDPATH. -(unset CDPATH) >/dev/null 2>&1 && unset CDPATH +$as_unset CDPATH + if test "x$CONFIG_SHELL" = x; then - as_bourne_compatible="if test -n \"\${ZSH_VERSION+set}\" && (emulate sh) >/dev/null 2>&1; then : - emulate sh - NULLCMD=: - # Pre-4.2 versions of Zsh do word splitting on \${1+\"\$@\"}, which - # is contrary to our usage. Disable this feature. - alias -g '\${1+\"\$@\"}'='\"\$@\"' - setopt NO_GLOB_SUBST + if (eval ":") 2>/dev/null; then + as_have_required=yes else - case \`(set -o) 2>/dev/null\` in #( - *posix*) : - set -o posix ;; #( - *) : - ;; -esac + as_have_required=no fi -" - as_required="as_fn_return () { (exit \$1); } -as_fn_success () { as_fn_return 0; } -as_fn_failure () { as_fn_return 1; } -as_fn_ret_success () { return 0; } -as_fn_ret_failure () { return 1; } + + if test $as_have_required = yes && (eval ": +(as_func_return () { + (exit \$1) +} +as_func_success () { + as_func_return 0 +} +as_func_failure () { + as_func_return 1 +} +as_func_ret_success () { + return 0 +} +as_func_ret_failure () { + return 1 +} exitcode=0 -as_fn_success || { exitcode=1; echo as_fn_success failed.; } -as_fn_failure && { exitcode=1; echo as_fn_failure succeeded.; } -as_fn_ret_success || { exitcode=1; echo as_fn_ret_success failed.; } -as_fn_ret_failure && { exitcode=1; echo as_fn_ret_failure succeeded.; } -if ( set x; as_fn_ret_success y && test x = \"\$1\" ); then : - -else - exitcode=1; echo positional parameters were not saved. -fi -test x\$exitcode = x0 || exit 1" - as_suggested=" as_lineno_1=";as_suggested=$as_suggested$LINENO;as_suggested=$as_suggested" as_lineno_1a=\$LINENO - as_lineno_2=";as_suggested=$as_suggested$LINENO;as_suggested=$as_suggested" as_lineno_2a=\$LINENO - eval 'test \"x\$as_lineno_1'\$as_run'\" != \"x\$as_lineno_2'\$as_run'\" && - test \"x\`expr \$as_lineno_1'\$as_run' + 1\`\" = \"x\$as_lineno_2'\$as_run'\"' || exit 1 -test \$(( 1 + 1 )) = 2 || exit 1" - if (eval "$as_required") 2>/dev/null; then : - as_have_required=yes +if as_func_success; then + : else - as_have_required=no + exitcode=1 + echo as_func_success failed. fi - if test x$as_have_required = xyes && (eval "$as_suggested") 2>/dev/null; then : +if as_func_failure; then + exitcode=1 + echo as_func_failure succeeded. +fi + +if as_func_ret_success; then + : else - as_save_IFS=$IFS; IFS=$PATH_SEPARATOR -as_found=false + exitcode=1 + echo as_func_ret_success failed. +fi + +if as_func_ret_failure; then + exitcode=1 + echo as_func_ret_failure succeeded. +fi + +if ( set x; as_func_ret_success y && test x = \"\$1\" ); then + : +else + exitcode=1 + echo positional parameters were not saved. +fi + +test \$exitcode = 0) || { (exit 1); exit 1; } + +( + as_lineno_1=\$LINENO + as_lineno_2=\$LINENO + test \"x\$as_lineno_1\" != \"x\$as_lineno_2\" && + test \"x\`expr \$as_lineno_1 + 1\`\" = \"x\$as_lineno_2\") || { (exit 1); exit 1; } +") 2> /dev/null; then + : +else + as_candidate_shells= + as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in /bin$PATH_SEPARATOR/usr/bin$PATH_SEPARATOR$PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - as_found=: - case $as_dir in #( + case $as_dir in /*) for as_base in sh bash ksh sh5; do - # Try only shells that exist, to save several forks. - as_shell=$as_dir/$as_base - if { test -f "$as_shell" || test -f "$as_shell.exe"; } && - { $as_echo "$as_bourne_compatible""$as_required" | as_run=a "$as_shell"; } 2>/dev/null; then : - CONFIG_SHELL=$as_shell as_have_required=yes - if { $as_echo "$as_bourne_compatible""$as_suggested" | as_run=a "$as_shell"; } 2>/dev/null; then : - break 2 -fi -fi + as_candidate_shells="$as_candidate_shells $as_dir/$as_base" done;; esac - as_found=false done -$as_found || { if { test -f "$SHELL" || test -f "$SHELL.exe"; } && - { $as_echo "$as_bourne_compatible""$as_required" | as_run=a "$SHELL"; } 2>/dev/null; then : - CONFIG_SHELL=$SHELL as_have_required=yes -fi; } IFS=$as_save_IFS - if test "x$CONFIG_SHELL" != x; then : - # We cannot yet assume a decent shell, so we have to provide a - # neutralization value for shells without unset; and this also - # works around shells that cannot unset nonexistent variables. - BASH_ENV=/dev/null - ENV=/dev/null - (unset BASH_ENV) >/dev/null 2>&1 && unset BASH_ENV ENV - export CONFIG_SHELL - exec "$CONFIG_SHELL" "$as_myself" ${1+"$@"} -fi + for as_shell in $as_candidate_shells $SHELL; do + # Try only shells that exist, to save several forks. + if { test -f "$as_shell" || test -f "$as_shell.exe"; } && + { ("$as_shell") 2> /dev/null <<\_ASEOF +if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then + emulate sh + NULLCMD=: + # Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which + # is contrary to our usage. Disable this feature. + alias -g '${1+"$@"}'='"$@"' + setopt NO_GLOB_SUBST +else + case `(set -o) 2>/dev/null` in + *posix*) set -o posix ;; +esac - if test x$as_have_required = xno; then : - $as_echo "$0: This script requires a shell more modern than all" - $as_echo "$0: the shells that I found on your system." - if test x${ZSH_VERSION+set} = xset ; then - $as_echo "$0: In particular, zsh $ZSH_VERSION has bugs and should" - $as_echo "$0: be upgraded to zsh 4.3.4 or later." - else - $as_echo "$0: Please tell bug-autoconf@gnu.org about your system, -$0: including any error possibly output before this -$0: message. Then install a modern shell, or manually run -$0: the script under such a shell if you do have one." - fi - exit 1 -fi fi + + +: +_ASEOF +}; then + CONFIG_SHELL=$as_shell + as_have_required=yes + if { "$as_shell" 2> /dev/null <<\_ASEOF +if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then + emulate sh + NULLCMD=: + # Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which + # is contrary to our usage. Disable this feature. + alias -g '${1+"$@"}'='"$@"' + setopt NO_GLOB_SUBST +else + case `(set -o) 2>/dev/null` in + *posix*) set -o posix ;; +esac + fi -SHELL=${CONFIG_SHELL-/bin/sh} -export SHELL -# Unset more variables known to interfere with behavior of common tools. -CLICOLOR_FORCE= GREP_OPTIONS= -unset CLICOLOR_FORCE GREP_OPTIONS -## --------------------- ## -## M4sh Shell Functions. ## -## --------------------- ## -# as_fn_unset VAR -# --------------- -# Portably unset VAR. -as_fn_unset () -{ - { eval $1=; unset $1;} + +: +(as_func_return () { + (exit $1) +} +as_func_success () { + as_func_return 0 +} +as_func_failure () { + as_func_return 1 +} +as_func_ret_success () { + return 0 +} +as_func_ret_failure () { + return 1 } -as_unset=as_fn_unset -# as_fn_set_status STATUS -# ----------------------- -# Set $? to STATUS, without forking. -as_fn_set_status () -{ - return $1 -} # as_fn_set_status +exitcode=0 +if as_func_success; then + : +else + exitcode=1 + echo as_func_success failed. +fi -# as_fn_exit STATUS -# ----------------- -# Exit the shell with STATUS, even in a "trap 0" or "set -e" context. -as_fn_exit () -{ - set +e - as_fn_set_status $1 - exit $1 -} # as_fn_exit - -# as_fn_mkdir_p -# ------------- -# Create "$as_dir" as a directory, including parents if necessary. -as_fn_mkdir_p () -{ +if as_func_failure; then + exitcode=1 + echo as_func_failure succeeded. +fi - case $as_dir in #( - -*) as_dir=./$as_dir;; - esac - test -d "$as_dir" || eval $as_mkdir_p || { - as_dirs= - while :; do - case $as_dir in #( - *\'*) as_qdir=`$as_echo "$as_dir" | sed "s/'/'\\\\\\\\''/g"`;; #'( - *) as_qdir=$as_dir;; - esac - as_dirs="'$as_qdir' $as_dirs" - as_dir=`$as_dirname -- "$as_dir" || -$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \ - X"$as_dir" : 'X\(//\)[^/]' \| \ - X"$as_dir" : 'X\(//\)$' \| \ - X"$as_dir" : 'X\(/\)' \| . 2>/dev/null || -$as_echo X"$as_dir" | - sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ - s//\1/ - q - } - /^X\(\/\/\)[^/].*/{ - s//\1/ - q - } - /^X\(\/\/\)$/{ - s//\1/ - q - } - /^X\(\/\).*/{ - s//\1/ - q - } - s/.*/./; q'` - test -d "$as_dir" && break - done - test -z "$as_dirs" || eval "mkdir $as_dirs" - } || test -d "$as_dir" || as_fn_error $? "cannot create directory $as_dir" - - -} # as_fn_mkdir_p -# as_fn_append VAR VALUE -# ---------------------- -# Append the text in VALUE to the end of the definition contained in VAR. Take -# advantage of any shell optimizations that allow amortized linear growth over -# repeated appends, instead of the typical quadratic growth present in naive -# implementations. -if (eval "as_var=1; as_var+=2; test x\$as_var = x12") 2>/dev/null; then : - eval 'as_fn_append () - { - eval $1+=\$2 - }' +if as_func_ret_success; then + : else - as_fn_append () - { - eval $1=\$$1\$2 - } -fi # as_fn_append - -# as_fn_arith ARG... -# ------------------ -# Perform arithmetic evaluation on the ARGs, and store the result in the -# global $as_val. Take advantage of shells that can avoid forks. The arguments -# must be portable across $(()) and expr. -if (eval "test \$(( 1 + 1 )) = 2") 2>/dev/null; then : - eval 'as_fn_arith () - { - as_val=$(( $* )) - }' + exitcode=1 + echo as_func_ret_success failed. +fi + +if as_func_ret_failure; then + exitcode=1 + echo as_func_ret_failure succeeded. +fi + +if ( set x; as_func_ret_success y && test x = "$1" ); then + : else - as_fn_arith () - { - as_val=`expr "$@" || test $? -eq 1` - } -fi # as_fn_arith + exitcode=1 + echo positional parameters were not saved. +fi +test $exitcode = 0) || { (exit 1); exit 1; } -# as_fn_error STATUS ERROR [LINENO LOG_FD] -# ---------------------------------------- -# Output "`basename $0`: error: ERROR" to stderr. If LINENO and LOG_FD are -# provided, also output the error to LOG_FD, referencing LINENO. Then exit the -# script with STATUS, using 1 if that was 0. -as_fn_error () -{ - as_status=$1; test $as_status -eq 0 && as_status=1 - if test "$4"; then - as_lineno=${as_lineno-"$3"} as_lineno_stack=as_lineno_stack=$as_lineno_stack - $as_echo "$as_me:${as_lineno-$LINENO}: error: $2" >&$4 - fi - $as_echo "$as_me: error: $2" >&2 - as_fn_exit $as_status -} # as_fn_error +( + as_lineno_1=$LINENO + as_lineno_2=$LINENO + test "x$as_lineno_1" != "x$as_lineno_2" && + test "x`expr $as_lineno_1 + 1`" = "x$as_lineno_2") || { (exit 1); exit 1; } -if expr a : '\(a\)' >/dev/null 2>&1 && - test "X`expr 00001 : '.*\(...\)'`" = X001; then - as_expr=expr +_ASEOF +}; then + break +fi + +fi + + done + + if test "x$CONFIG_SHELL" != x; then + for as_var in BASH_ENV ENV + do ($as_unset $as_var) >/dev/null 2>&1 && $as_unset $as_var + done + export CONFIG_SHELL + exec "$CONFIG_SHELL" "$as_myself" ${1+"$@"} +fi + + + if test $as_have_required = no; then + echo This script requires a shell more modern than all the + echo shells that I found on your system. Please install a + echo modern shell, or manually run the script under such a + echo shell if you do have one. + { (exit 1); exit 1; } +fi + + +fi + +fi + + + +(eval "as_func_return () { + (exit \$1) +} +as_func_success () { + as_func_return 0 +} +as_func_failure () { + as_func_return 1 +} +as_func_ret_success () { + return 0 +} +as_func_ret_failure () { + return 1 +} + +exitcode=0 +if as_func_success; then + : else - as_expr=false + exitcode=1 + echo as_func_success failed. fi -if (basename -- /) >/dev/null 2>&1 && test "X`basename -- / 2>&1`" = "X/"; then - as_basename=basename +if as_func_failure; then + exitcode=1 + echo as_func_failure succeeded. +fi + +if as_func_ret_success; then + : else - as_basename=false + exitcode=1 + echo as_func_ret_success failed. fi -if (as_dir=`dirname -- /` && test "X$as_dir" = X/) >/dev/null 2>&1; then - as_dirname=dirname +if as_func_ret_failure; then + exitcode=1 + echo as_func_ret_failure succeeded. +fi + +if ( set x; as_func_ret_success y && test x = \"\$1\" ); then + : else - as_dirname=false + exitcode=1 + echo positional parameters were not saved. fi -as_me=`$as_basename -- "$0" || -$as_expr X/"$0" : '.*/\([^/][^/]*\)/*$' \| \ - X"$0" : 'X\(//\)$' \| \ - X"$0" : 'X\(/\)' \| . 2>/dev/null || -$as_echo X/"$0" | - sed '/^.*\/\([^/][^/]*\)\/*$/{ - s//\1/ - q - } - /^X\/\(\/\/\)$/{ - s//\1/ - q - } - /^X\/\(\/\).*/{ - s//\1/ - q - } - s/.*/./; q'` +test \$exitcode = 0") || { + echo No shell found that supports shell functions. + echo Please tell bug-autoconf@gnu.org about your system, + echo including any error possibly output before this message. + echo This can help us improve future autoconf versions. + echo Configuration will now proceed without shell functions. +} + -# Avoid depending upon Character Ranges. -as_cr_letters='abcdefghijklmnopqrstuvwxyz' -as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ' -as_cr_Letters=$as_cr_letters$as_cr_LETTERS -as_cr_digits='0123456789' -as_cr_alnum=$as_cr_Letters$as_cr_digits + as_lineno_1=$LINENO + as_lineno_2=$LINENO + test "x$as_lineno_1" != "x$as_lineno_2" && + test "x`expr $as_lineno_1 + 1`" = "x$as_lineno_2" || { - as_lineno_1=$LINENO as_lineno_1a=$LINENO - as_lineno_2=$LINENO as_lineno_2a=$LINENO - eval 'test "x$as_lineno_1'$as_run'" != "x$as_lineno_2'$as_run'" && - test "x`expr $as_lineno_1'$as_run' + 1`" = "x$as_lineno_2'$as_run'"' || { - # Blame Lee E. McMahon (1931-1989) for sed's syntax. :-) + # Create $as_me.lineno as a copy of $as_myself, but with $LINENO + # uniformly replaced by the line number. The first 'sed' inserts a + # line-number line after each line using $LINENO; the second 'sed' + # does the real work. The second script uses 'N' to pair each + # line-number line with the line containing $LINENO, and appends + # trailing '-' during substitution so that $LINENO is not a special + # case at line end. + # (Raja R Harinath suggested sed '=', and Paul Eggert wrote the + # scripts with optimization help from Paolo Bonzini. Blame Lee + # E. McMahon (1931-1989) for sed's syntax. :-) sed -n ' p /[$]LINENO/= @@ -439,7 +471,8 @@ as_cr_alnum=$as_cr_Letters$as_cr_digits s/-\n.*// ' >$as_me.lineno && chmod +x "$as_me.lineno" || - { $as_echo "$as_me: error: cannot create $as_me.lineno; rerun with a POSIX shell" >&2; as_fn_exit 1; } + { $as_echo "$as_me: error: cannot create $as_me.lineno; rerun with a POSIX shell" >&2 + { (exit 1); exit 1; }; } # Don't try to exec as it changes $[0], causing all sort of problems # (the dirname of $[0] is not the place where we might find the @@ -449,18 +482,29 @@ as_cr_alnum=$as_cr_Letters$as_cr_digits exit } + +if (as_dir=`dirname -- /` && test "X$as_dir" = X/) >/dev/null 2>&1; then + as_dirname=dirname +else + as_dirname=false +fi + ECHO_C= ECHO_N= ECHO_T= -case `echo -n x` in #((((( +case `echo -n x` in -n*) - case `echo 'xy\c'` in + case `echo 'x\c'` in *c*) ECHO_T=' ';; # ECHO_T is single tab character. - xy) ECHO_C='\c';; - *) echo `echo ksh88 bug on AIX 6.1` > /dev/null - ECHO_T=' ';; + *) ECHO_C='\c';; esac;; *) ECHO_N='-n';; esac +if expr a : '\(a\)' >/dev/null 2>&1 && + test "X`expr 00001 : '.*\(...\)'`" = X001; then + as_expr=expr +else + as_expr=false +fi rm -f conf$$ conf$$.exe conf$$.file if test -d conf$$.dir; then @@ -490,7 +534,7 @@ rm -f conf$$ conf$$.exe conf$$.dir/conf$$.file conf$$.file rmdir conf$$.dir 2>/dev/null if mkdir -p . 2>/dev/null; then - as_mkdir_p='mkdir -p "$as_dir"' + as_mkdir_p=: else test -d ./-p && rmdir ./-p as_mkdir_p=false @@ -509,10 +553,10 @@ else if test -d "$1"; then test -d "$1/."; else - case $1 in #( + case $1 in -*)set "./$1";; esac; - case `ls -ld'$as_ls_L_option' "$1" 2>/dev/null` in #(( + case `ls -ld'$as_ls_L_option' "$1" 2>/dev/null` in ???[sx]*):;;*)false;;esac;fi '\'' sh ' @@ -526,11 +570,11 @@ as_tr_cpp="eval sed 'y%*$as_cr_letters%P$as_cr_LETTERS%;s%[^_$as_cr_alnum]%_%g'" as_tr_sh="eval sed 'y%*+%pp%;s%[^_$as_cr_alnum]%_%g'" -test -n "$DJDIR" || exec 7<&0 &1 + +exec 7<&0 &1 # Name of the host. -# hostname on some systems (SVR3.2, old GNU/Linux) returns a bogus exit status, +# hostname on some systems (SVR3.2, Linux) returns a bogus exit status, # so uname gets run too. ac_hostname=`(hostname || uname -n) 2>/dev/null | sed 1q` @@ -545,14 +589,14 @@ cross_compiling=no subdirs= MFLAGS= MAKEFLAGS= +SHELL=${CONFIG_SHELL-/bin/sh} # Identity of this package. PACKAGE_NAME='gtfold' PACKAGE_TARNAME='gtfold' -PACKAGE_VERSION='1.18' -PACKAGE_STRING='gtfold 1.18' +PACKAGE_VERSION='2.0' +PACKAGE_STRING='gtfold 2.0' PACKAGE_BUGREPORT='' -PACKAGE_URL='' ac_unique_file="README" # Factoring default headers for most tests. @@ -688,7 +732,6 @@ bindir program_transform_name prefix exec_prefix -PACKAGE_URL PACKAGE_BUGREPORT PACKAGE_STRING PACKAGE_VERSION @@ -778,9 +821,8 @@ do fi case $ac_option in - *=?*) ac_optarg=`expr "X$ac_option" : '[^=]*=\(.*\)'` ;; - *=) ac_optarg= ;; - *) ac_optarg=yes ;; + *=*) ac_optarg=`expr "X$ac_option" : '[^=]*=\(.*\)'` ;; + *) ac_optarg=yes ;; esac # Accept the important Cygnus configure options, so we can diagnose typos. @@ -825,7 +867,8 @@ do ac_useropt=`expr "x$ac_option" : 'x-*disable-\(.*\)'` # Reject names that are not valid shell variable names. expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null && - as_fn_error $? "invalid feature name: $ac_useropt" + { $as_echo "$as_me: error: invalid feature name: $ac_useropt" >&2 + { (exit 1); exit 1; }; } ac_useropt_orig=$ac_useropt ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'` case $ac_user_opts in @@ -851,7 +894,8 @@ do ac_useropt=`expr "x$ac_option" : 'x-*enable-\([^=]*\)'` # Reject names that are not valid shell variable names. expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null && - as_fn_error $? "invalid feature name: $ac_useropt" + { $as_echo "$as_me: error: invalid feature name: $ac_useropt" >&2 + { (exit 1); exit 1; }; } ac_useropt_orig=$ac_useropt ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'` case $ac_user_opts in @@ -1055,7 +1099,8 @@ do ac_useropt=`expr "x$ac_option" : 'x-*with-\([^=]*\)'` # Reject names that are not valid shell variable names. expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null && - as_fn_error $? "invalid package name: $ac_useropt" + { $as_echo "$as_me: error: invalid package name: $ac_useropt" >&2 + { (exit 1); exit 1; }; } ac_useropt_orig=$ac_useropt ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'` case $ac_user_opts in @@ -1071,7 +1116,8 @@ do ac_useropt=`expr "x$ac_option" : 'x-*without-\(.*\)'` # Reject names that are not valid shell variable names. expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null && - as_fn_error $? "invalid package name: $ac_useropt" + { $as_echo "$as_me: error: invalid package name: $ac_useropt" >&2 + { (exit 1); exit 1; }; } ac_useropt_orig=$ac_useropt ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'` case $ac_user_opts in @@ -1101,17 +1147,17 @@ do | --x-librar=* | --x-libra=* | --x-libr=* | --x-lib=* | --x-li=* | --x-l=*) x_libraries=$ac_optarg ;; - -*) as_fn_error $? "unrecognized option: \`$ac_option' -Try \`$0 --help' for more information" + -*) { $as_echo "$as_me: error: unrecognized option: $ac_option +Try \`$0 --help' for more information." >&2 + { (exit 1); exit 1; }; } ;; *=*) ac_envvar=`expr "x$ac_option" : 'x\([^=]*\)='` # Reject names that are not valid shell variable names. - case $ac_envvar in #( - '' | [0-9]* | *[!_$as_cr_alnum]* ) - as_fn_error $? "invalid variable name: \`$ac_envvar'" ;; - esac + expr "x$ac_envvar" : ".*[^_$as_cr_alnum]" >/dev/null && + { $as_echo "$as_me: error: invalid variable name: $ac_envvar" >&2 + { (exit 1); exit 1; }; } eval $ac_envvar=\$ac_optarg export $ac_envvar ;; @@ -1128,13 +1174,15 @@ done if test -n "$ac_prev"; then ac_option=--`echo $ac_prev | sed 's/_/-/g'` - as_fn_error $? "missing argument to $ac_option" + { $as_echo "$as_me: error: missing argument to $ac_option" >&2 + { (exit 1); exit 1; }; } fi if test -n "$ac_unrecognized_opts"; then case $enable_option_checking in no) ;; - fatal) as_fn_error $? "unrecognized options: $ac_unrecognized_opts" ;; + fatal) { $as_echo "$as_me: error: unrecognized options: $ac_unrecognized_opts" >&2 + { (exit 1); exit 1; }; } ;; *) $as_echo "$as_me: WARNING: unrecognized options: $ac_unrecognized_opts" >&2 ;; esac fi @@ -1157,7 +1205,8 @@ do [\\/$]* | ?:[\\/]* ) continue;; NONE | '' ) case $ac_var in *prefix ) continue;; esac;; esac - as_fn_error $? "expected an absolute directory name for --$ac_var: $ac_val" + { $as_echo "$as_me: error: expected an absolute directory name for --$ac_var: $ac_val" >&2 + { (exit 1); exit 1; }; } done # There might be people who depend on the old broken behavior: `$host' @@ -1171,8 +1220,8 @@ target=$target_alias if test "x$host_alias" != x; then if test "x$build_alias" = x; then cross_compiling=maybe - $as_echo "$as_me: WARNING: if you wanted to set the --build type, don't use --host. - If a cross compiler is detected then cross compile mode will be used" >&2 + $as_echo "$as_me: WARNING: If you wanted to set the --build type, don't use --host. + If a cross compiler is detected then cross compile mode will be used." >&2 elif test "x$build_alias" != "x$host_alias"; then cross_compiling=yes fi @@ -1187,9 +1236,11 @@ test "$silent" = yes && exec 6>/dev/null ac_pwd=`pwd` && test -n "$ac_pwd" && ac_ls_di=`ls -di .` && ac_pwd_ls_di=`cd "$ac_pwd" && ls -di .` || - as_fn_error $? "working directory cannot be determined" + { $as_echo "$as_me: error: working directory cannot be determined" >&2 + { (exit 1); exit 1; }; } test "X$ac_ls_di" = "X$ac_pwd_ls_di" || - as_fn_error $? "pwd does not report name of working directory" + { $as_echo "$as_me: error: pwd does not report name of working directory" >&2 + { (exit 1); exit 1; }; } # Find the source files, if location was not specified. @@ -1228,11 +1279,13 @@ else fi if test ! -r "$srcdir/$ac_unique_file"; then test "$ac_srcdir_defaulted" = yes && srcdir="$ac_confdir or .." - as_fn_error $? "cannot find sources ($ac_unique_file) in $srcdir" + { $as_echo "$as_me: error: cannot find sources ($ac_unique_file) in $srcdir" >&2 + { (exit 1); exit 1; }; } fi ac_msg="sources are in $srcdir, but \`cd $srcdir' does not work" ac_abs_confdir=`( - cd "$srcdir" && test -r "./$ac_unique_file" || as_fn_error $? "$ac_msg" + cd "$srcdir" && test -r "./$ac_unique_file" || { $as_echo "$as_me: error: $ac_msg" >&2 + { (exit 1); exit 1; }; } pwd)` # When building in place, set srcdir=. if test "$ac_abs_confdir" = "$ac_pwd"; then @@ -1258,7 +1311,7 @@ if test "$ac_init_help" = "long"; then # Omit some internal or obsolete options to make the list less imposing. # This message is too long to be a string in the A/UX 3.1 sh. cat <<_ACEOF -\`configure' configures gtfold 1.18 to adapt to many kinds of systems. +\`configure' configures gtfold 2.0 to adapt to many kinds of systems. Usage: $0 [OPTION]... [VAR=VALUE]... @@ -1272,7 +1325,7 @@ Configuration: --help=short display options specific to this package --help=recursive display the short help of all the included packages -V, --version display version information and exit - -q, --quiet, --silent do not print \`checking ...' messages + -q, --quiet, --silent do not print \`checking...' messages --cache-file=FILE cache test results in FILE [disabled] -C, --config-cache alias for \`--cache-file=config.cache' -n, --no-create do not create output files @@ -1329,7 +1382,7 @@ fi if test -n "$ac_init_help"; then case $ac_init_help in - short | recursive ) echo "Configuration of gtfold 1.18:";; + short | recursive ) echo "Configuration of gtfold 2.0:";; esac cat <<\_ACEOF @@ -1349,537 +1402,93 @@ Some influential environment variables: LDFLAGS linker flags, e.g. -L if you have libraries in a nonstandard directory LIBS libraries to pass to the linker, e.g. -l - CPPFLAGS (Objective) C/C++ preprocessor flags, e.g. -I if + CPPFLAGS C/C++/Objective C preprocessor flags, e.g. -I if you have headers in a nonstandard directory CXX C++ compiler command - CXXFLAGS C++ compiler flags - CPP C preprocessor - -Use these variables to override the choices made by `configure' or to help -it to find libraries and programs with nonstandard names/locations. - -Report bugs to the package provider. -_ACEOF -ac_status=$? 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Invocation command line was +It was created by gtfold $as_me 2.0, which was +generated by GNU Autoconf 2.63. Invocation command line was $ $0 $@ @@ -1915,8 +1524,8 @@ for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - $as_echo "PATH: $as_dir" - done + $as_echo "PATH: $as_dir" +done IFS=$as_save_IFS } >&5 @@ -1953,9 +1562,9 @@ do ac_arg=`$as_echo "$ac_arg" | sed "s/'/'\\\\\\\\''/g"` ;; esac case $ac_pass in - 1) as_fn_append ac_configure_args0 " '$ac_arg'" ;; + 1) ac_configure_args0="$ac_configure_args0 '$ac_arg'" ;; 2) - as_fn_append ac_configure_args1 " '$ac_arg'" + ac_configure_args1="$ac_configure_args1 '$ac_arg'" if test $ac_must_keep_next = true; then ac_must_keep_next=false # Got value, back to normal. else @@ -1971,13 +1580,13 @@ do -* ) ac_must_keep_next=true ;; esac fi - as_fn_append ac_configure_args " '$ac_arg'" + ac_configure_args="$ac_configure_args '$ac_arg'" ;; esac done done -{ ac_configure_args0=; unset ac_configure_args0;} -{ ac_configure_args1=; unset ac_configure_args1;} +$as_unset ac_configure_args0 || test "${ac_configure_args0+set}" != set || { ac_configure_args0=; export ac_configure_args0; } +$as_unset ac_configure_args1 || test "${ac_configure_args1+set}" != set || { ac_configure_args1=; export ac_configure_args1; } # When interrupted or exit'd, cleanup temporary files, and complete # config.log. We remove comments because anyway the quotes in there @@ -1989,9 +1598,11 @@ trap 'exit_status=$? { echo - $as_echo "## ---------------- ## + cat <<\_ASBOX +## ---------------- ## ## Cache variables. ## -## ---------------- ##" +## ---------------- ## +_ASBOX echo # The following way of writing the cache mishandles newlines in values, ( @@ -2000,13 +1611,13 @@ trap 'exit_status=$? case $ac_val in #( *${as_nl}*) case $ac_var in #( - *_cv_*) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: cache variable $ac_var contains a newline" >&5 + *_cv_*) { $as_echo "$as_me:$LINENO: WARNING: cache variable $ac_var contains a newline" >&5 $as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;; esac case $ac_var in #( _ | IFS | as_nl) ;; #( BASH_ARGV | BASH_SOURCE) eval $ac_var= ;; #( - *) { eval $ac_var=; unset $ac_var;} ;; + *) $as_unset $ac_var ;; esac ;; esac done @@ -2025,9 +1636,11 @@ $as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;; ) echo - $as_echo "## ----------------- ## + cat <<\_ASBOX +## ----------------- ## ## Output variables. ## -## ----------------- ##" +## ----------------- ## +_ASBOX echo for ac_var in $ac_subst_vars do @@ -2040,9 +1653,11 @@ $as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;; echo if test -n "$ac_subst_files"; then - $as_echo "## ------------------- ## + cat <<\_ASBOX +## ------------------- ## ## File substitutions. ## -## ------------------- ##" +## ------------------- ## +_ASBOX echo for ac_var in $ac_subst_files do @@ -2056,9 +1671,11 @@ $as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;; fi if test -s confdefs.h; then - $as_echo "## ----------- ## + cat <<\_ASBOX +## ----------- ## ## confdefs.h. ## -## ----------- ##" +## ----------- ## +_ASBOX echo cat confdefs.h echo @@ -2072,39 +1689,37 @@ $as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;; exit $exit_status ' 0 for ac_signal in 1 2 13 15; do - trap 'ac_signal='$ac_signal'; as_fn_exit 1' $ac_signal + trap 'ac_signal='$ac_signal'; { (exit 1); exit 1; }' $ac_signal done ac_signal=0 # confdefs.h avoids OS command line length limits that DEFS can exceed. rm -f -r conftest* confdefs.h -$as_echo "/* confdefs.h */" > confdefs.h - # Predefined preprocessor variables. cat >>confdefs.h <<_ACEOF #define PACKAGE_NAME "$PACKAGE_NAME" _ACEOF + cat >>confdefs.h <<_ACEOF #define PACKAGE_TARNAME "$PACKAGE_TARNAME" _ACEOF + cat >>confdefs.h <<_ACEOF #define PACKAGE_VERSION "$PACKAGE_VERSION" _ACEOF + cat >>confdefs.h <<_ACEOF #define PACKAGE_STRING "$PACKAGE_STRING" _ACEOF -cat >>confdefs.h <<_ACEOF -#define PACKAGE_BUGREPORT "$PACKAGE_BUGREPORT" -_ACEOF cat >>confdefs.h <<_ACEOF -#define PACKAGE_URL "$PACKAGE_URL" +#define PACKAGE_BUGREPORT "$PACKAGE_BUGREPORT" _ACEOF @@ -2113,12 +1728,7 @@ _ACEOF ac_site_file1=NONE ac_site_file2=NONE if test -n "$CONFIG_SITE"; then - # We do not want a PATH search for config.site. - case $CONFIG_SITE in #(( - -*) ac_site_file1=./$CONFIG_SITE;; - */*) ac_site_file1=$CONFIG_SITE;; - *) ac_site_file1=./$CONFIG_SITE;; - esac + ac_site_file1=$CONFIG_SITE elif test "x$prefix" != xNONE; then ac_site_file1=$prefix/share/config.site ac_site_file2=$prefix/etc/config.site @@ -2129,23 +1739,19 @@ fi for ac_site_file in "$ac_site_file1" "$ac_site_file2" do test "x$ac_site_file" = xNONE && continue - if test /dev/null != "$ac_site_file" && test -r "$ac_site_file"; then - { $as_echo "$as_me:${as_lineno-$LINENO}: loading site script $ac_site_file" >&5 + if test -r "$ac_site_file"; then + { $as_echo "$as_me:$LINENO: loading site script $ac_site_file" >&5 $as_echo "$as_me: loading site script $ac_site_file" >&6;} sed 's/^/| /' "$ac_site_file" >&5 - . "$ac_site_file" \ - || { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 -$as_echo "$as_me: error: in \`$ac_pwd':" >&2;} -as_fn_error $? "failed to load site script $ac_site_file -See \`config.log' for more details" "$LINENO" 5 ; } + . "$ac_site_file" fi done if test -r "$cache_file"; then - # Some versions of bash will fail to source /dev/null (special files - # actually), so we avoid doing that. DJGPP emulates it as a regular file. - if test /dev/null != "$cache_file" && test -f "$cache_file"; then - { $as_echo "$as_me:${as_lineno-$LINENO}: loading cache $cache_file" >&5 + # Some versions of bash will fail to source /dev/null (special + # files actually), so we avoid doing that. + if test -f "$cache_file"; then + { $as_echo "$as_me:$LINENO: loading cache $cache_file" >&5 $as_echo "$as_me: loading cache $cache_file" >&6;} case $cache_file in [\\/]* | ?:[\\/]* ) . "$cache_file";; @@ -2153,7 +1759,7 @@ $as_echo "$as_me: loading cache $cache_file" >&6;} esac fi else - { $as_echo "$as_me:${as_lineno-$LINENO}: creating cache $cache_file" >&5 + { $as_echo "$as_me:$LINENO: creating cache $cache_file" >&5 $as_echo "$as_me: creating cache $cache_file" >&6;} >$cache_file fi @@ -2168,11 +1774,11 @@ for ac_var in $ac_precious_vars; do eval ac_new_val=\$ac_env_${ac_var}_value case $ac_old_set,$ac_new_set in set,) - { $as_echo "$as_me:${as_lineno-$LINENO}: error: \`$ac_var' was set to \`$ac_old_val' in the previous run" >&5 + { $as_echo "$as_me:$LINENO: error: \`$ac_var' was set to \`$ac_old_val' in the previous run" >&5 $as_echo "$as_me: error: \`$ac_var' was set to \`$ac_old_val' in the previous run" >&2;} ac_cache_corrupted=: ;; ,set) - { $as_echo "$as_me:${as_lineno-$LINENO}: error: \`$ac_var' was not set in the previous run" >&5 + { $as_echo "$as_me:$LINENO: error: \`$ac_var' was not set in the previous run" >&5 $as_echo "$as_me: error: \`$ac_var' was not set in the previous run" >&2;} ac_cache_corrupted=: ;; ,);; @@ -2182,17 +1788,17 @@ $as_echo "$as_me: error: \`$ac_var' was not set in the previous run" >&2;} ac_old_val_w=`echo x $ac_old_val` ac_new_val_w=`echo x $ac_new_val` if test "$ac_old_val_w" != "$ac_new_val_w"; then - { $as_echo "$as_me:${as_lineno-$LINENO}: error: \`$ac_var' has changed since the previous run:" >&5 + { $as_echo "$as_me:$LINENO: error: \`$ac_var' has changed since the previous run:" >&5 $as_echo "$as_me: error: \`$ac_var' has changed since the previous run:" >&2;} ac_cache_corrupted=: else - { $as_echo "$as_me:${as_lineno-$LINENO}: warning: ignoring whitespace changes in \`$ac_var' since the previous run:" >&5 + { $as_echo "$as_me:$LINENO: warning: ignoring whitespace changes in \`$ac_var' since the previous run:" >&5 $as_echo "$as_me: warning: ignoring whitespace changes in \`$ac_var' since the previous run:" >&2;} eval $ac_var=\$ac_old_val fi - { $as_echo "$as_me:${as_lineno-$LINENO}: former value: \`$ac_old_val'" >&5 + { $as_echo "$as_me:$LINENO: former value: \`$ac_old_val'" >&5 $as_echo "$as_me: former value: \`$ac_old_val'" >&2;} - { $as_echo "$as_me:${as_lineno-$LINENO}: current value: \`$ac_new_val'" >&5 + { $as_echo "$as_me:$LINENO: current value: \`$ac_new_val'" >&5 $as_echo "$as_me: current value: \`$ac_new_val'" >&2;} fi;; esac @@ -2204,20 +1810,43 @@ $as_echo "$as_me: current value: \`$ac_new_val'" >&2;} esac case " $ac_configure_args " in *" '$ac_arg' "*) ;; # Avoid dups. Use of quotes ensures accuracy. - *) as_fn_append ac_configure_args " '$ac_arg'" ;; + *) ac_configure_args="$ac_configure_args '$ac_arg'" ;; esac fi done if $ac_cache_corrupted; then - { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 + { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5 $as_echo "$as_me: error: in \`$ac_pwd':" >&2;} - { $as_echo "$as_me:${as_lineno-$LINENO}: error: changes in the environment can compromise the build" >&5 + { $as_echo "$as_me:$LINENO: error: changes in the environment can compromise the build" >&5 $as_echo "$as_me: error: changes in the environment can compromise the build" >&2;} - as_fn_error $? "run \`make distclean' and/or \`rm $cache_file' and start over" "$LINENO" 5 + { { $as_echo "$as_me:$LINENO: error: run \`make distclean' and/or \`rm $cache_file' and start over" >&5 +$as_echo "$as_me: error: run \`make distclean' and/or \`rm $cache_file' and start over" >&2;} + { (exit 1); exit 1; }; } fi -## -------------------- ## -## Main body of script. ## -## -------------------- ## + + + + + + + + + + + + + + + + + + + + + + + + ac_ext=c ac_cpp='$CPP $CPPFLAGS' @@ -2249,7 +1878,9 @@ for ac_dir in "$srcdir" "$srcdir/.." "$srcdir/../.."; do fi done if test -z "$ac_aux_dir"; then - as_fn_error $? "cannot find install-sh, install.sh, or shtool in \"$srcdir\" \"$srcdir/..\" \"$srcdir/../..\"" "$LINENO" 5 + { { $as_echo "$as_me:$LINENO: error: cannot find install-sh or install.sh in \"$srcdir\" \"$srcdir/..\" \"$srcdir/../..\"" >&5 +$as_echo "$as_me: error: cannot find install-sh or install.sh in \"$srcdir\" \"$srcdir/..\" \"$srcdir/../..\"" >&2;} + { (exit 1); exit 1; }; } fi # These three variables are undocumented and unsupported, @@ -2263,27 +1894,35 @@ ac_configure="$SHELL $ac_aux_dir/configure" # Please don't use this var. # Make sure we can run config.sub. $SHELL "$ac_aux_dir/config.sub" sun4 >/dev/null 2>&1 || - as_fn_error $? "cannot run $SHELL $ac_aux_dir/config.sub" "$LINENO" 5 + { { $as_echo "$as_me:$LINENO: error: cannot run $SHELL $ac_aux_dir/config.sub" >&5 +$as_echo "$as_me: error: cannot run $SHELL $ac_aux_dir/config.sub" >&2;} + { (exit 1); exit 1; }; } -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking build system type" >&5 +{ $as_echo "$as_me:$LINENO: checking build system type" >&5 $as_echo_n "checking build system type... " >&6; } -if test "${ac_cv_build+set}" = set; then : +if test "${ac_cv_build+set}" = set; then $as_echo_n "(cached) " >&6 else ac_build_alias=$build_alias test "x$ac_build_alias" = x && ac_build_alias=`$SHELL "$ac_aux_dir/config.guess"` test "x$ac_build_alias" = x && - as_fn_error $? "cannot guess build type; you must specify one" "$LINENO" 5 + { { $as_echo "$as_me:$LINENO: error: cannot guess build type; you must specify one" >&5 +$as_echo "$as_me: error: cannot guess build type; you must specify one" >&2;} + { (exit 1); exit 1; }; } ac_cv_build=`$SHELL "$ac_aux_dir/config.sub" $ac_build_alias` || - as_fn_error $? "$SHELL $ac_aux_dir/config.sub $ac_build_alias failed" "$LINENO" 5 + { { $as_echo "$as_me:$LINENO: error: $SHELL $ac_aux_dir/config.sub $ac_build_alias failed" >&5 +$as_echo "$as_me: error: $SHELL $ac_aux_dir/config.sub $ac_build_alias failed" >&2;} + { (exit 1); exit 1; }; } fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_build" >&5 +{ $as_echo "$as_me:$LINENO: result: $ac_cv_build" >&5 $as_echo "$ac_cv_build" >&6; } case $ac_cv_build in *-*-*) ;; -*) as_fn_error $? "invalid value of canonical build" "$LINENO" 5 ;; +*) { { $as_echo "$as_me:$LINENO: error: invalid value of canonical build" >&5 +$as_echo "$as_me: error: invalid value of canonical build" >&2;} + { (exit 1); exit 1; }; };; esac build=$ac_cv_build ac_save_IFS=$IFS; IFS='-' @@ -2299,24 +1938,28 @@ IFS=$ac_save_IFS case $build_os in *\ *) build_os=`echo "$build_os" | sed 's/ /-/g'`;; esac -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking host system type" >&5 +{ $as_echo "$as_me:$LINENO: checking host system type" >&5 $as_echo_n "checking host system type... " >&6; } -if test "${ac_cv_host+set}" = set; then : +if test "${ac_cv_host+set}" = set; then $as_echo_n "(cached) " >&6 else if test "x$host_alias" = x; then ac_cv_host=$ac_cv_build else ac_cv_host=`$SHELL "$ac_aux_dir/config.sub" $host_alias` || - as_fn_error $? "$SHELL $ac_aux_dir/config.sub $host_alias failed" "$LINENO" 5 + { { $as_echo "$as_me:$LINENO: error: $SHELL $ac_aux_dir/config.sub $host_alias failed" >&5 +$as_echo "$as_me: error: $SHELL $ac_aux_dir/config.sub $host_alias failed" >&2;} + { (exit 1); exit 1; }; } fi fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_host" >&5 +{ $as_echo "$as_me:$LINENO: result: $ac_cv_host" >&5 $as_echo "$ac_cv_host" >&6; } case $ac_cv_host in *-*-*) ;; -*) as_fn_error $? "invalid value of canonical host" "$LINENO" 5 ;; +*) { { $as_echo "$as_me:$LINENO: error: invalid value of canonical host" >&5 +$as_echo "$as_me: error: invalid value of canonical host" >&2;} + { (exit 1); exit 1; }; };; esac host=$ac_cv_host ac_save_IFS=$IFS; IFS='-' @@ -2332,24 +1975,28 @@ IFS=$ac_save_IFS case $host_os in *\ *) host_os=`echo "$host_os" | sed 's/ /-/g'`;; esac -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking target system type" >&5 +{ $as_echo "$as_me:$LINENO: checking target system type" >&5 $as_echo_n "checking target system type... " >&6; } -if test "${ac_cv_target+set}" = set; then : +if test "${ac_cv_target+set}" = set; then $as_echo_n "(cached) " >&6 else if test "x$target_alias" = x; then ac_cv_target=$ac_cv_host else ac_cv_target=`$SHELL "$ac_aux_dir/config.sub" $target_alias` || - as_fn_error $? "$SHELL $ac_aux_dir/config.sub $target_alias failed" "$LINENO" 5 + { { $as_echo "$as_me:$LINENO: error: $SHELL $ac_aux_dir/config.sub $target_alias failed" >&5 +$as_echo "$as_me: error: $SHELL $ac_aux_dir/config.sub $target_alias failed" >&2;} + { (exit 1); exit 1; }; } fi fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_target" >&5 +{ $as_echo "$as_me:$LINENO: result: $ac_cv_target" >&5 $as_echo "$ac_cv_target" >&6; } case $ac_cv_target in *-*-*) ;; -*) as_fn_error $? "invalid value of canonical target" "$LINENO" 5 ;; +*) { { $as_echo "$as_me:$LINENO: error: invalid value of canonical target" >&5 +$as_echo "$as_me: error: invalid value of canonical target" >&2;} + { (exit 1); exit 1; }; };; esac target=$ac_cv_target ac_save_IFS=$IFS; IFS='-' @@ -2372,7 +2019,6 @@ test -n "$target_alias" && NONENONEs,x,x, && program_prefix=${target_alias}- - am__api_version='1.11' # Find a good install program. We prefer a C program (faster), @@ -2389,10 +2035,10 @@ am__api_version='1.11' # OS/2's system install, which has a completely different semantic # ./install, which can be erroneously created by make from ./install.sh. # Reject install programs that cannot install multiple files. -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for a BSD-compatible install" >&5 +{ $as_echo "$as_me:$LINENO: checking for a BSD-compatible install" >&5 $as_echo_n "checking for a BSD-compatible install... " >&6; } if test -z "$INSTALL"; then -if test "${ac_cv_path_install+set}" = set; then : +if test "${ac_cv_path_install+set}" = set; then $as_echo_n "(cached) " >&6 else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR @@ -2400,11 +2046,11 @@ for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - # Account for people who put trailing slashes in PATH elements. -case $as_dir/ in #(( - ./ | .// | /[cC]/* | \ + # Account for people who put trailing slashes in PATH elements. +case $as_dir/ in + ./ | .// | /cC/* | \ /etc/* | /usr/sbin/* | /usr/etc/* | /sbin/* | /usr/afsws/bin/* | \ - ?:[\\/]os2[\\/]install[\\/]* | ?:[\\/]OS2[\\/]INSTALL[\\/]* | \ + ?:\\/os2\\/install\\/* | ?:\\/OS2\\/INSTALL\\/* | \ /usr/ucb/* ) ;; *) # OSF1 and SCO ODT 3.0 have their own names for install. @@ -2441,7 +2087,7 @@ case $as_dir/ in #(( ;; esac - done +done IFS=$as_save_IFS rm -rf conftest.one conftest.two conftest.dir @@ -2457,7 +2103,7 @@ fi INSTALL=$ac_install_sh fi fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $INSTALL" >&5 +{ $as_echo "$as_me:$LINENO: result: $INSTALL" >&5 $as_echo "$INSTALL" >&6; } # Use test -z because SunOS4 sh mishandles braces in ${var-val}. @@ -2468,7 +2114,7 @@ test -z "$INSTALL_SCRIPT" && INSTALL_SCRIPT='${INSTALL}' test -z "$INSTALL_DATA" && INSTALL_DATA='${INSTALL} -m 644' -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether build environment is sane" >&5 +{ $as_echo "$as_me:$LINENO: checking whether build environment is sane" >&5 $as_echo_n "checking whether build environment is sane... " >&6; } # Just in case sleep 1 @@ -2479,11 +2125,15 @@ am_lf=' ' case `pwd` in *[\\\"\#\$\&\'\`$am_lf]*) - as_fn_error $? "unsafe absolute working directory name" "$LINENO" 5 ;; + { { $as_echo "$as_me:$LINENO: error: unsafe absolute working directory name" >&5 +$as_echo "$as_me: error: unsafe absolute working directory name" >&2;} + { (exit 1); exit 1; }; };; esac case $srcdir in *[\\\"\#\$\&\'\`$am_lf\ \ ]*) - as_fn_error $? "unsafe srcdir value: \`$srcdir'" "$LINENO" 5 ;; + { { $as_echo "$as_me:$LINENO: error: unsafe srcdir value: \`$srcdir'" >&5 +$as_echo "$as_me: error: unsafe srcdir value: \`$srcdir'" >&2;} + { (exit 1); exit 1; }; };; esac # Do `set' in a subshell so we don't clobber the current shell's @@ -2505,8 +2155,11 @@ if ( # if, for instance, CONFIG_SHELL is bash and it inherits a # broken ls alias from the environment. This has actually # happened. Such a system could not be considered "sane". - as_fn_error $? "ls -t appears to fail. Make sure there is not a broken -alias in your environment" "$LINENO" 5 + { { $as_echo "$as_me:$LINENO: error: ls -t appears to fail. Make sure there is not a broken +alias in your environment" >&5 +$as_echo "$as_me: error: ls -t appears to fail. Make sure there is not a broken +alias in your environment" >&2;} + { (exit 1); exit 1; }; } fi test "$2" = conftest.file @@ -2515,10 +2168,13 @@ then # Ok. : else - as_fn_error $? "newly created file is older than distributed files! -Check your system clock" "$LINENO" 5 + { { $as_echo "$as_me:$LINENO: error: newly created file is older than distributed files! +Check your system clock" >&5 +$as_echo "$as_me: error: newly created file is older than distributed files! +Check your system clock" >&2;} + { (exit 1); exit 1; }; } fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5 +{ $as_echo "$as_me:$LINENO: result: yes" >&5 $as_echo "yes" >&6; } test "$program_prefix" != NONE && program_transform_name="s&^&$program_prefix&;$program_transform_name" @@ -2546,7 +2202,7 @@ if eval "$MISSING --run true"; then am_missing_run="$MISSING --run " else am_missing_run= - { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: \`missing' script is too old or missing" >&5 + { $as_echo "$as_me:$LINENO: WARNING: \`missing' script is too old or missing" >&5 $as_echo "$as_me: WARNING: \`missing' script is too old or missing" >&2;} fi @@ -2567,9 +2223,9 @@ if test "$cross_compiling" != no; then if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}strip", so it can be a program name with args. set dummy ${ac_tool_prefix}strip; ac_word=$2 -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } -if test "${ac_cv_prog_STRIP+set}" = set; then : +if test "${ac_cv_prog_STRIP+set}" = set; then $as_echo_n "(cached) " >&6 else if test -n "$STRIP"; then @@ -2580,24 +2236,24 @@ for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - for ac_exec_ext in '' $ac_executable_extensions; do + for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_STRIP="${ac_tool_prefix}strip" - $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 + $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done - done +done IFS=$as_save_IFS fi fi STRIP=$ac_cv_prog_STRIP if test -n "$STRIP"; then - { $as_echo "$as_me:${as_lineno-$LINENO}: result: $STRIP" >&5 + { $as_echo "$as_me:$LINENO: result: $STRIP" >&5 $as_echo "$STRIP" >&6; } else - { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 + { $as_echo "$as_me:$LINENO: result: no" >&5 $as_echo "no" >&6; } fi @@ -2607,9 +2263,9 @@ if test -z "$ac_cv_prog_STRIP"; then ac_ct_STRIP=$STRIP # Extract the first word of "strip", so it can be a program name with args. set dummy strip; ac_word=$2 -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } -if test "${ac_cv_prog_ac_ct_STRIP+set}" = set; then : +if test "${ac_cv_prog_ac_ct_STRIP+set}" = set; then $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_STRIP"; then @@ -2620,24 +2276,24 @@ for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - for ac_exec_ext in '' $ac_executable_extensions; do + for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_ac_ct_STRIP="strip" - $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 + $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done - done +done IFS=$as_save_IFS fi fi ac_ct_STRIP=$ac_cv_prog_ac_ct_STRIP if test -n "$ac_ct_STRIP"; then - { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_STRIP" >&5 + { $as_echo "$as_me:$LINENO: result: $ac_ct_STRIP" >&5 $as_echo "$ac_ct_STRIP" >&6; } else - { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 + { $as_echo "$as_me:$LINENO: result: no" >&5 $as_echo "no" >&6; } fi @@ -2646,7 +2302,7 @@ fi else case $cross_compiling:$ac_tool_warned in yes:) -{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 +{ $as_echo "$as_me:$LINENO: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac @@ -2659,10 +2315,10 @@ fi fi INSTALL_STRIP_PROGRAM="\$(install_sh) -c -s" -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for a thread-safe mkdir -p" >&5 +{ $as_echo "$as_me:$LINENO: checking for a thread-safe mkdir -p" >&5 $as_echo_n "checking for a thread-safe mkdir -p... " >&6; } if test -z "$MKDIR_P"; then - if test "${ac_cv_path_mkdir+set}" = set; then : + if test "${ac_cv_path_mkdir+set}" = set; then $as_echo_n "(cached) " >&6 else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR @@ -2670,7 +2326,7 @@ for as_dir in $PATH$PATH_SEPARATOR/opt/sfw/bin do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - for ac_prog in mkdir gmkdir; do + for ac_prog in mkdir gmkdir; do for ac_exec_ext in '' $ac_executable_extensions; do { test -f "$as_dir/$ac_prog$ac_exec_ext" && $as_test_x "$as_dir/$ac_prog$ac_exec_ext"; } || continue case `"$as_dir/$ac_prog$ac_exec_ext" --version 2>&1` in #( @@ -2682,12 +2338,11 @@ do esac done done - done +done IFS=$as_save_IFS fi - test -d ./--version && rmdir ./--version if test "${ac_cv_path_mkdir+set}" = set; then MKDIR_P="$ac_cv_path_mkdir -p" else @@ -2695,10 +2350,11 @@ fi # value for MKDIR_P within a source directory, because that will # break other packages using the cache if that directory is # removed, or if the value is a relative name. + test -d ./--version && rmdir ./--version MKDIR_P="$ac_install_sh -d" fi fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $MKDIR_P" >&5 +{ $as_echo "$as_me:$LINENO: result: $MKDIR_P" >&5 $as_echo "$MKDIR_P" >&6; } mkdir_p="$MKDIR_P" @@ -2711,9 +2367,9 @@ for ac_prog in gawk mawk nawk awk do # Extract the first word of "$ac_prog", so it can be a program name with args. set dummy $ac_prog; ac_word=$2 -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } -if test "${ac_cv_prog_AWK+set}" = set; then : +if test "${ac_cv_prog_AWK+set}" = set; then $as_echo_n "(cached) " >&6 else if test -n "$AWK"; then @@ -2724,24 +2380,24 @@ for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - for ac_exec_ext in '' $ac_executable_extensions; do + for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_AWK="$ac_prog" - $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 + $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done - done +done IFS=$as_save_IFS fi fi AWK=$ac_cv_prog_AWK if test -n "$AWK"; then - { $as_echo "$as_me:${as_lineno-$LINENO}: result: $AWK" >&5 + { $as_echo "$as_me:$LINENO: result: $AWK" >&5 $as_echo "$AWK" >&6; } else - { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 + { $as_echo "$as_me:$LINENO: result: no" >&5 $as_echo "no" >&6; } fi @@ -2749,11 +2405,11 @@ fi test -n "$AWK" && break done -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether ${MAKE-make} sets \$(MAKE)" >&5 +{ $as_echo "$as_me:$LINENO: checking whether ${MAKE-make} sets \$(MAKE)" >&5 $as_echo_n "checking whether ${MAKE-make} sets \$(MAKE)... " >&6; } set x ${MAKE-make} ac_make=`$as_echo "$2" | sed 's/+/p/g; s/[^a-zA-Z0-9_]/_/g'` -if eval "test \"\${ac_cv_prog_make_${ac_make}_set+set}\"" = set; then : +if { as_var=ac_cv_prog_make_${ac_make}_set; eval "test \"\${$as_var+set}\" = set"; }; then $as_echo_n "(cached) " >&6 else cat >conftest.make <<\_ACEOF @@ -2761,7 +2417,7 @@ SHELL = /bin/sh all: @echo '@@@%%%=$(MAKE)=@@@%%%' _ACEOF -# GNU make sometimes prints "make[1]: Entering ...", which would confuse us. +# GNU make sometimes prints "make[1]: Entering...", which would confuse us. case `${MAKE-make} -f conftest.make 2>/dev/null` in *@@@%%%=?*=@@@%%%*) eval ac_cv_prog_make_${ac_make}_set=yes;; @@ -2771,11 +2427,11 @@ esac rm -f conftest.make fi if eval test \$ac_cv_prog_make_${ac_make}_set = yes; then - { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5 + { $as_echo "$as_me:$LINENO: result: yes" >&5 $as_echo "yes" >&6; } SET_MAKE= else - { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 + { $as_echo "$as_me:$LINENO: result: no" >&5 $as_echo "no" >&6; } SET_MAKE="MAKE=${MAKE-make}" fi @@ -2795,7 +2451,9 @@ if test "`cd $srcdir && pwd`" != "`pwd`"; then am__isrc=' -I$(srcdir)' # test to see if srcdir already configured if test -f $srcdir/config.status; then - as_fn_error $? "source directory already configured; run \"make distclean\" there first" "$LINENO" 5 + { { $as_echo "$as_me:$LINENO: error: source directory already configured; run \"make distclean\" there first" >&5 +$as_echo "$as_me: error: source directory already configured; run \"make distclean\" there first" >&2;} + { (exit 1); exit 1; }; } fi fi @@ -2811,7 +2469,7 @@ fi # Define the identity of the package. PACKAGE='gtfold' - VERSION='1.18' + VERSION='2.0' cat >>confdefs.h <<_ACEOF @@ -2853,11 +2511,13 @@ am__tar='${AMTAR} chof - "$$tardir"'; am__untar='${AMTAR} xf -' # Check whether --enable-64bit was given. -if test "${enable_64bit+set}" = set; then : +if test "${enable_64bit+set}" = set; then enableval=$enable_64bit; case "${enableval}" in "" | y | ye | yes) gtfold_cv_enable_64bit=yes ;; n | no) gtfold_cv_enable_64bit=no ;; - *) as_fn_error $? "bad value ${enableval} for --enable-64bit" "$LINENO" 5 ;; + *) { { $as_echo "$as_me:$LINENO: error: bad value ${enableval} for --enable-64bit" >&5 +$as_echo "$as_me: error: bad value ${enableval} for --enable-64bit" >&2;} + { (exit 1); exit 1; }; } ;; esac else gtfold_cv_enable_64bit=no @@ -2888,9 +2548,9 @@ if test -n "$ac_tool_prefix"; then do # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args. set dummy $ac_tool_prefix$ac_prog; ac_word=$2 -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } -if test "${ac_cv_prog_CC+set}" = set; then : +if test "${ac_cv_prog_CC+set}" = set; then $as_echo_n "(cached) " >&6 else if test -n "$CC"; then @@ -2901,24 +2561,24 @@ for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - for ac_exec_ext in '' $ac_executable_extensions; do + for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_CC="$ac_tool_prefix$ac_prog" - $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 + $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done - done +done IFS=$as_save_IFS fi fi CC=$ac_cv_prog_CC if test -n "$CC"; then - { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5 + { $as_echo "$as_me:$LINENO: result: $CC" >&5 $as_echo "$CC" >&6; } else - { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 + { $as_echo "$as_me:$LINENO: result: no" >&5 $as_echo "no" >&6; } fi @@ -2932,9 +2592,9 @@ if test -z "$CC"; then do # Extract the first word of "$ac_prog", so it can be a program name with args. set dummy $ac_prog; ac_word=$2 -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } -if test "${ac_cv_prog_ac_ct_CC+set}" = set; then : +if test "${ac_cv_prog_ac_ct_CC+set}" = set; then $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_CC"; then @@ -2945,24 +2605,24 @@ for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - for ac_exec_ext in '' $ac_executable_extensions; do + for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_ac_ct_CC="$ac_prog" - $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 + $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done - done +done IFS=$as_save_IFS fi fi ac_ct_CC=$ac_cv_prog_ac_ct_CC if test -n "$ac_ct_CC"; then - { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_CC" >&5 + { $as_echo "$as_me:$LINENO: result: $ac_ct_CC" >&5 $as_echo "$ac_ct_CC" >&6; } else - { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 + { $as_echo "$as_me:$LINENO: result: no" >&5 $as_echo "no" >&6; } fi @@ -2975,7 +2635,7 @@ done else case $cross_compiling:$ac_tool_warned in yes:) -{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 +{ $as_echo "$as_me:$LINENO: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac @@ -2984,37 +2644,57 @@ esac fi -test -z "$CC" && { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 +test -z "$CC" && { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5 $as_echo "$as_me: error: in \`$ac_pwd':" >&2;} -as_fn_error $? "no acceptable C compiler found in \$PATH -See \`config.log' for more details" "$LINENO" 5 ; } +{ { $as_echo "$as_me:$LINENO: error: no acceptable C compiler found in \$PATH +See \`config.log' for more details." >&5 +$as_echo "$as_me: error: no acceptable C compiler found in \$PATH +See \`config.log' for more details." >&2;} + { (exit 1); exit 1; }; }; } # Provide some information about the compiler. -$as_echo "$as_me:${as_lineno-$LINENO}: checking for C compiler version" >&5 +$as_echo "$as_me:$LINENO: checking for C compiler version" >&5 set X $ac_compile ac_compiler=$2 -for ac_option in --version -v -V -qversion; do - { { ac_try="$ac_compiler $ac_option >&5" +{ (ac_try="$ac_compiler --version >&5" case "(($ac_try" in *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; *) ac_try_echo=$ac_try;; esac -eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\"" -$as_echo "$ac_try_echo"; } >&5 - (eval "$ac_compiler $ac_option >&5") 2>conftest.err +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compiler --version >&5") 2>&5 ac_status=$? - if test -s conftest.err; then - sed '10a\ -... rest of stderr output deleted ... - 10q' conftest.err >conftest.er1 - cat conftest.er1 >&5 - fi - rm -f conftest.er1 conftest.err - $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 - test $ac_status = 0; } -done + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } +{ (ac_try="$ac_compiler -v >&5" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compiler -v >&5") 2>&5 + ac_status=$? + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } +{ (ac_try="$ac_compiler -V >&5" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compiler -V >&5") 2>&5 + ac_status=$? + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } -cat confdefs.h - <<_ACEOF >conftest.$ac_ext +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ int @@ -3030,8 +2710,8 @@ ac_clean_files="$ac_clean_files a.out a.out.dSYM a.exe b.out" # Try to create an executable without -o first, disregard a.out. # It will help us diagnose broken compilers, and finding out an intuition # of exeext. -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether the C compiler works" >&5 -$as_echo_n "checking whether the C compiler works... " >&6; } +{ $as_echo "$as_me:$LINENO: checking for C compiler default output file name" >&5 +$as_echo_n "checking for C compiler default output file name... " >&6; } ac_link_default=`$as_echo "$ac_link" | sed 's/ -o *conftest[^ ]*//'` # The possible output files: @@ -3047,17 +2727,17 @@ do done rm -f $ac_rmfiles -if { { ac_try="$ac_link_default" +if { (ac_try="$ac_link_default" case "(($ac_try" in *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; *) ac_try_echo=$ac_try;; esac -eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\"" -$as_echo "$ac_try_echo"; } >&5 +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 (eval "$ac_link_default") 2>&5 ac_status=$? - $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 - test $ac_status = 0; }; then : + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; then # Autoconf-2.13 could set the ac_cv_exeext variable to `no'. # So ignore a value of `no', otherwise this would lead to `EXEEXT = no' # in a Makefile. We should not override ac_cv_exeext if it was cached, @@ -3074,7 +2754,7 @@ do # certainly right. break;; *.* ) - if test "${ac_cv_exeext+set}" = set && test "$ac_cv_exeext" != no; + if test "${ac_cv_exeext+set}" = set && test "$ac_cv_exeext" != no; then :; else ac_cv_exeext=`expr "$ac_file" : '[^.]*\(\..*\)'` fi @@ -3093,132 +2773,124 @@ test "$ac_cv_exeext" = no && ac_cv_exeext= else ac_file='' fi -if test -z "$ac_file"; then : - { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 -$as_echo "no" >&6; } -$as_echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 -{ { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 -$as_echo "$as_me: error: in \`$ac_pwd':" >&2;} -as_fn_error 77 "C compiler cannot create executables -See \`config.log' for more details" "$LINENO" 5 ; } -else - { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5 -$as_echo "yes" >&6; } -fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for C compiler default output file name" >&5 -$as_echo_n "checking for C compiler default output file name... " >&6; } -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_file" >&5 +{ $as_echo "$as_me:$LINENO: result: $ac_file" >&5 $as_echo "$ac_file" >&6; } -ac_exeext=$ac_cv_exeext +if test -z "$ac_file"; then + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 -rm -f -r a.out a.out.dSYM a.exe conftest$ac_cv_exeext b.out -ac_clean_files=$ac_clean_files_save -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for suffix of executables" >&5 -$as_echo_n "checking for suffix of executables... " >&6; } -if { { ac_try="$ac_link" -case "(($ac_try" in - *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; - *) ac_try_echo=$ac_try;; -esac -eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\"" -$as_echo "$ac_try_echo"; } >&5 - (eval "$ac_link") 2>&5 - ac_status=$? - $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 - test $ac_status = 0; }; then : - # If both `conftest.exe' and `conftest' are `present' (well, observable) -# catch `conftest.exe'. For instance with Cygwin, `ls conftest' will -# work properly (i.e., refer to `conftest.exe'), while it won't with -# `rm'. -for ac_file in conftest.exe conftest conftest.*; do - test -f "$ac_file" || continue - case $ac_file in - *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.map | *.inf | *.dSYM | *.o | *.obj ) ;; - *.* ) ac_cv_exeext=`expr "$ac_file" : '[^.]*\(\..*\)'` - break;; - * ) break;; - esac -done -else - { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 +{ { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5 $as_echo "$as_me: error: in \`$ac_pwd':" >&2;} -as_fn_error $? "cannot compute suffix of executables: cannot compile and link -See \`config.log' for more details" "$LINENO" 5 ; } +{ { $as_echo "$as_me:$LINENO: error: C compiler cannot create executables +See \`config.log' for more details." >&5 +$as_echo "$as_me: error: C compiler cannot create executables +See \`config.log' for more details." >&2;} + { (exit 77); exit 77; }; }; } fi -rm -f conftest conftest$ac_cv_exeext -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_exeext" >&5 -$as_echo "$ac_cv_exeext" >&6; } -rm -f conftest.$ac_ext -EXEEXT=$ac_cv_exeext -ac_exeext=$EXEEXT -cat confdefs.h - <<_ACEOF >conftest.$ac_ext -/* end confdefs.h. */ -#include -int -main () -{ -FILE *f = fopen ("conftest.out", "w"); - return ferror (f) || fclose (f) != 0; +ac_exeext=$ac_cv_exeext - ; - return 0; -} -_ACEOF -ac_clean_files="$ac_clean_files conftest.out" # Check that the compiler produces executables we can run. If not, either # the compiler is broken, or we cross compile. -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether we are cross compiling" >&5 -$as_echo_n "checking whether we are cross compiling... " >&6; } +{ $as_echo "$as_me:$LINENO: checking whether the C compiler works" >&5 +$as_echo_n "checking whether the C compiler works... " >&6; } +# FIXME: These cross compiler hacks should be removed for Autoconf 3.0 +# If not cross compiling, check that we can run a simple program. if test "$cross_compiling" != yes; then - { { ac_try="$ac_link" -case "(($ac_try" in - *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; - *) ac_try_echo=$ac_try;; -esac -eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\"" -$as_echo "$ac_try_echo"; } >&5 - (eval "$ac_link") 2>&5 - ac_status=$? - $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 - test $ac_status = 0; } - if { ac_try='./conftest$ac_cv_exeext' - { { case "(($ac_try" in + if { ac_try='./$ac_file' + { (case "(($ac_try" in *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; *) ac_try_echo=$ac_try;; esac -eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\"" -$as_echo "$ac_try_echo"; } >&5 +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 (eval "$ac_try") 2>&5 ac_status=$? - $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 - test $ac_status = 0; }; }; then + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then cross_compiling=no else if test "$cross_compiling" = maybe; then cross_compiling=yes else - { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 + { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5 $as_echo "$as_me: error: in \`$ac_pwd':" >&2;} -as_fn_error $? "cannot run C compiled programs. +{ { $as_echo "$as_me:$LINENO: error: cannot run C compiled programs. If you meant to cross compile, use \`--host'. -See \`config.log' for more details" "$LINENO" 5 ; } +See \`config.log' for more details." >&5 +$as_echo "$as_me: error: cannot run C compiled programs. +If you meant to cross compile, use \`--host'. +See \`config.log' for more details." >&2;} + { (exit 1); exit 1; }; }; } fi fi fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $cross_compiling" >&5 -$as_echo "$cross_compiling" >&6; } +{ $as_echo "$as_me:$LINENO: result: yes" >&5 +$as_echo "yes" >&6; } -rm -f conftest.$ac_ext conftest$ac_cv_exeext conftest.out +rm -f -r a.out a.out.dSYM a.exe conftest$ac_cv_exeext b.out ac_clean_files=$ac_clean_files_save -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for suffix of object files" >&5 +# Check that the compiler produces executables we can run. If not, either +# the compiler is broken, or we cross compile. +{ $as_echo "$as_me:$LINENO: checking whether we are cross compiling" >&5 +$as_echo_n "checking whether we are cross compiling... " >&6; } +{ $as_echo "$as_me:$LINENO: result: $cross_compiling" >&5 +$as_echo "$cross_compiling" >&6; } + +{ $as_echo "$as_me:$LINENO: checking for suffix of executables" >&5 +$as_echo_n "checking for suffix of executables... " >&6; } +if { (ac_try="$ac_link" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_link") 2>&5 + ac_status=$? + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; then + # If both `conftest.exe' and `conftest' are `present' (well, observable) +# catch `conftest.exe'. For instance with Cygwin, `ls conftest' will +# work properly (i.e., refer to `conftest.exe'), while it won't with +# `rm'. +for ac_file in conftest.exe conftest conftest.*; do + test -f "$ac_file" || continue + case $ac_file in + *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.map | *.inf | *.dSYM | *.o | *.obj ) ;; + *.* ) ac_cv_exeext=`expr "$ac_file" : '[^.]*\(\..*\)'` + break;; + * ) break;; + esac +done +else + { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5 +$as_echo "$as_me: error: in \`$ac_pwd':" >&2;} +{ { $as_echo "$as_me:$LINENO: error: cannot compute suffix of executables: cannot compile and link +See \`config.log' for more details." >&5 +$as_echo "$as_me: error: cannot compute suffix of executables: cannot compile and link +See \`config.log' for more details." >&2;} + { (exit 1); exit 1; }; }; } +fi + +rm -f conftest$ac_cv_exeext +{ $as_echo "$as_me:$LINENO: result: $ac_cv_exeext" >&5 +$as_echo "$ac_cv_exeext" >&6; } + +rm -f conftest.$ac_ext +EXEEXT=$ac_cv_exeext +ac_exeext=$EXEEXT +{ $as_echo "$as_me:$LINENO: checking for suffix of object files" >&5 $as_echo_n "checking for suffix of object files... " >&6; } -if test "${ac_cv_objext+set}" = set; then : +if test "${ac_cv_objext+set}" = set; then $as_echo_n "(cached) " >&6 else - cat confdefs.h - <<_ACEOF >conftest.$ac_ext + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ int @@ -3230,17 +2902,17 @@ main () } _ACEOF rm -f conftest.o conftest.obj -if { { ac_try="$ac_compile" +if { (ac_try="$ac_compile" case "(($ac_try" in *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; *) ac_try_echo=$ac_try;; esac -eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\"" -$as_echo "$ac_try_echo"; } >&5 +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 (eval "$ac_compile") 2>&5 ac_status=$? - $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 - test $ac_status = 0; }; then : + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; then for ac_file in conftest.o conftest.obj conftest.*; do test -f "$ac_file" || continue; case $ac_file in @@ -3253,23 +2925,31 @@ else $as_echo "$as_me: failed program was:" >&5 sed 's/^/| /' conftest.$ac_ext >&5 -{ { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 +{ { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5 $as_echo "$as_me: error: in \`$ac_pwd':" >&2;} -as_fn_error $? "cannot compute suffix of object files: cannot compile -See \`config.log' for more details" "$LINENO" 5 ; } +{ { $as_echo "$as_me:$LINENO: error: cannot compute suffix of object files: cannot compile +See \`config.log' for more details." >&5 +$as_echo "$as_me: error: cannot compute suffix of object files: cannot compile +See \`config.log' for more details." >&2;} + { (exit 1); exit 1; }; }; } fi + rm -f conftest.$ac_cv_objext conftest.$ac_ext fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_objext" >&5 +{ $as_echo "$as_me:$LINENO: result: $ac_cv_objext" >&5 $as_echo "$ac_cv_objext" >&6; } OBJEXT=$ac_cv_objext ac_objext=$OBJEXT -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether we are using the GNU C compiler" >&5 +{ $as_echo "$as_me:$LINENO: checking whether we are using the GNU C compiler" >&5 $as_echo_n "checking whether we are using the GNU C compiler... " >&6; } -if test "${ac_cv_c_compiler_gnu+set}" = set; then : +if test "${ac_cv_c_compiler_gnu+set}" = set; then $as_echo_n "(cached) " >&6 else - cat confdefs.h - <<_ACEOF >conftest.$ac_ext + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ int @@ -3283,16 +2963,37 @@ main () return 0; } _ACEOF -if ac_fn_c_try_compile "$LINENO"; then : +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then ac_compiler_gnu=yes else - ac_compiler_gnu=no + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_compiler_gnu=no fi + rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext ac_cv_c_compiler_gnu=$ac_compiler_gnu fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_c_compiler_gnu" >&5 +{ $as_echo "$as_me:$LINENO: result: $ac_cv_c_compiler_gnu" >&5 $as_echo "$ac_cv_c_compiler_gnu" >&6; } if test $ac_compiler_gnu = yes; then GCC=yes @@ -3301,16 +3002,20 @@ else fi ac_test_CFLAGS=${CFLAGS+set} ac_save_CFLAGS=$CFLAGS -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $CC accepts -g" >&5 +{ $as_echo "$as_me:$LINENO: checking whether $CC accepts -g" >&5 $as_echo_n "checking whether $CC accepts -g... " >&6; } -if test "${ac_cv_prog_cc_g+set}" = set; then : +if test "${ac_cv_prog_cc_g+set}" = set; then $as_echo_n "(cached) " >&6 else ac_save_c_werror_flag=$ac_c_werror_flag ac_c_werror_flag=yes ac_cv_prog_cc_g=no CFLAGS="-g" - cat confdefs.h - <<_ACEOF >conftest.$ac_ext + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ int @@ -3321,11 +3026,35 @@ main () return 0; } _ACEOF -if ac_fn_c_try_compile "$LINENO"; then : +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then ac_cv_prog_cc_g=yes else - CFLAGS="" - cat confdefs.h - <<_ACEOF >conftest.$ac_ext + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + CFLAGS="" + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ int @@ -3336,12 +3065,36 @@ main () return 0; } _ACEOF -if ac_fn_c_try_compile "$LINENO"; then : - +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + : else - ac_c_werror_flag=$ac_save_c_werror_flag + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_c_werror_flag=$ac_save_c_werror_flag CFLAGS="-g" - cat confdefs.h - <<_ACEOF >conftest.$ac_ext + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ int @@ -3352,17 +3105,42 @@ main () return 0; } _ACEOF -if ac_fn_c_try_compile "$LINENO"; then : +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then ac_cv_prog_cc_g=yes +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + fi + rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext fi + rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext fi + rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext ac_c_werror_flag=$ac_save_c_werror_flag fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cc_g" >&5 +{ $as_echo "$as_me:$LINENO: result: $ac_cv_prog_cc_g" >&5 $as_echo "$ac_cv_prog_cc_g" >&6; } if test "$ac_test_CFLAGS" = set; then CFLAGS=$ac_save_CFLAGS @@ -3379,14 +3157,18 @@ else CFLAGS= fi fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $CC option to accept ISO C89" >&5 +{ $as_echo "$as_me:$LINENO: checking for $CC option to accept ISO C89" >&5 $as_echo_n "checking for $CC option to accept ISO C89... " >&6; } -if test "${ac_cv_prog_cc_c89+set}" = set; then : +if test "${ac_cv_prog_cc_c89+set}" = set; then $as_echo_n "(cached) " >&6 else ac_cv_prog_cc_c89=no ac_save_CC=$CC -cat confdefs.h - <<_ACEOF >conftest.$ac_ext +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ #include #include @@ -3443,9 +3225,32 @@ for ac_arg in '' -qlanglvl=extc89 -qlanglvl=ansi -std \ -Ae "-Aa -D_HPUX_SOURCE" "-Xc -D__EXTENSIONS__" do CC="$ac_save_CC $ac_arg" - if ac_fn_c_try_compile "$LINENO"; then : + rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then ac_cv_prog_cc_c89=$ac_arg +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + fi + rm -f core conftest.err conftest.$ac_objext test "x$ac_cv_prog_cc_c89" != "xno" && break done @@ -3456,19 +3261,17 @@ fi # AC_CACHE_VAL case "x$ac_cv_prog_cc_c89" in x) - { $as_echo "$as_me:${as_lineno-$LINENO}: result: none needed" >&5 + { $as_echo "$as_me:$LINENO: result: none needed" >&5 $as_echo "none needed" >&6; } ;; xno) - { $as_echo "$as_me:${as_lineno-$LINENO}: result: unsupported" >&5 + { $as_echo "$as_me:$LINENO: result: unsupported" >&5 $as_echo "unsupported" >&6; } ;; *) CC="$CC $ac_cv_prog_cc_c89" - { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cc_c89" >&5 + { $as_echo "$as_me:$LINENO: result: $ac_cv_prog_cc_c89" >&5 $as_echo "$ac_cv_prog_cc_c89" >&6; } ;; esac -if test "x$ac_cv_prog_cc_c89" != xno; then : -fi ac_ext=c ac_cpp='$CPP $CPPFLAGS' @@ -3487,7 +3290,7 @@ am__doit: .PHONY: am__doit END # If we don't find an include directive, just comment out the code. -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for style of include used by $am_make" >&5 +{ $as_echo "$as_me:$LINENO: checking for style of include used by $am_make" >&5 $as_echo_n "checking for style of include used by $am_make... " >&6; } am__include="#" am__quote= @@ -3515,12 +3318,12 @@ if test "$am__include" = "#"; then fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $_am_result" >&5 +{ $as_echo "$as_me:$LINENO: result: $_am_result" >&5 $as_echo "$_am_result" >&6; } rm -f confinc confmf # Check whether --enable-dependency-tracking was given. -if test "${enable_dependency_tracking+set}" = set; then : +if test "${enable_dependency_tracking+set}" = set; then enableval=$enable_dependency_tracking; fi @@ -3540,9 +3343,9 @@ fi depcc="$CC" am_compiler_list= -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking dependency style of $depcc" >&5 +{ $as_echo "$as_me:$LINENO: checking dependency style of $depcc" >&5 $as_echo_n "checking dependency style of $depcc... " >&6; } -if test "${am_cv_CC_dependencies_compiler_type+set}" = set; then : +if test "${am_cv_CC_dependencies_compiler_type+set}" = set; then $as_echo_n "(cached) " >&6 else if test -z "$AMDEP_TRUE" && test -f "$am_depcomp"; then @@ -3650,7 +3453,7 @@ else fi fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $am_cv_CC_dependencies_compiler_type" >&5 +{ $as_echo "$as_me:$LINENO: result: $am_cv_CC_dependencies_compiler_type" >&5 $as_echo "$am_cv_CC_dependencies_compiler_type" >&6; } CCDEPMODE=depmode=$am_cv_CC_dependencies_compiler_type @@ -3679,9 +3482,9 @@ if test -z "$CXX"; then do # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args. set dummy $ac_tool_prefix$ac_prog; ac_word=$2 -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } -if test "${ac_cv_prog_CXX+set}" = set; then : +if test "${ac_cv_prog_CXX+set}" = set; then $as_echo_n "(cached) " >&6 else if test -n "$CXX"; then @@ -3692,24 +3495,24 @@ for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - for ac_exec_ext in '' $ac_executable_extensions; do + for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_CXX="$ac_tool_prefix$ac_prog" - $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 + $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done - done +done IFS=$as_save_IFS fi fi CXX=$ac_cv_prog_CXX if test -n "$CXX"; then - { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CXX" >&5 + { $as_echo "$as_me:$LINENO: result: $CXX" >&5 $as_echo "$CXX" >&6; } else - { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 + { $as_echo "$as_me:$LINENO: result: no" >&5 $as_echo "no" >&6; } fi @@ -3723,9 +3526,9 @@ if test -z "$CXX"; then do # Extract the first word of "$ac_prog", so it can be a program name with args. set dummy $ac_prog; ac_word=$2 -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } -if test "${ac_cv_prog_ac_ct_CXX+set}" = set; then : +if test "${ac_cv_prog_ac_ct_CXX+set}" = set; then $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_CXX"; then @@ -3736,24 +3539,24 @@ for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - for ac_exec_ext in '' $ac_executable_extensions; do + for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_ac_ct_CXX="$ac_prog" - $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 + $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done - done +done IFS=$as_save_IFS fi fi ac_ct_CXX=$ac_cv_prog_ac_ct_CXX if test -n "$ac_ct_CXX"; then - { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_CXX" >&5 + { $as_echo "$as_me:$LINENO: result: $ac_ct_CXX" >&5 $as_echo "$ac_ct_CXX" >&6; } else - { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 + { $as_echo "$as_me:$LINENO: result: no" >&5 $as_echo "no" >&6; } fi @@ -3766,7 +3569,7 @@ done else case $cross_compiling:$ac_tool_warned in yes:) -{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 +{ $as_echo "$as_me:$LINENO: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac @@ -3777,36 +3580,53 @@ fi fi fi # Provide some information about the compiler. -$as_echo "$as_me:${as_lineno-$LINENO}: checking for C++ compiler version" >&5 +$as_echo "$as_me:$LINENO: checking for C++ compiler version" >&5 set X $ac_compile ac_compiler=$2 -for ac_option in --version -v -V -qversion; do - { { ac_try="$ac_compiler $ac_option >&5" +{ (ac_try="$ac_compiler --version >&5" case "(($ac_try" in *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; *) ac_try_echo=$ac_try;; esac -eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\"" -$as_echo "$ac_try_echo"; } >&5 - (eval "$ac_compiler $ac_option >&5") 2>conftest.err +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compiler --version >&5") 2>&5 ac_status=$? - if test -s conftest.err; then - sed '10a\ -... rest of stderr output deleted ... - 10q' conftest.err >conftest.er1 - cat conftest.er1 >&5 - fi - rm -f conftest.er1 conftest.err - $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 - test $ac_status = 0; } -done + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } +{ (ac_try="$ac_compiler -v >&5" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compiler -v >&5") 2>&5 + ac_status=$? + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } +{ (ac_try="$ac_compiler -V >&5" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compiler -V >&5") 2>&5 + ac_status=$? + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether we are using the GNU C++ compiler" >&5 +{ $as_echo "$as_me:$LINENO: checking whether we are using the GNU C++ compiler" >&5 $as_echo_n "checking whether we are using the GNU C++ compiler... " >&6; } -if test "${ac_cv_cxx_compiler_gnu+set}" = set; then : +if test "${ac_cv_cxx_compiler_gnu+set}" = set; then $as_echo_n "(cached) " >&6 else - cat confdefs.h - <<_ACEOF >conftest.$ac_ext + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ int @@ -3820,16 +3640,37 @@ main () return 0; } _ACEOF -if ac_fn_cxx_try_compile "$LINENO"; then : +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_cxx_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then ac_compiler_gnu=yes else - ac_compiler_gnu=no + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_compiler_gnu=no fi + rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext ac_cv_cxx_compiler_gnu=$ac_compiler_gnu fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_cxx_compiler_gnu" >&5 +{ $as_echo "$as_me:$LINENO: result: $ac_cv_cxx_compiler_gnu" >&5 $as_echo "$ac_cv_cxx_compiler_gnu" >&6; } if test $ac_compiler_gnu = yes; then GXX=yes @@ -3838,16 +3679,20 @@ else fi ac_test_CXXFLAGS=${CXXFLAGS+set} ac_save_CXXFLAGS=$CXXFLAGS -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $CXX accepts -g" >&5 +{ $as_echo "$as_me:$LINENO: checking whether $CXX accepts -g" >&5 $as_echo_n "checking whether $CXX accepts -g... " >&6; } -if test "${ac_cv_prog_cxx_g+set}" = set; then : +if test "${ac_cv_prog_cxx_g+set}" = set; then $as_echo_n "(cached) " >&6 else ac_save_cxx_werror_flag=$ac_cxx_werror_flag ac_cxx_werror_flag=yes ac_cv_prog_cxx_g=no CXXFLAGS="-g" - cat confdefs.h - <<_ACEOF >conftest.$ac_ext + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ int @@ -3858,11 +3703,35 @@ main () return 0; } _ACEOF -if ac_fn_cxx_try_compile "$LINENO"; then : +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_cxx_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then ac_cv_prog_cxx_g=yes else - CXXFLAGS="" - cat confdefs.h - <<_ACEOF >conftest.$ac_ext + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + CXXFLAGS="" + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ int @@ -3873,12 +3742,36 @@ main () return 0; } _ACEOF -if ac_fn_cxx_try_compile "$LINENO"; then : - +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_cxx_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + : else - ac_cxx_werror_flag=$ac_save_cxx_werror_flag + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_cxx_werror_flag=$ac_save_cxx_werror_flag CXXFLAGS="-g" - cat confdefs.h - <<_ACEOF >conftest.$ac_ext + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ int @@ -3889,17 +3782,42 @@ main () return 0; } _ACEOF -if ac_fn_cxx_try_compile "$LINENO"; then : +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_cxx_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then ac_cv_prog_cxx_g=yes +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + fi + rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext fi + rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext fi + rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext ac_cxx_werror_flag=$ac_save_cxx_werror_flag fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cxx_g" >&5 +{ $as_echo "$as_me:$LINENO: result: $ac_cv_prog_cxx_g" >&5 $as_echo "$ac_cv_prog_cxx_g" >&6; } if test "$ac_test_CXXFLAGS" = set; then CXXFLAGS=$ac_save_CXXFLAGS @@ -3924,9 +3842,9 @@ ac_compiler_gnu=$ac_cv_c_compiler_gnu depcc="$CXX" am_compiler_list= -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking dependency style of $depcc" >&5 +{ $as_echo "$as_me:$LINENO: checking dependency style of $depcc" >&5 $as_echo_n "checking dependency style of $depcc... " >&6; } -if test "${am_cv_CXX_dependencies_compiler_type+set}" = set; then : +if test "${am_cv_CXX_dependencies_compiler_type+set}" = set; then $as_echo_n "(cached) " >&6 else if test -z "$AMDEP_TRUE" && test -f "$am_depcomp"; then @@ -4034,7 +3952,7 @@ else fi fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $am_cv_CXX_dependencies_compiler_type" >&5 +{ $as_echo "$as_me:$LINENO: result: $am_cv_CXX_dependencies_compiler_type" >&5 $as_echo "$am_cv_CXX_dependencies_compiler_type" >&6; } CXXDEPMODE=depmode=$am_cv_CXX_dependencies_compiler_type @@ -4049,25 +3967,116 @@ else fi -#AC_PROG_LIBTOOL +#AC_PROG_LIBTOOL +# Find a good install program. We prefer a C program (faster), +# so one script is as good as another. But avoid the broken or +# incompatible versions: +# SysV /etc/install, /usr/sbin/install +# SunOS /usr/etc/install +# IRIX /sbin/install +# AIX /bin/install +# AmigaOS /C/install, which installs bootblocks on floppy discs +# AIX 4 /usr/bin/installbsd, which doesn't work without a -g flag +# AFS /usr/afsws/bin/install, which mishandles nonexistent args +# SVR4 /usr/ucb/install, which tries to use the nonexistent group "staff" +# OS/2's system install, which has a completely different semantic +# ./install, which can be erroneously created by make from ./install.sh. +# Reject install programs that cannot install multiple files. +{ $as_echo "$as_me:$LINENO: checking for a BSD-compatible install" >&5 +$as_echo_n "checking for a BSD-compatible install... " >&6; } +if test -z "$INSTALL"; then +if test "${ac_cv_path_install+set}" = set; then + $as_echo_n "(cached) " >&6 +else + as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + # Account for people who put trailing slashes in PATH elements. +case $as_dir/ in + ./ | .// | /cC/* | \ + /etc/* | /usr/sbin/* | /usr/etc/* | /sbin/* | /usr/afsws/bin/* | \ + ?:\\/os2\\/install\\/* | ?:\\/OS2\\/INSTALL\\/* | \ + /usr/ucb/* ) ;; + *) + # OSF1 and SCO ODT 3.0 have their own names for install. + # Don't use installbsd from OSF since it installs stuff as root + # by default. + for ac_prog in ginstall scoinst install; do + for ac_exec_ext in '' $ac_executable_extensions; do + if { test -f "$as_dir/$ac_prog$ac_exec_ext" && $as_test_x "$as_dir/$ac_prog$ac_exec_ext"; }; then + if test $ac_prog = install && + grep dspmsg "$as_dir/$ac_prog$ac_exec_ext" >/dev/null 2>&1; then + # AIX install. It has an incompatible calling convention. + : + elif test $ac_prog = install && + grep pwplus "$as_dir/$ac_prog$ac_exec_ext" >/dev/null 2>&1; then + # program-specific install script used by HP pwplus--don't use. + : + else + rm -rf conftest.one conftest.two conftest.dir + echo one > conftest.one + echo two > conftest.two + mkdir conftest.dir + if "$as_dir/$ac_prog$ac_exec_ext" -c conftest.one conftest.two "`pwd`/conftest.dir" && + test -s conftest.one && test -s conftest.two && + test -s conftest.dir/conftest.one && + test -s conftest.dir/conftest.two + then + ac_cv_path_install="$as_dir/$ac_prog$ac_exec_ext -c" + break 3 + fi + fi + fi + done + done + ;; +esac + +done +IFS=$as_save_IFS + +rm -rf conftest.one conftest.two conftest.dir + +fi + if test "${ac_cv_path_install+set}" = set; then + INSTALL=$ac_cv_path_install + else + # As a last resort, use the slow shell script. Don't cache a + # value for INSTALL within a source directory, because that will + # break other packages using the cache if that directory is + # removed, or if the value is a relative name. + INSTALL=$ac_install_sh + fi +fi +{ $as_echo "$as_me:$LINENO: result: $INSTALL" >&5 +$as_echo "$INSTALL" >&6; } + +# Use test -z because SunOS4 sh mishandles braces in ${var-val}. +# It thinks the first close brace ends the variable substitution. +test -z "$INSTALL_PROGRAM" && INSTALL_PROGRAM='${INSTALL}' + +test -z "$INSTALL_SCRIPT" && INSTALL_SCRIPT='${INSTALL}' + +test -z "$INSTALL_DATA" && INSTALL_DATA='${INSTALL} -m 644' OPENMP_CFLAGS= # Check whether --enable-openmp was given. -if test "${enable_openmp+set}" = set; then : +if test "${enable_openmp+set}" = set; then enableval=$enable_openmp; fi if test "$enable_openmp" != no; then - { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $CC option to support OpenMP" >&5 + { $as_echo "$as_me:$LINENO: checking for $CC option to support OpenMP" >&5 $as_echo_n "checking for $CC option to support OpenMP... " >&6; } -if test "${ac_cv_prog_c_openmp+set}" = set; then : +if test "${ac_cv_prog_c_openmp+set}" = set; then $as_echo_n "(cached) " >&6 else - cat confdefs.h - <<_ACEOF >conftest.$ac_ext -/* end confdefs.h. */ + cat >conftest.$ac_ext <<_ACEOF #ifndef _OPENMP choke me @@ -4076,15 +4085,37 @@ else int main () { return omp_get_num_threads (); } _ACEOF -if ac_fn_c_try_link "$LINENO"; then : +rm -f conftest.$ac_objext conftest$ac_exeext +if { (ac_try="$ac_link" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_link") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest$ac_exeext && { + test "$cross_compiling" = yes || + $as_test_x conftest$ac_exeext + }; then ac_cv_prog_c_openmp='none needed' else - ac_cv_prog_c_openmp='unsupported' + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_cv_prog_c_openmp='unsupported' for ac_option in -fopenmp -xopenmp -openmp -mp -omp -qsmp=omp; do ac_save_CFLAGS=$CFLAGS CFLAGS="$CFLAGS $ac_option" - cat confdefs.h - <<_ACEOF >conftest.$ac_ext -/* end confdefs.h. */ + cat >conftest.$ac_ext <<_ACEOF #ifndef _OPENMP choke me @@ -4093,27 +4124,56 @@ else int main () { return omp_get_num_threads (); } _ACEOF -if ac_fn_c_try_link "$LINENO"; then : +rm -f conftest.$ac_objext conftest$ac_exeext +if { (ac_try="$ac_link" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_link") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest$ac_exeext && { + test "$cross_compiling" = yes || + $as_test_x conftest$ac_exeext + }; then ac_cv_prog_c_openmp=$ac_option +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + fi -rm -f core conftest.err conftest.$ac_objext \ - conftest$ac_exeext conftest.$ac_ext + +rm -rf conftest.dSYM +rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \ + conftest$ac_exeext conftest.$ac_ext CFLAGS=$ac_save_CFLAGS if test "$ac_cv_prog_c_openmp" != unsupported; then break fi done fi -rm -f core conftest.err conftest.$ac_objext \ - conftest$ac_exeext conftest.$ac_ext + +rm -rf conftest.dSYM +rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \ + conftest$ac_exeext conftest.$ac_ext fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_c_openmp" >&5 +{ $as_echo "$as_me:$LINENO: result: $ac_cv_prog_c_openmp" >&5 $as_echo "$ac_cv_prog_c_openmp" >&6; } case $ac_cv_prog_c_openmp in #( "none needed" | unsupported) - ;; #( + ;; #( *) - OPENMP_CFLAGS=$ac_cv_prog_c_openmp ;; + OPENMP_CFLAGS=$ac_cv_prog_c_openmp ;; esac fi @@ -4121,14 +4181,18 @@ $as_echo "$ac_cv_prog_c_openmp" >&6; } #AC_DEFINE([_RAND],[],[RNG library to use]) -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for log2 in -lm" >&5 +{ $as_echo "$as_me:$LINENO: checking for log2 in -lm" >&5 $as_echo_n "checking for log2 in -lm... " >&6; } -if test "${ac_cv_lib_m_log2+set}" = set; then : +if test "${ac_cv_lib_m_log2+set}" = set; then $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-lm $LIBS" -cat confdefs.h - <<_ACEOF >conftest.$ac_ext +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ /* Override any GCC internal prototype to avoid an error. @@ -4146,20 +4210,47 @@ return log2 (); return 0; } _ACEOF -if ac_fn_c_try_link "$LINENO"; then : +rm -f conftest.$ac_objext conftest$ac_exeext +if { (ac_try="$ac_link" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_link") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest$ac_exeext && { + test "$cross_compiling" = yes || + $as_test_x conftest$ac_exeext + }; then ac_cv_lib_m_log2=yes else - ac_cv_lib_m_log2=no + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_cv_lib_m_log2=no fi -rm -f core conftest.err conftest.$ac_objext \ - conftest$ac_exeext conftest.$ac_ext + +rm -rf conftest.dSYM +rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \ + conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_m_log2" >&5 +{ $as_echo "$as_me:$LINENO: result: $ac_cv_lib_m_log2" >&5 $as_echo "$ac_cv_lib_m_log2" >&6; } -if test "x$ac_cv_lib_m_log2" = x""yes; then : +if test "x$ac_cv_lib_m_log2" = x""yes; then -$as_echo "#define HAVE_LOG2 /**/" >>confdefs.h +cat >>confdefs.h <<\_ACEOF +#define HAVE_LOG2 /**/ +_ACEOF fi @@ -4169,14 +4260,14 @@ ac_cpp='$CPP $CPPFLAGS' ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' ac_compiler_gnu=$ac_cv_c_compiler_gnu -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking how to run the C preprocessor" >&5 +{ $as_echo "$as_me:$LINENO: checking how to run the C preprocessor" >&5 $as_echo_n "checking how to run the C preprocessor... " >&6; } # On Suns, sometimes $CPP names a directory. if test -n "$CPP" && test -d "$CPP"; then CPP= fi if test -z "$CPP"; then - if test "${ac_cv_prog_CPP+set}" = set; then : + if test "${ac_cv_prog_CPP+set}" = set; then $as_echo_n "(cached) " >&6 else # Double quotes because CPP needs to be expanded @@ -4191,7 +4282,11 @@ do # exists even on freestanding compilers. # On the NeXT, cc -E runs the code through the compiler's parser, # not just through cpp. "Syntax error" is here to catch this case. - cat confdefs.h - <<_ACEOF >conftest.$ac_ext + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ #ifdef __STDC__ # include @@ -4200,34 +4295,78 @@ do #endif Syntax error _ACEOF -if ac_fn_c_try_cpp "$LINENO"; then : - +if { (ac_try="$ac_cpp conftest.$ac_ext" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } >/dev/null && { + test -z "$ac_c_preproc_warn_flag$ac_c_werror_flag" || + test ! -s conftest.err + }; then + : else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + # Broken: fails on valid input. continue fi -rm -f conftest.err conftest.i conftest.$ac_ext + +rm -f conftest.err conftest.$ac_ext # OK, works on sane cases. Now check whether nonexistent headers # can be detected and how. - cat confdefs.h - <<_ACEOF >conftest.$ac_ext + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ #include _ACEOF -if ac_fn_c_try_cpp "$LINENO"; then : +if { (ac_try="$ac_cpp conftest.$ac_ext" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } >/dev/null && { + test -z "$ac_c_preproc_warn_flag$ac_c_werror_flag" || + test ! -s conftest.err + }; then # Broken: success on invalid input. continue else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + # Passes both tests. ac_preproc_ok=: break fi -rm -f conftest.err conftest.i conftest.$ac_ext + +rm -f conftest.err conftest.$ac_ext done # Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped. -rm -f conftest.i conftest.err conftest.$ac_ext -if $ac_preproc_ok; then : +rm -f conftest.err conftest.$ac_ext +if $ac_preproc_ok; then break fi @@ -4239,7 +4378,7 @@ fi else ac_cv_prog_CPP=$CPP fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $CPP" >&5 +{ $as_echo "$as_me:$LINENO: result: $CPP" >&5 $as_echo "$CPP" >&6; } ac_preproc_ok=false for ac_c_preproc_warn_flag in '' yes @@ -4250,7 +4389,11 @@ do # exists even on freestanding compilers. # On the NeXT, cc -E runs the code through the compiler's parser, # not just through cpp. "Syntax error" is here to catch this case. - cat confdefs.h - <<_ACEOF >conftest.$ac_ext + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ #ifdef __STDC__ # include @@ -4259,40 +4402,87 @@ do #endif Syntax error _ACEOF -if ac_fn_c_try_cpp "$LINENO"; then : - +if { (ac_try="$ac_cpp conftest.$ac_ext" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } >/dev/null && { + test -z "$ac_c_preproc_warn_flag$ac_c_werror_flag" || + test ! -s conftest.err + }; then + : else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + # Broken: fails on valid input. continue fi -rm -f conftest.err conftest.i conftest.$ac_ext + +rm -f conftest.err conftest.$ac_ext # OK, works on sane cases. Now check whether nonexistent headers # can be detected and how. - cat confdefs.h - <<_ACEOF >conftest.$ac_ext + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ #include _ACEOF -if ac_fn_c_try_cpp "$LINENO"; then : +if { (ac_try="$ac_cpp conftest.$ac_ext" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } >/dev/null && { + test -z "$ac_c_preproc_warn_flag$ac_c_werror_flag" || + test ! -s conftest.err + }; then # Broken: success on invalid input. continue else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + # Passes both tests. ac_preproc_ok=: break fi -rm -f conftest.err conftest.i conftest.$ac_ext + +rm -f conftest.err conftest.$ac_ext done # Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped. -rm -f conftest.i conftest.err conftest.$ac_ext -if $ac_preproc_ok; then : - +rm -f conftest.err conftest.$ac_ext +if $ac_preproc_ok; then + : else - { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 + { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5 $as_echo "$as_me: error: in \`$ac_pwd':" >&2;} -as_fn_error $? "C preprocessor \"$CPP\" fails sanity check -See \`config.log' for more details" "$LINENO" 5 ; } +{ { $as_echo "$as_me:$LINENO: error: C preprocessor \"$CPP\" fails sanity check +See \`config.log' for more details." >&5 +$as_echo "$as_me: error: C preprocessor \"$CPP\" fails sanity check +See \`config.log' for more details." >&2;} + { (exit 1); exit 1; }; }; } fi ac_ext=c @@ -4302,9 +4492,9 @@ ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $ ac_compiler_gnu=$ac_cv_c_compiler_gnu -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for grep that handles long lines and -e" >&5 +{ $as_echo "$as_me:$LINENO: checking for grep that handles long lines and -e" >&5 $as_echo_n "checking for grep that handles long lines and -e... " >&6; } -if test "${ac_cv_path_GREP+set}" = set; then : +if test "${ac_cv_path_GREP+set}" = set; then $as_echo_n "(cached) " >&6 else if test -z "$GREP"; then @@ -4315,7 +4505,7 @@ for as_dir in $PATH$PATH_SEPARATOR/usr/xpg4/bin do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - for ac_prog in grep ggrep; do + for ac_prog in grep ggrep; do for ac_exec_ext in '' $ac_executable_extensions; do ac_path_GREP="$as_dir/$ac_prog$ac_exec_ext" { test -f "$ac_path_GREP" && $as_test_x "$ac_path_GREP"; } || continue @@ -4335,7 +4525,7 @@ case `"$ac_path_GREP" --version 2>&1` in $as_echo 'GREP' >> "conftest.nl" "$ac_path_GREP" -e 'GREP$' -e '-(cannot match)-' < "conftest.nl" >"conftest.out" 2>/dev/null || break diff "conftest.out" "conftest.nl" >/dev/null 2>&1 || break - as_fn_arith $ac_count + 1 && ac_count=$as_val + ac_count=`expr $ac_count + 1` if test $ac_count -gt ${ac_path_GREP_max-0}; then # Best one so far, save it but keep looking for a better one ac_cv_path_GREP="$ac_path_GREP" @@ -4350,24 +4540,26 @@ esac $ac_path_GREP_found && break 3 done done - done +done IFS=$as_save_IFS if test -z "$ac_cv_path_GREP"; then - as_fn_error $? "no acceptable grep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" "$LINENO" 5 + { { $as_echo "$as_me:$LINENO: error: no acceptable grep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" >&5 +$as_echo "$as_me: error: no acceptable grep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" >&2;} + { (exit 1); exit 1; }; } fi else ac_cv_path_GREP=$GREP fi fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_path_GREP" >&5 +{ $as_echo "$as_me:$LINENO: result: $ac_cv_path_GREP" >&5 $as_echo "$ac_cv_path_GREP" >&6; } GREP="$ac_cv_path_GREP" -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for egrep" >&5 +{ $as_echo "$as_me:$LINENO: checking for egrep" >&5 $as_echo_n "checking for egrep... " >&6; } -if test "${ac_cv_path_EGREP+set}" = set; then : +if test "${ac_cv_path_EGREP+set}" = set; then $as_echo_n "(cached) " >&6 else if echo a | $GREP -E '(a|b)' >/dev/null 2>&1 @@ -4381,7 +4573,7 @@ for as_dir in $PATH$PATH_SEPARATOR/usr/xpg4/bin do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - for ac_prog in egrep; do + for ac_prog in egrep; do for ac_exec_ext in '' $ac_executable_extensions; do ac_path_EGREP="$as_dir/$ac_prog$ac_exec_ext" { test -f "$ac_path_EGREP" && $as_test_x "$ac_path_EGREP"; } || continue @@ -4401,7 +4593,7 @@ case `"$ac_path_EGREP" --version 2>&1` in $as_echo 'EGREP' >> "conftest.nl" "$ac_path_EGREP" 'EGREP$' < "conftest.nl" >"conftest.out" 2>/dev/null || break diff "conftest.out" "conftest.nl" >/dev/null 2>&1 || break - as_fn_arith $ac_count + 1 && ac_count=$as_val + ac_count=`expr $ac_count + 1` if test $ac_count -gt ${ac_path_EGREP_max-0}; then # Best one so far, save it but keep looking for a better one ac_cv_path_EGREP="$ac_path_EGREP" @@ -4416,10 +4608,12 @@ esac $ac_path_EGREP_found && break 3 done done - done +done IFS=$as_save_IFS if test -z "$ac_cv_path_EGREP"; then - as_fn_error $? "no acceptable egrep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" "$LINENO" 5 + { { $as_echo "$as_me:$LINENO: error: no acceptable egrep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" >&5 +$as_echo "$as_me: error: no acceptable egrep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" >&2;} + { (exit 1); exit 1; }; } fi else ac_cv_path_EGREP=$EGREP @@ -4427,17 +4621,21 @@ fi fi fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_path_EGREP" >&5 +{ $as_echo "$as_me:$LINENO: result: $ac_cv_path_EGREP" >&5 $as_echo "$ac_cv_path_EGREP" >&6; } EGREP="$ac_cv_path_EGREP" -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for ANSI C header files" >&5 +{ $as_echo "$as_me:$LINENO: checking for ANSI C header files" >&5 $as_echo_n "checking for ANSI C header files... " >&6; } -if test "${ac_cv_header_stdc+set}" = set; then : +if test "${ac_cv_header_stdc+set}" = set; then $as_echo_n "(cached) " >&6 else - cat confdefs.h - <<_ACEOF >conftest.$ac_ext + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ #include #include @@ -4452,23 +4650,48 @@ main () return 0; } _ACEOF -if ac_fn_c_try_compile "$LINENO"; then : +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then ac_cv_header_stdc=yes else - ac_cv_header_stdc=no + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_cv_header_stdc=no fi + rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext if test $ac_cv_header_stdc = yes; then # SunOS 4.x string.h does not declare mem*, contrary to ANSI. - cat confdefs.h - <<_ACEOF >conftest.$ac_ext + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ #include _ACEOF if (eval "$ac_cpp conftest.$ac_ext") 2>&5 | - $EGREP "memchr" >/dev/null 2>&1; then : - + $EGREP "memchr" >/dev/null 2>&1; then + : else ac_cv_header_stdc=no fi @@ -4478,14 +4701,18 @@ fi if test $ac_cv_header_stdc = yes; then # ISC 2.0.2 stdlib.h does not declare free, contrary to ANSI. - cat confdefs.h - <<_ACEOF >conftest.$ac_ext + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ #include _ACEOF if (eval "$ac_cpp conftest.$ac_ext") 2>&5 | - $EGREP "free" >/dev/null 2>&1; then : - + $EGREP "free" >/dev/null 2>&1; then + : else ac_cv_header_stdc=no fi @@ -4495,10 +4722,14 @@ fi if test $ac_cv_header_stdc = yes; then # /bin/cc in Irix-4.0.5 gets non-ANSI ctype macros unless using -ansi. - if test "$cross_compiling" = yes; then : + if test "$cross_compiling" = yes; then : else - cat confdefs.h - <<_ACEOF >conftest.$ac_ext + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ #include #include @@ -4525,49 +4756,269 @@ main () return 0; } _ACEOF -if ac_fn_c_try_run "$LINENO"; then : - +rm -f conftest$ac_exeext +if { (ac_try="$ac_link" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_link") 2>&5 + ac_status=$? + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { ac_try='./conftest$ac_exeext' + { (case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_try") 2>&5 + ac_status=$? + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + : else - ac_cv_header_stdc=no + $as_echo "$as_me: program exited with status $ac_status" >&5 +$as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +( exit $ac_status ) +ac_cv_header_stdc=no fi -rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext \ - conftest.$ac_objext conftest.beam conftest.$ac_ext +rm -rf conftest.dSYM +rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext fi + fi fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_header_stdc" >&5 +{ $as_echo "$as_me:$LINENO: result: $ac_cv_header_stdc" >&5 $as_echo "$ac_cv_header_stdc" >&6; } if test $ac_cv_header_stdc = yes; then -$as_echo "#define STDC_HEADERS 1" >>confdefs.h +cat >>confdefs.h <<\_ACEOF +#define STDC_HEADERS 1 +_ACEOF fi #AC_CHECK_HEADERS(sys/resource.h) #AC_CHECK_HEADERS(getopt.h) # On IRIX 5.3, sys/types and inttypes.h are conflicting. + + + + + + + + + for ac_header in sys/types.h sys/stat.h stdlib.h string.h memory.h strings.h \ inttypes.h stdint.h unistd.h -do : - as_ac_Header=`$as_echo "ac_cv_header_$ac_header" | $as_tr_sh` -ac_fn_c_check_header_compile "$LINENO" "$ac_header" "$as_ac_Header" "$ac_includes_default -" -if eval test \"x\$"$as_ac_Header"\" = x"yes"; then : +do +as_ac_Header=`$as_echo "ac_cv_header_$ac_header" | $as_tr_sh` +{ $as_echo "$as_me:$LINENO: checking for $ac_header" >&5 +$as_echo_n "checking for $ac_header... " >&6; } +if { as_var=$as_ac_Header; eval "test \"\${$as_var+set}\" = set"; }; then + $as_echo_n "(cached) " >&6 +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_includes_default + +#include <$ac_header> +_ACEOF +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + eval "$as_ac_Header=yes" +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + eval "$as_ac_Header=no" +fi + +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +fi +ac_res=`eval 'as_val=${'$as_ac_Header'} + $as_echo "$as_val"'` + { $as_echo "$as_me:$LINENO: result: $ac_res" >&5 +$as_echo "$ac_res" >&6; } +as_val=`eval 'as_val=${'$as_ac_Header'} + $as_echo "$as_val"'` + if test "x$as_val" = x""yes; then cat >>confdefs.h <<_ACEOF #define `$as_echo "HAVE_$ac_header" | $as_tr_cpp` 1 _ACEOF fi - -done - - -for ac_header in stdlib.h string.h sys/time.h -do : - as_ac_Header=`$as_echo "ac_cv_header_$ac_header" | $as_tr_sh` -ac_fn_c_check_header_mongrel "$LINENO" "$ac_header" "$as_ac_Header" "$ac_includes_default" -if eval test \"x\$"$as_ac_Header"\" = x"yes"; then : + +done + + + + + +for ac_header in stdlib.h string.h sys/time.h +do +as_ac_Header=`$as_echo "ac_cv_header_$ac_header" | $as_tr_sh` +if { as_var=$as_ac_Header; eval "test \"\${$as_var+set}\" = set"; }; then + { $as_echo "$as_me:$LINENO: checking for $ac_header" >&5 +$as_echo_n "checking for $ac_header... " >&6; } +if { as_var=$as_ac_Header; eval "test \"\${$as_var+set}\" = set"; }; then + $as_echo_n "(cached) " >&6 +fi +ac_res=`eval 'as_val=${'$as_ac_Header'} + $as_echo "$as_val"'` + { $as_echo "$as_me:$LINENO: result: $ac_res" >&5 +$as_echo "$ac_res" >&6; } +else + # Is the header compilable? +{ $as_echo "$as_me:$LINENO: checking $ac_header usability" >&5 +$as_echo_n "checking $ac_header usability... " >&6; } +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_includes_default +#include <$ac_header> +_ACEOF +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + ac_header_compiler=yes +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_header_compiler=no +fi + +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +{ $as_echo "$as_me:$LINENO: result: $ac_header_compiler" >&5 +$as_echo "$ac_header_compiler" >&6; } + +# Is the header present? +{ $as_echo "$as_me:$LINENO: checking $ac_header presence" >&5 +$as_echo_n "checking $ac_header presence... " >&6; } +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +#include <$ac_header> +_ACEOF +if { (ac_try="$ac_cpp conftest.$ac_ext" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } >/dev/null && { + test -z "$ac_c_preproc_warn_flag$ac_c_werror_flag" || + test ! -s conftest.err + }; then + ac_header_preproc=yes +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_header_preproc=no +fi + +rm -f conftest.err conftest.$ac_ext +{ $as_echo "$as_me:$LINENO: result: $ac_header_preproc" >&5 +$as_echo "$ac_header_preproc" >&6; } + +# So? What about this header? +case $ac_header_compiler:$ac_header_preproc:$ac_c_preproc_warn_flag in + yes:no: ) + { $as_echo "$as_me:$LINENO: WARNING: $ac_header: accepted by the compiler, rejected by the preprocessor!" >&5 +$as_echo "$as_me: WARNING: $ac_header: accepted by the compiler, rejected by the preprocessor!" >&2;} + { $as_echo "$as_me:$LINENO: WARNING: $ac_header: proceeding with the compiler's result" >&5 +$as_echo "$as_me: WARNING: $ac_header: proceeding with the compiler's result" >&2;} + ac_header_preproc=yes + ;; + no:yes:* ) + { $as_echo "$as_me:$LINENO: WARNING: $ac_header: present but cannot be compiled" >&5 +$as_echo "$as_me: WARNING: $ac_header: present but cannot be compiled" >&2;} + { $as_echo "$as_me:$LINENO: WARNING: $ac_header: check for missing prerequisite headers?" >&5 +$as_echo "$as_me: WARNING: $ac_header: check for missing prerequisite headers?" >&2;} + { $as_echo "$as_me:$LINENO: WARNING: $ac_header: see the Autoconf documentation" >&5 +$as_echo "$as_me: WARNING: $ac_header: see the Autoconf documentation" >&2;} + { $as_echo "$as_me:$LINENO: WARNING: $ac_header: section \"Present But Cannot Be Compiled\"" >&5 +$as_echo "$as_me: WARNING: $ac_header: section \"Present But Cannot Be Compiled\"" >&2;} + { $as_echo "$as_me:$LINENO: WARNING: $ac_header: proceeding with the preprocessor's result" >&5 +$as_echo "$as_me: WARNING: $ac_header: proceeding with the preprocessor's result" >&2;} + { $as_echo "$as_me:$LINENO: WARNING: $ac_header: in the future, the compiler will take precedence" >&5 +$as_echo "$as_me: WARNING: $ac_header: in the future, the compiler will take precedence" >&2;} + + ;; +esac +{ $as_echo "$as_me:$LINENO: checking for $ac_header" >&5 +$as_echo_n "checking for $ac_header... " >&6; } +if { as_var=$as_ac_Header; eval "test \"\${$as_var+set}\" = set"; }; then + $as_echo_n "(cached) " >&6 +else + eval "$as_ac_Header=\$ac_header_preproc" +fi +ac_res=`eval 'as_val=${'$as_ac_Header'} + $as_echo "$as_val"'` + { $as_echo "$as_me:$LINENO: result: $ac_res" >&5 +$as_echo "$ac_res" >&6; } + +fi +as_val=`eval 'as_val=${'$as_ac_Header'} + $as_echo "$as_val"'` + if test "x$as_val" = x""yes; then cat >>confdefs.h <<_ACEOF #define `$as_echo "HAVE_$ac_header" | $as_tr_cpp` 1 _ACEOF @@ -4577,12 +5028,16 @@ fi done -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for an ANSI C-conforming const" >&5 +{ $as_echo "$as_me:$LINENO: checking for an ANSI C-conforming const" >&5 $as_echo_n "checking for an ANSI C-conforming const... " >&6; } -if test "${ac_cv_c_const+set}" = set; then : +if test "${ac_cv_c_const+set}" = set; then $as_echo_n "(cached) " >&6 else - cat confdefs.h - <<_ACEOF >conftest.$ac_ext + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ int @@ -4642,29 +5097,56 @@ main () return 0; } _ACEOF -if ac_fn_c_try_compile "$LINENO"; then : +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then ac_cv_c_const=yes else - ac_cv_c_const=no + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_cv_c_const=no fi + rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_c_const" >&5 +{ $as_echo "$as_me:$LINENO: result: $ac_cv_c_const" >&5 $as_echo "$ac_cv_c_const" >&6; } if test $ac_cv_c_const = no; then -$as_echo "#define const /**/" >>confdefs.h +cat >>confdefs.h <<\_ACEOF +#define const /**/ +_ACEOF fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for inline" >&5 +{ $as_echo "$as_me:$LINENO: checking for inline" >&5 $as_echo_n "checking for inline... " >&6; } -if test "${ac_cv_c_inline+set}" = set; then : +if test "${ac_cv_c_inline+set}" = set; then $as_echo_n "(cached) " >&6 else ac_cv_c_inline=no for ac_kw in inline __inline__ __inline; do - cat confdefs.h - <<_ACEOF >conftest.$ac_ext + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ #ifndef __cplusplus typedef int foo_t; @@ -4673,17 +5155,41 @@ $ac_kw foo_t foo () {return 0; } #endif _ACEOF -if ac_fn_c_try_compile "$LINENO"; then : +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then ac_cv_c_inline=$ac_kw +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + fi + rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext test "$ac_cv_c_inline" != no && break done fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_c_inline" >&5 +{ $as_echo "$as_me:$LINENO: result: $ac_cv_c_inline" >&5 $as_echo "$ac_cv_c_inline" >&6; } + case $ac_cv_c_inline in inline | yes) ;; *) @@ -4699,9 +5205,102 @@ _ACEOF ;; esac -ac_fn_c_check_type "$LINENO" "size_t" "ac_cv_type_size_t" "$ac_includes_default" -if test "x$ac_cv_type_size_t" = x""yes; then : +{ $as_echo "$as_me:$LINENO: checking for size_t" >&5 +$as_echo_n "checking for size_t... " >&6; } +if test "${ac_cv_type_size_t+set}" = set; then + $as_echo_n "(cached) " >&6 +else + ac_cv_type_size_t=no +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_includes_default +int +main () +{ +if (sizeof (size_t)) + return 0; + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_includes_default +int +main () +{ +if (sizeof ((size_t))) + return 0; + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + : +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_cv_type_size_t=yes +fi + +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + +fi +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +fi +{ $as_echo "$as_me:$LINENO: result: $ac_cv_type_size_t" >&5 +$as_echo "$ac_cv_type_size_t" >&6; } +if test "x$ac_cv_type_size_t" = x""yes; then + : else cat >>confdefs.h <<_ACEOF @@ -4710,12 +5309,16 @@ _ACEOF fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether time.h and sys/time.h may both be included" >&5 +{ $as_echo "$as_me:$LINENO: checking whether time.h and sys/time.h may both be included" >&5 $as_echo_n "checking whether time.h and sys/time.h may both be included... " >&6; } -if test "${ac_cv_header_time+set}" = set; then : +if test "${ac_cv_header_time+set}" = set; then $as_echo_n "(cached) " >&6 else - cat confdefs.h - <<_ACEOF >conftest.$ac_ext + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ #include #include @@ -4730,27 +5333,54 @@ return 0; return 0; } _ACEOF -if ac_fn_c_try_compile "$LINENO"; then : +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then ac_cv_header_time=yes else - ac_cv_header_time=no + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_cv_header_time=no fi + rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_header_time" >&5 +{ $as_echo "$as_me:$LINENO: result: $ac_cv_header_time" >&5 $as_echo "$ac_cv_header_time" >&6; } if test $ac_cv_header_time = yes; then -$as_echo "#define TIME_WITH_SYS_TIME 1" >>confdefs.h +cat >>confdefs.h <<\_ACEOF +#define TIME_WITH_SYS_TIME 1 +_ACEOF fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether struct tm is in sys/time.h or time.h" >&5 +{ $as_echo "$as_me:$LINENO: checking whether struct tm is in sys/time.h or time.h" >&5 $as_echo_n "checking whether struct tm is in sys/time.h or time.h... " >&6; } -if test "${ac_cv_struct_tm+set}" = set; then : +if test "${ac_cv_struct_tm+set}" = set; then $as_echo_n "(cached) " >&6 else - cat confdefs.h - <<_ACEOF >conftest.$ac_ext + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ #include #include @@ -4765,18 +5395,41 @@ struct tm tm; return 0; } _ACEOF -if ac_fn_c_try_compile "$LINENO"; then : +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then ac_cv_struct_tm=time.h else - ac_cv_struct_tm=sys/time.h + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_cv_struct_tm=sys/time.h fi + rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_struct_tm" >&5 +{ $as_echo "$as_me:$LINENO: result: $ac_cv_struct_tm" >&5 $as_echo "$ac_cv_struct_tm" >&6; } if test $ac_cv_struct_tm = sys/time.h; then -$as_echo "#define TM_IN_SYS_TIME 1" >>confdefs.h +cat >>confdefs.h <<\_ACEOF +#define TM_IN_SYS_TIME 1 +_ACEOF fi @@ -4799,10 +5452,14 @@ if test "x$GXX" = "xyes"; then fi -If Sun cc is present, define appropriate compiler flags -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for Sun C compiler" >&5 +#If Sun cc is present, define appropriate compiler flags +{ $as_echo "$as_me:$LINENO: checking for Sun C compiler" >&5 $as_echo_n "checking for Sun C compiler... " >&6; } -cat confdefs.h - <<_ACEOF >conftest.$ac_ext +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ int @@ -4816,22 +5473,47 @@ main () return 0; } _ACEOF -if ac_fn_c_try_compile "$LINENO"; then : - { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5 +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + { $as_echo "$as_me:$LINENO: result: yes" >&5 $as_echo "yes" >&6; } gtfold_cv_check_sunpro_cc=yes else - { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + { $as_echo "$as_me:$LINENO: result: no" >&5 $as_echo "no" >&6; } gtfold_cv_check_sunpro_cc=no fi + rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext if test "$gtfold_cv_check_sunpro_cc" == "yes"; then - { $as_echo "$as_me:${as_lineno-$LINENO}: checking for Sun C compiler architecture target" >&5 + { $as_echo "$as_me:$LINENO: checking for Sun C compiler architecture target" >&5 $as_echo_n "checking for Sun C compiler architecture target... " >&6; } - cat confdefs.h - <<_ACEOF >conftest.$ac_ext + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ int @@ -4845,15 +5527,36 @@ main () return 0; } _ACEOF -if ac_fn_c_try_compile "$LINENO"; then : - { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5 +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + { $as_echo "$as_me:$LINENO: result: yes" >&5 $as_echo "yes" >&6; } gtfold_cv_check_sun_sparc=yes else - { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + { $as_echo "$as_me:$LINENO: result: no" >&5 $as_echo "no" >&6; } gtfold_cv_check_sun_sparc=no fi + rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext fi @@ -4861,9 +5564,13 @@ if test "$gtfold_cv_check_sunpro_cc" == "yes"; then if test "$gtfold_cv_check_sun_sparc" == "yes"; then - { $as_echo "$as_me:${as_lineno-$LINENO}: checking for Sun sparc v9 architecture" >&5 + { $as_echo "$as_me:$LINENO: checking for Sun sparc v9 architecture" >&5 $as_echo_n "checking for Sun sparc v9 architecture... " >&6; } - cat confdefs.h - <<_ACEOF >conftest.$ac_ext + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ int @@ -4877,15 +5584,36 @@ main () return 0; } _ACEOF -if ac_fn_c_try_compile "$LINENO"; then : - { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5 +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + { $as_echo "$as_me:$LINENO: result: yes" >&5 $as_echo "yes" >&6; } gtfold_cv_check_sun_sparcv9=yes else - { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + { $as_echo "$as_me:$LINENO: result: no" >&5 $as_echo "no" >&6; } gtfold_cv_check_sun_sparcv9=no fi + rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext fi fi @@ -4908,14 +5636,18 @@ fi if test "$enable_openmp" != 'no'; then if test "x${GCC}" = "xyes"; then - { $as_echo "$as_me:${as_lineno-$LINENO}: checking for GOMP_parallel_start in -lomp" >&5 + { $as_echo "$as_me:$LINENO: checking for GOMP_parallel_start in -lomp" >&5 $as_echo_n "checking for GOMP_parallel_start in -lomp... " >&6; } -if test "${ac_cv_lib_omp_GOMP_parallel_start+set}" = set; then : +if test "${ac_cv_lib_omp_GOMP_parallel_start+set}" = set; then $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-lomp $LIBS" -cat confdefs.h - <<_ACEOF >conftest.$ac_ext +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ /* Override any GCC internal prototype to avoid an error. @@ -4933,29 +5665,58 @@ return GOMP_parallel_start (); return 0; } _ACEOF -if ac_fn_c_try_link "$LINENO"; then : +rm -f conftest.$ac_objext conftest$ac_exeext +if { (ac_try="$ac_link" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_link") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest$ac_exeext && { + test "$cross_compiling" = yes || + $as_test_x conftest$ac_exeext + }; then ac_cv_lib_omp_GOMP_parallel_start=yes else - ac_cv_lib_omp_GOMP_parallel_start=no + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_cv_lib_omp_GOMP_parallel_start=no fi -rm -f core conftest.err conftest.$ac_objext \ - conftest$ac_exeext conftest.$ac_ext + +rm -rf conftest.dSYM +rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \ + conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_omp_GOMP_parallel_start" >&5 +{ $as_echo "$as_me:$LINENO: result: $ac_cv_lib_omp_GOMP_parallel_start" >&5 $as_echo "$ac_cv_lib_omp_GOMP_parallel_start" >&6; } -if test "x$ac_cv_lib_omp_GOMP_parallel_start" = x""yes; then : +if test "x$ac_cv_lib_omp_GOMP_parallel_start" = x""yes; then LIB_OMP="-lgomp" fi - { $as_echo "$as_me:${as_lineno-$LINENO}: checking for GOMP_parallel_start in -lgomp" >&5 + { $as_echo "$as_me:$LINENO: checking for GOMP_parallel_start in -lgomp" >&5 $as_echo_n "checking for GOMP_parallel_start in -lgomp... " >&6; } -if test "${ac_cv_lib_gomp_GOMP_parallel_start+set}" = set; then : +if test "${ac_cv_lib_gomp_GOMP_parallel_start+set}" = set; then $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-lgomp $LIBS" -cat confdefs.h - <<_ACEOF >conftest.$ac_ext +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ /* Override any GCC internal prototype to avoid an error. @@ -4973,30 +5734,59 @@ return GOMP_parallel_start (); return 0; } _ACEOF -if ac_fn_c_try_link "$LINENO"; then : +rm -f conftest.$ac_objext conftest$ac_exeext +if { (ac_try="$ac_link" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_link") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest$ac_exeext && { + test "$cross_compiling" = yes || + $as_test_x conftest$ac_exeext + }; then ac_cv_lib_gomp_GOMP_parallel_start=yes else - ac_cv_lib_gomp_GOMP_parallel_start=no + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_cv_lib_gomp_GOMP_parallel_start=no fi -rm -f core conftest.err conftest.$ac_objext \ - conftest$ac_exeext conftest.$ac_ext + +rm -rf conftest.dSYM +rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \ + conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_gomp_GOMP_parallel_start" >&5 +{ $as_echo "$as_me:$LINENO: result: $ac_cv_lib_gomp_GOMP_parallel_start" >&5 $as_echo "$ac_cv_lib_gomp_GOMP_parallel_start" >&6; } -if test "x$ac_cv_lib_gomp_GOMP_parallel_start" = x""yes; then : +if test "x$ac_cv_lib_gomp_GOMP_parallel_start" = x""yes; then GOMP_LIBS="-lgomp" fi else - { $as_echo "$as_me:${as_lineno-$LINENO}: checking for sunw_mp_register_warn in -lmtsk" >&5 + { $as_echo "$as_me:$LINENO: checking for sunw_mp_register_warn in -lmtsk" >&5 $as_echo_n "checking for sunw_mp_register_warn in -lmtsk... " >&6; } -if test "${ac_cv_lib_mtsk_sunw_mp_register_warn+set}" = set; then : +if test "${ac_cv_lib_mtsk_sunw_mp_register_warn+set}" = set; then $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-lmtsk $LIBS" -cat confdefs.h - <<_ACEOF >conftest.$ac_ext +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ /* Override any GCC internal prototype to avoid an error. @@ -5014,29 +5804,58 @@ return sunw_mp_register_warn (); return 0; } _ACEOF -if ac_fn_c_try_link "$LINENO"; then : +rm -f conftest.$ac_objext conftest$ac_exeext +if { (ac_try="$ac_link" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_link") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest$ac_exeext && { + test "$cross_compiling" = yes || + $as_test_x conftest$ac_exeext + }; then ac_cv_lib_mtsk_sunw_mp_register_warn=yes else - ac_cv_lib_mtsk_sunw_mp_register_warn=no + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_cv_lib_mtsk_sunw_mp_register_warn=no fi -rm -f core conftest.err conftest.$ac_objext \ - conftest$ac_exeext conftest.$ac_ext + +rm -rf conftest.dSYM +rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \ + conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_mtsk_sunw_mp_register_warn" >&5 +{ $as_echo "$as_me:$LINENO: result: $ac_cv_lib_mtsk_sunw_mp_register_warn" >&5 $as_echo "$ac_cv_lib_mtsk_sunw_mp_register_warn" >&6; } -if test "x$ac_cv_lib_mtsk_sunw_mp_register_warn" = x""yes; then : +if test "x$ac_cv_lib_mtsk_sunw_mp_register_warn" = x""yes; then LIB_OMP="-lmtsk" fi - { $as_echo "$as_me:${as_lineno-$LINENO}: checking for sunw_mp_register_warn in -lmtsk" >&5 + { $as_echo "$as_me:$LINENO: checking for sunw_mp_register_warn in -lmtsk" >&5 $as_echo_n "checking for sunw_mp_register_warn in -lmtsk... " >&6; } -if test "${ac_cv_lib_mtsk_sunw_mp_register_warn+set}" = set; then : +if test "${ac_cv_lib_mtsk_sunw_mp_register_warn+set}" = set; then $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-lmtsk $LIBS" -cat confdefs.h - <<_ACEOF >conftest.$ac_ext +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ /* Override any GCC internal prototype to avoid an error. @@ -5045,40 +5864,156 @@ cat confdefs.h - <<_ACEOF >conftest.$ac_ext #ifdef __cplusplus extern "C" #endif -char sunw_mp_register_warn (); +char sunw_mp_register_warn (); +int +main () +{ +return sunw_mp_register_warn (); + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (ac_try="$ac_link" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_link") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest$ac_exeext && { + test "$cross_compiling" = yes || + $as_test_x conftest$ac_exeext + }; then + ac_cv_lib_mtsk_sunw_mp_register_warn=yes +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_cv_lib_mtsk_sunw_mp_register_warn=no +fi + +rm -rf conftest.dSYM +rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \ + conftest$ac_exeext conftest.$ac_ext +LIBS=$ac_check_lib_save_LIBS +fi +{ $as_echo "$as_me:$LINENO: result: $ac_cv_lib_mtsk_sunw_mp_register_warn" >&5 +$as_echo "$ac_cv_lib_mtsk_sunw_mp_register_warn" >&6; } +if test "x$ac_cv_lib_mtsk_sunw_mp_register_warn" = x""yes; then + GOMP_LIBS="-lmtsk" +fi + + fi + LIBS="$GOMP_LIBS $LIBS" +fi + + + + + +for ac_func in floor gettimeofday pow +do +as_ac_var=`$as_echo "ac_cv_func_$ac_func" | $as_tr_sh` +{ $as_echo "$as_me:$LINENO: checking for $ac_func" >&5 +$as_echo_n "checking for $ac_func... " >&6; } +if { as_var=$as_ac_var; eval "test \"\${$as_var+set}\" = set"; }; then + $as_echo_n "(cached) " >&6 +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +/* Define $ac_func to an innocuous variant, in case declares $ac_func. + For example, HP-UX 11i declares gettimeofday. */ +#define $ac_func innocuous_$ac_func + +/* System header to define __stub macros and hopefully few prototypes, + which can conflict with char $ac_func (); below. + Prefer to if __STDC__ is defined, since + exists even on freestanding compilers. */ + +#ifdef __STDC__ +# include +#else +# include +#endif + +#undef $ac_func + +/* Override any GCC internal prototype to avoid an error. + Use char because int might match the return type of a GCC + builtin and then its argument prototype would still apply. */ +#ifdef __cplusplus +extern "C" +#endif +char $ac_func (); +/* The GNU C library defines this for functions which it implements + to always fail with ENOSYS. Some functions are actually named + something starting with __ and the normal name is an alias. */ +#if defined __stub_$ac_func || defined __stub___$ac_func +choke me +#endif + int main () { -return sunw_mp_register_warn (); +return $ac_func (); ; return 0; } _ACEOF -if ac_fn_c_try_link "$LINENO"; then : - ac_cv_lib_mtsk_sunw_mp_register_warn=yes +rm -f conftest.$ac_objext conftest$ac_exeext +if { (ac_try="$ac_link" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_link") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest$ac_exeext && { + test "$cross_compiling" = yes || + $as_test_x conftest$ac_exeext + }; then + eval "$as_ac_var=yes" else - ac_cv_lib_mtsk_sunw_mp_register_warn=no -fi -rm -f core conftest.err conftest.$ac_objext \ - conftest$ac_exeext conftest.$ac_ext -LIBS=$ac_check_lib_save_LIBS -fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_mtsk_sunw_mp_register_warn" >&5 -$as_echo "$ac_cv_lib_mtsk_sunw_mp_register_warn" >&6; } -if test "x$ac_cv_lib_mtsk_sunw_mp_register_warn" = x""yes; then : - GOMP_LIBS="-lmtsk" -fi + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 - fi - LIBS="$GOMP_LIBS $LIBS" + eval "$as_ac_var=no" fi - -for ac_func in floor gettimeofday pow -do : - as_ac_var=`$as_echo "ac_cv_func_$ac_func" | $as_tr_sh` -ac_fn_c_check_func "$LINENO" "$ac_func" "$as_ac_var" -if eval test \"x\$"$as_ac_var"\" = x"yes"; then : +rm -rf conftest.dSYM +rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \ + conftest$ac_exeext conftest.$ac_ext +fi +ac_res=`eval 'as_val=${'$as_ac_var'} + $as_echo "$as_val"'` + { $as_echo "$as_me:$LINENO: result: $ac_res" >&5 +$as_echo "$ac_res" >&6; } +as_val=`eval 'as_val=${'$as_ac_var'} + $as_echo "$as_val"'` + if test "x$as_val" = x""yes; then cat >>confdefs.h <<_ACEOF #define `$as_echo "HAVE_$ac_func" | $as_tr_cpp` 1 _ACEOF @@ -5088,12 +6023,14 @@ done # Check whether --enable-debug was given. -if test "${enable_debug+set}" = set; then : +if test "${enable_debug+set}" = set; then enableval=$enable_debug; case "${enableval}" in "" | y | ye | yes) debug=true; CFLAGS=$(echo $CFLAGS -g | sed -e 's/-O\|-O2\|-O3//g') ;; n | no) debug=false ;; - *) as_fn_error $? "bad value ${enableval} for --enable-debug" "$LINENO" 5 ;; + *) { { $as_echo "$as_me:$LINENO: error: bad value ${enableval} for --enable-debug" >&5 +$as_echo "$as_me: error: bad value ${enableval} for --enable-debug" >&2;} + { (exit 1); exit 1; }; } ;; esac else debug=false @@ -5110,7 +6047,7 @@ fi ac_config_files="$ac_config_files Makefile src/Makefile data/Makefile include/Makefile" -ac_config_files="$ac_config_files data/Turner99/Makefile data/Turner04/Makefile data/Andronescu/Makefile" +ac_config_files="$ac_config_files data/Turner99/Makefile data/Turner04/Makefile data/Andronescu/Makefile data/UNAParams/Makefile data/RNAParams/Makefile" cat >confcache <<\_ACEOF @@ -5140,13 +6077,13 @@ _ACEOF case $ac_val in #( *${as_nl}*) case $ac_var in #( - *_cv_*) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: cache variable $ac_var contains a newline" >&5 + *_cv_*) { $as_echo "$as_me:$LINENO: WARNING: cache variable $ac_var contains a newline" >&5 $as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;; esac case $ac_var in #( _ | IFS | as_nl) ;; #( BASH_ARGV | BASH_SOURCE) eval $ac_var= ;; #( - *) { eval $ac_var=; unset $ac_var;} ;; + *) $as_unset $ac_var ;; esac ;; esac done @@ -5154,8 +6091,8 @@ $as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;; (set) 2>&1 | case $as_nl`(ac_space=' '; set) 2>&1` in #( *${as_nl}ac_space=\ *) - # `set' does not quote correctly, so add quotes: double-quote - # substitution turns \\\\ into \\, and sed turns \\ into \. + # `set' does not quote correctly, so add quotes (double-quote + # substitution turns \\\\ into \\, and sed turns \\ into \). sed -n \ "s/'/'\\\\''/g; s/^\\([_$as_cr_alnum]*_cv_[_$as_cr_alnum]*\\)=\\(.*\\)/\\1='\\2'/p" @@ -5178,11 +6115,11 @@ $as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;; if diff "$cache_file" confcache >/dev/null 2>&1; then :; else if test -w "$cache_file"; then test "x$cache_file" != "x/dev/null" && - { $as_echo "$as_me:${as_lineno-$LINENO}: updating cache $cache_file" >&5 + { $as_echo "$as_me:$LINENO: updating cache $cache_file" >&5 $as_echo "$as_me: updating cache $cache_file" >&6;} cat confcache >$cache_file else - { $as_echo "$as_me:${as_lineno-$LINENO}: not updating unwritable cache $cache_file" >&5 + { $as_echo "$as_me:$LINENO: not updating unwritable cache $cache_file" >&5 $as_echo "$as_me: not updating unwritable cache $cache_file" >&6;} fi fi @@ -5196,15 +6133,14 @@ DEFS=-DHAVE_CONFIG_H ac_libobjs= ac_ltlibobjs= -U= for ac_i in : $LIBOBJS; do test "x$ac_i" = x: && continue # 1. Remove the extension, and $U if already installed. ac_script='s/\$U\././;s/\.o$//;s/\.obj$//' ac_i=`$as_echo "$ac_i" | sed "$ac_script"` # 2. Prepend LIBOBJDIR. When used with automake>=1.10 LIBOBJDIR # will be set to the directory where LIBOBJS objects are built. - as_fn_append ac_libobjs " \${LIBOBJDIR}$ac_i\$U.$ac_objext" - as_fn_append ac_ltlibobjs " \${LIBOBJDIR}$ac_i"'$U.lo' + ac_libobjs="$ac_libobjs \${LIBOBJDIR}$ac_i\$U.$ac_objext" + ac_ltlibobjs="$ac_ltlibobjs \${LIBOBJDIR}$ac_i"'$U.lo' done LIBOBJS=$ac_libobjs @@ -5220,30 +6156,41 @@ else fi if test -z "${AMDEP_TRUE}" && test -z "${AMDEP_FALSE}"; then - as_fn_error $? "conditional \"AMDEP\" was never defined. -Usually this means the macro was only invoked conditionally." "$LINENO" 5 + { { $as_echo "$as_me:$LINENO: error: conditional \"AMDEP\" was never defined. +Usually this means the macro was only invoked conditionally." >&5 +$as_echo "$as_me: error: conditional \"AMDEP\" was never defined. +Usually this means the macro was only invoked conditionally." >&2;} + { (exit 1); exit 1; }; } fi if test -z "${am__fastdepCC_TRUE}" && test -z "${am__fastdepCC_FALSE}"; then - as_fn_error $? "conditional \"am__fastdepCC\" was never defined. -Usually this means the macro was only invoked conditionally." "$LINENO" 5 + { { $as_echo "$as_me:$LINENO: error: conditional \"am__fastdepCC\" was never defined. +Usually this means the macro was only invoked conditionally." >&5 +$as_echo "$as_me: error: conditional \"am__fastdepCC\" was never defined. +Usually this means the macro was only invoked conditionally." >&2;} + { (exit 1); exit 1; }; } fi if test -z "${am__fastdepCXX_TRUE}" && test -z "${am__fastdepCXX_FALSE}"; then - as_fn_error $? "conditional \"am__fastdepCXX\" was never defined. -Usually this means the macro was only invoked conditionally." "$LINENO" 5 + { { $as_echo "$as_me:$LINENO: error: conditional \"am__fastdepCXX\" was never defined. +Usually this means the macro was only invoked conditionally." >&5 +$as_echo "$as_me: error: conditional \"am__fastdepCXX\" was never defined. +Usually this means the macro was only invoked conditionally." >&2;} + { (exit 1); exit 1; }; } fi if test -z "${GTFOLD_DEBUG_TRUE}" && test -z "${GTFOLD_DEBUG_FALSE}"; then - as_fn_error $? "conditional \"GTFOLD_DEBUG\" was never defined. -Usually this means the macro was only invoked conditionally." "$LINENO" 5 + { { $as_echo "$as_me:$LINENO: error: conditional \"GTFOLD_DEBUG\" was never defined. +Usually this means the macro was only invoked conditionally." >&5 +$as_echo "$as_me: error: conditional \"GTFOLD_DEBUG\" was never defined. +Usually this means the macro was only invoked conditionally." >&2;} + { (exit 1); exit 1; }; } fi : ${CONFIG_STATUS=./config.status} ac_write_fail=0 ac_clean_files_save=$ac_clean_files ac_clean_files="$ac_clean_files $CONFIG_STATUS" -{ $as_echo "$as_me:${as_lineno-$LINENO}: creating $CONFIG_STATUS" >&5 +{ $as_echo "$as_me:$LINENO: creating $CONFIG_STATUS" >&5 $as_echo "$as_me: creating $CONFIG_STATUS" >&6;} -as_write_fail=0 -cat >$CONFIG_STATUS <<_ASEOF || as_write_fail=1 +cat >$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 #! $SHELL # Generated by $as_me. # Run this file to recreate the current configuration. @@ -5253,18 +6200,17 @@ cat >$CONFIG_STATUS <<_ASEOF || as_write_fail=1 debug=false ac_cs_recheck=false ac_cs_silent=false - SHELL=\${CONFIG_SHELL-$SHELL} -export SHELL -_ASEOF -cat >>$CONFIG_STATUS <<\_ASEOF || as_write_fail=1 -## -------------------- ## -## M4sh Initialization. ## -## -------------------- ## +_ACEOF + +cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 +## --------------------- ## +## M4sh Initialization. ## +## --------------------- ## # Be more Bourne compatible DUALCASE=1; export DUALCASE # for MKS sh -if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then : +if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then emulate sh NULLCMD=: # Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which @@ -5272,15 +6218,23 @@ if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then : alias -g '${1+"$@"}'='"$@"' setopt NO_GLOB_SUBST else - case `(set -o) 2>/dev/null` in #( - *posix*) : - set -o posix ;; #( - *) : - ;; + case `(set -o) 2>/dev/null` in + *posix*) set -o posix ;; esac + fi + + +# PATH needs CR +# Avoid depending upon Character Ranges. +as_cr_letters='abcdefghijklmnopqrstuvwxyz' +as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ' +as_cr_Letters=$as_cr_letters$as_cr_LETTERS +as_cr_digits='0123456789' +as_cr_alnum=$as_cr_Letters$as_cr_digits + as_nl=' ' export as_nl @@ -5288,13 +6242,7 @@ export as_nl as_echo='\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\' as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo$as_echo -# Prefer a ksh shell builtin over an external printf program on Solaris, -# but without wasting forks for bash or zsh. -if test -z "$BASH_VERSION$ZSH_VERSION" \ - && (test "X`print -r -- $as_echo`" = "X$as_echo") 2>/dev/null; then - as_echo='print -r --' - as_echo_n='print -rn --' -elif (test "X`printf %s $as_echo`" = "X$as_echo") 2>/dev/null; then +if (test "X`printf %s $as_echo`" = "X$as_echo") 2>/dev/null; then as_echo='printf %s\n' as_echo_n='printf %s' else @@ -5305,7 +6253,7 @@ else as_echo_body='eval expr "X$1" : "X\\(.*\\)"' as_echo_n_body='eval arg=$1; - case $arg in #( + case $arg in *"$as_nl"*) expr "X$arg" : "X\\(.*\\)$as_nl"; arg=`expr "X$arg" : ".*$as_nl\\(.*\\)"`;; @@ -5328,6 +6276,13 @@ if test "${PATH_SEPARATOR+set}" != set; then } fi +# Support unset when possible. +if ( (MAIL=60; unset MAIL) || exit) >/dev/null 2>&1; then + as_unset=unset +else + as_unset=false +fi + # IFS # We need space, tab and new line, in precisely that order. Quoting is @@ -5337,15 +6292,15 @@ fi IFS=" "" $as_nl" # Find who we are. Look in the path if we contain no directory separator. -case $0 in #(( +case $0 in *[\\/]* ) as_myself=$0 ;; *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break - done + test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break +done IFS=$as_save_IFS ;; @@ -5357,16 +6312,12 @@ if test "x$as_myself" = x; then fi if test ! -f "$as_myself"; then $as_echo "$as_myself: error: cannot find myself; rerun with an absolute file name" >&2 - exit 1 + { (exit 1); exit 1; } fi -# Unset variables that we do not need and which cause bugs (e.g. in -# pre-3.0 UWIN ksh). But do not cause bugs in bash 2.01; the "|| exit 1" -# suppresses any "Segmentation fault" message there. '((' could -# trigger a bug in pdksh 5.2.14. -for as_var in BASH_ENV ENV MAIL MAILPATH -do eval test x\${$as_var+set} = xset \ - && ( (unset $as_var) || exit 1) >/dev/null 2>&1 && unset $as_var || : +# Work around bugs in pre-3.0 UWIN ksh. +for as_var in ENV MAIL MAILPATH +do ($as_unset $as_var) >/dev/null 2>&1 && $as_unset $as_var done PS1='$ ' PS2='> ' @@ -5378,89 +6329,7 @@ export LC_ALL LANGUAGE=C export LANGUAGE -# CDPATH. -(unset CDPATH) >/dev/null 2>&1 && unset CDPATH - - -# as_fn_error STATUS ERROR [LINENO LOG_FD] -# ---------------------------------------- -# Output "`basename $0`: error: ERROR" to stderr. If LINENO and LOG_FD are -# provided, also output the error to LOG_FD, referencing LINENO. Then exit the -# script with STATUS, using 1 if that was 0. -as_fn_error () -{ - as_status=$1; test $as_status -eq 0 && as_status=1 - if test "$4"; then - as_lineno=${as_lineno-"$3"} as_lineno_stack=as_lineno_stack=$as_lineno_stack - $as_echo "$as_me:${as_lineno-$LINENO}: error: $2" >&$4 - fi - $as_echo "$as_me: error: $2" >&2 - as_fn_exit $as_status -} # as_fn_error - - -# as_fn_set_status STATUS -# ----------------------- -# Set $? to STATUS, without forking. -as_fn_set_status () -{ - return $1 -} # as_fn_set_status - -# as_fn_exit STATUS -# ----------------- -# Exit the shell with STATUS, even in a "trap 0" or "set -e" context. -as_fn_exit () -{ - set +e - as_fn_set_status $1 - exit $1 -} # as_fn_exit - -# as_fn_unset VAR -# --------------- -# Portably unset VAR. -as_fn_unset () -{ - { eval $1=; unset $1;} -} -as_unset=as_fn_unset -# as_fn_append VAR VALUE -# ---------------------- -# Append the text in VALUE to the end of the definition contained in VAR. Take -# advantage of any shell optimizations that allow amortized linear growth over -# repeated appends, instead of the typical quadratic growth present in naive -# implementations. -if (eval "as_var=1; as_var+=2; test x\$as_var = x12") 2>/dev/null; then : - eval 'as_fn_append () - { - eval $1+=\$2 - }' -else - as_fn_append () - { - eval $1=\$$1\$2 - } -fi # as_fn_append - -# as_fn_arith ARG... -# ------------------ -# Perform arithmetic evaluation on the ARGs, and store the result in the -# global $as_val. Take advantage of shells that can avoid forks. The arguments -# must be portable across $(()) and expr. -if (eval "test \$(( 1 + 1 )) = 2") 2>/dev/null; then : - eval 'as_fn_arith () - { - as_val=$(( $* )) - }' -else - as_fn_arith () - { - as_val=`expr "$@" || test $? -eq 1` - } -fi # as_fn_arith - - +# Required to use basename. if expr a : '\(a\)' >/dev/null 2>&1 && test "X`expr 00001 : '.*\(...\)'`" = X001; then as_expr=expr @@ -5474,12 +6343,8 @@ else as_basename=false fi -if (as_dir=`dirname -- /` && test "X$as_dir" = X/) >/dev/null 2>&1; then - as_dirname=dirname -else - as_dirname=false -fi +# Name of the executable. as_me=`$as_basename -- "$0" || $as_expr X/"$0" : '.*/\([^/][^/]*\)/*$' \| \ X"$0" : 'X\(//\)$' \| \ @@ -5499,25 +6364,76 @@ $as_echo X/"$0" | } s/.*/./; q'` -# Avoid depending upon Character Ranges. -as_cr_letters='abcdefghijklmnopqrstuvwxyz' -as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ' -as_cr_Letters=$as_cr_letters$as_cr_LETTERS -as_cr_digits='0123456789' -as_cr_alnum=$as_cr_Letters$as_cr_digits +# CDPATH. +$as_unset CDPATH + + + + as_lineno_1=$LINENO + as_lineno_2=$LINENO + test "x$as_lineno_1" != "x$as_lineno_2" && + test "x`expr $as_lineno_1 + 1`" = "x$as_lineno_2" || { + + # Create $as_me.lineno as a copy of $as_myself, but with $LINENO + # uniformly replaced by the line number. The first 'sed' inserts a + # line-number line after each line using $LINENO; the second 'sed' + # does the real work. The second script uses 'N' to pair each + # line-number line with the line containing $LINENO, and appends + # trailing '-' during substitution so that $LINENO is not a special + # case at line end. + # (Raja R Harinath suggested sed '=', and Paul Eggert wrote the + # scripts with optimization help from Paolo Bonzini. Blame Lee + # E. McMahon (1931-1989) for sed's syntax. :-) + sed -n ' + p + /[$]LINENO/= + ' <$as_myself | + sed ' + s/[$]LINENO.*/&-/ + t lineno + b + :lineno + N + :loop + s/[$]LINENO\([^'$as_cr_alnum'_].*\n\)\(.*\)/\2\1\2/ + t loop + s/-\n.*// + ' >$as_me.lineno && + chmod +x "$as_me.lineno" || + { $as_echo "$as_me: error: cannot create $as_me.lineno; rerun with a POSIX shell" >&2 + { (exit 1); exit 1; }; } + + # Don't try to exec as it changes $[0], causing all sort of problems + # (the dirname of $[0] is not the place where we might find the + # original and so on. Autoconf is especially sensitive to this). + . "./$as_me.lineno" + # Exit status is that of the last command. + exit +} + + +if (as_dir=`dirname -- /` && test "X$as_dir" = X/) >/dev/null 2>&1; then + as_dirname=dirname +else + as_dirname=false +fi ECHO_C= ECHO_N= ECHO_T= -case `echo -n x` in #((((( +case `echo -n x` in -n*) - case `echo 'xy\c'` in + case `echo 'x\c'` in *c*) ECHO_T=' ';; # ECHO_T is single tab character. - xy) ECHO_C='\c';; - *) echo `echo ksh88 bug on AIX 6.1` > /dev/null - ECHO_T=' ';; + *) ECHO_C='\c';; esac;; *) ECHO_N='-n';; esac +if expr a : '\(a\)' >/dev/null 2>&1 && + test "X`expr 00001 : '.*\(...\)'`" = X001; then + as_expr=expr +else + as_expr=false +fi rm -f conf$$ conf$$.exe conf$$.file if test -d conf$$.dir; then @@ -5546,56 +6462,8 @@ fi rm -f conf$$ conf$$.exe conf$$.dir/conf$$.file conf$$.file rmdir conf$$.dir 2>/dev/null - -# as_fn_mkdir_p -# ------------- -# Create "$as_dir" as a directory, including parents if necessary. -as_fn_mkdir_p () -{ - - case $as_dir in #( - -*) as_dir=./$as_dir;; - esac - test -d "$as_dir" || eval $as_mkdir_p || { - as_dirs= - while :; do - case $as_dir in #( - *\'*) as_qdir=`$as_echo "$as_dir" | sed "s/'/'\\\\\\\\''/g"`;; #'( - *) as_qdir=$as_dir;; - esac - as_dirs="'$as_qdir' $as_dirs" - as_dir=`$as_dirname -- "$as_dir" || -$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \ - X"$as_dir" : 'X\(//\)[^/]' \| \ - X"$as_dir" : 'X\(//\)$' \| \ - X"$as_dir" : 'X\(/\)' \| . 2>/dev/null || -$as_echo X"$as_dir" | - sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ - s//\1/ - q - } - /^X\(\/\/\)[^/].*/{ - s//\1/ - q - } - /^X\(\/\/\)$/{ - s//\1/ - q - } - /^X\(\/\).*/{ - s//\1/ - q - } - s/.*/./; q'` - test -d "$as_dir" && break - done - test -z "$as_dirs" || eval "mkdir $as_dirs" - } || test -d "$as_dir" || as_fn_error $? "cannot create directory $as_dir" - - -} # as_fn_mkdir_p if mkdir -p . 2>/dev/null; then - as_mkdir_p='mkdir -p "$as_dir"' + as_mkdir_p=: else test -d ./-p && rmdir ./-p as_mkdir_p=false @@ -5614,10 +6482,10 @@ else if test -d "$1"; then test -d "$1/."; else - case $1 in #( + case $1 in -*)set "./$1";; esac; - case `ls -ld'$as_ls_L_option' "$1" 2>/dev/null` in #(( + case `ls -ld'$as_ls_L_option' "$1" 2>/dev/null` in ???[sx]*):;;*)false;;esac;fi '\'' sh ' @@ -5632,19 +6500,13 @@ as_tr_sh="eval sed 'y%*+%pp%;s%[^_$as_cr_alnum]%_%g'" exec 6>&1 -## ----------------------------------- ## -## Main body of $CONFIG_STATUS script. ## -## ----------------------------------- ## -_ASEOF -test $as_write_fail = 0 && chmod +x $CONFIG_STATUS || ac_write_fail=1 -cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 -# Save the log message, to keep $0 and so on meaningful, and to +# Save the log message, to keep $[0] and so on meaningful, and to # report actual input values of CONFIG_FILES etc. instead of their # values after options handling. ac_log=" -This file was extended by gtfold $as_me 1.18, which was -generated by GNU Autoconf 2.67. Invocation command line was +This file was extended by gtfold $as_me 2.0, which was +generated by GNU Autoconf 2.63. Invocation command line was CONFIG_FILES = $CONFIG_FILES CONFIG_HEADERS = $CONFIG_HEADERS @@ -5676,15 +6538,13 @@ _ACEOF cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 ac_cs_usage="\ -\`$as_me' instantiates files and other configuration actions -from templates according to the current configuration. Unless the files -and actions are specified as TAGs, all are instantiated by default. +\`$as_me' instantiates files from templates according to the +current configuration. -Usage: $0 [OPTION]... [TAG]... +Usage: $0 [OPTION]... [FILE]... -h, --help print this help, then exit -V, --version print version number and configuration settings, then exit - --config print configuration, then exit -q, --quiet, --silent do not print progress messages -d, --debug don't remove temporary files @@ -5703,17 +6563,16 @@ $config_headers Configuration commands: $config_commands -Report bugs to the package provider." +Report bugs to ." _ACEOF cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 -ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`" ac_cs_version="\\ -gtfold config.status 1.18 -configured by $0, generated by GNU Autoconf 2.67, - with options \\"\$ac_cs_config\\" +gtfold config.status 2.0 +configured by $0, generated by GNU Autoconf 2.63, + with options \\"`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`\\" -Copyright (C) 2010 Free Software Foundation, Inc. +Copyright (C) 2008 Free Software Foundation, Inc. This config.status script is free software; the Free Software Foundation gives unlimited permission to copy, distribute and modify it." @@ -5731,16 +6590,11 @@ ac_need_defaults=: while test $# != 0 do case $1 in - --*=?*) + --*=*) ac_option=`expr "X$1" : 'X\([^=]*\)='` ac_optarg=`expr "X$1" : 'X[^=]*=\(.*\)'` ac_shift=: ;; - --*=) - ac_option=`expr "X$1" : 'X\([^=]*\)='` - ac_optarg= - ac_shift=: - ;; *) ac_option=$1 ac_optarg=$2 @@ -5754,29 +6608,27 @@ do ac_cs_recheck=: ;; --version | --versio | --versi | --vers | --ver | --ve | --v | -V ) $as_echo "$ac_cs_version"; exit ;; - --config | --confi | --conf | --con | --co | --c ) - $as_echo "$ac_cs_config"; exit ;; --debug | --debu | --deb | --de | --d | -d ) debug=: ;; --file | --fil | --fi | --f ) $ac_shift case $ac_optarg in *\'*) ac_optarg=`$as_echo "$ac_optarg" | sed "s/'/'\\\\\\\\''/g"` ;; - '') as_fn_error $? "missing file argument" ;; esac - as_fn_append CONFIG_FILES " '$ac_optarg'" + CONFIG_FILES="$CONFIG_FILES '$ac_optarg'" ac_need_defaults=false;; --header | --heade | --head | --hea ) $ac_shift case $ac_optarg in *\'*) ac_optarg=`$as_echo "$ac_optarg" | sed "s/'/'\\\\\\\\''/g"` ;; esac - as_fn_append CONFIG_HEADERS " '$ac_optarg'" + CONFIG_HEADERS="$CONFIG_HEADERS '$ac_optarg'" ac_need_defaults=false;; --he | --h) # Conflict between --help and --header - as_fn_error $? "ambiguous option: \`$1' -Try \`$0 --help' for more information.";; + { $as_echo "$as_me: error: ambiguous option: $1 +Try \`$0 --help' for more information." >&2 + { (exit 1); exit 1; }; };; --help | --hel | -h ) $as_echo "$ac_cs_usage"; exit ;; -q | -quiet | --quiet | --quie | --qui | --qu | --q \ @@ -5784,10 +6636,11 @@ Try \`$0 --help' for more information.";; ac_cs_silent=: ;; # This is an error. - -*) as_fn_error $? "unrecognized option: \`$1' -Try \`$0 --help' for more information." ;; + -*) { $as_echo "$as_me: error: unrecognized option: $1 +Try \`$0 --help' for more information." >&2 + { (exit 1); exit 1; }; } ;; - *) as_fn_append ac_config_targets " $1" + *) ac_config_targets="$ac_config_targets $1" ac_need_defaults=false ;; esac @@ -5847,8 +6700,12 @@ do "data/Turner99/Makefile") CONFIG_FILES="$CONFIG_FILES data/Turner99/Makefile" ;; "data/Turner04/Makefile") CONFIG_FILES="$CONFIG_FILES data/Turner04/Makefile" ;; "data/Andronescu/Makefile") CONFIG_FILES="$CONFIG_FILES data/Andronescu/Makefile" ;; + "data/UNAParams/Makefile") CONFIG_FILES="$CONFIG_FILES data/UNAParams/Makefile" ;; + "data/RNAParams/Makefile") CONFIG_FILES="$CONFIG_FILES data/RNAParams/Makefile" ;; - *) as_fn_error $? "invalid argument: \`$ac_config_target'" "$LINENO" 5 ;; + *) { { $as_echo "$as_me:$LINENO: error: invalid argument: $ac_config_target" >&5 +$as_echo "$as_me: error: invalid argument: $ac_config_target" >&2;} + { (exit 1); exit 1; }; };; esac done @@ -5875,7 +6732,7 @@ $debug || trap 'exit_status=$? { test -z "$tmp" || test ! -d "$tmp" || rm -fr "$tmp"; } && exit $exit_status ' 0 - trap 'as_fn_exit 1' 1 2 13 15 + trap '{ (exit 1); exit 1; }' 1 2 13 15 } # Create a (secure) tmp directory for tmp files. @@ -5886,7 +6743,11 @@ $debug || { tmp=./conf$$-$RANDOM (umask 077 && mkdir "$tmp") -} || as_fn_error $? "cannot create a temporary directory in ." "$LINENO" 5 +} || +{ + $as_echo "$as_me: cannot create a temporary directory in ." >&2 + { (exit 1); exit 1; } +} # Set up the scripts for CONFIG_FILES section. # No need to generate them if there are no CONFIG_FILES. @@ -5894,13 +6755,7 @@ $debug || if test -n "$CONFIG_FILES"; then -ac_cr=`echo X | tr X '\015'` -# On cygwin, bash can eat \r inside `` if the user requested igncr. -# But we know of no other shell where ac_cr would be empty at this -# point, so we can use a bashism as a fallback. -if test "x$ac_cr" = x; then - eval ac_cr=\$\'\\r\' -fi +ac_cr=' ' ac_cs_awk_cr=`$AWK 'BEGIN { print "a\rb" }' /dev/null` if test "$ac_cs_awk_cr" = "a${ac_cr}b"; then ac_cs_awk_cr='\\r' @@ -5917,18 +6772,24 @@ _ACEOF echo "$ac_subst_vars" | sed 's/.*/&!$&$ac_delim/' && echo "_ACEOF" } >conf$$subs.sh || - as_fn_error $? "could not make $CONFIG_STATUS" "$LINENO" 5 -ac_delim_num=`echo "$ac_subst_vars" | grep -c '^'` + { { $as_echo "$as_me:$LINENO: error: could not make $CONFIG_STATUS" >&5 +$as_echo "$as_me: error: could not make $CONFIG_STATUS" >&2;} + { (exit 1); exit 1; }; } +ac_delim_num=`echo "$ac_subst_vars" | grep -c '$'` ac_delim='%!_!# ' for ac_last_try in false false false false false :; do . ./conf$$subs.sh || - as_fn_error $? "could not make $CONFIG_STATUS" "$LINENO" 5 + { { $as_echo "$as_me:$LINENO: error: could not make $CONFIG_STATUS" >&5 +$as_echo "$as_me: error: could not make $CONFIG_STATUS" >&2;} + { (exit 1); exit 1; }; } ac_delim_n=`sed -n "s/.*$ac_delim\$/X/p" conf$$subs.awk | grep -c X` if test $ac_delim_n = $ac_delim_num; then break elif $ac_last_try; then - as_fn_error $? "could not make $CONFIG_STATUS" "$LINENO" 5 + { { $as_echo "$as_me:$LINENO: error: could not make $CONFIG_STATUS" >&5 +$as_echo "$as_me: error: could not make $CONFIG_STATUS" >&2;} + { (exit 1); exit 1; }; } else ac_delim="$ac_delim!$ac_delim _$ac_delim!! " fi @@ -5950,7 +6811,7 @@ s/'"$ac_delim"'$// t delim :nl h -s/\(.\{148\}\)..*/\1/ +s/\(.\{148\}\).*/\1/ t more1 s/["\\]/\\&/g; s/^/"/; s/$/\\n"\\/ p @@ -5964,7 +6825,7 @@ s/.\{148\}// t nl :delim h -s/\(.\{148\}\)..*/\1/ +s/\(.\{148\}\).*/\1/ t more2 s/["\\]/\\&/g; s/^/"/; s/$/"/ p @@ -6017,28 +6878,22 @@ if sed "s/$ac_cr//" < /dev/null > /dev/null 2>&1; then else cat fi < "$tmp/subs1.awk" > "$tmp/subs.awk" \ - || as_fn_error $? "could not setup config files machinery" "$LINENO" 5 + || { { $as_echo "$as_me:$LINENO: error: could not setup config files machinery" >&5 +$as_echo "$as_me: error: could not setup config files machinery" >&2;} + { (exit 1); exit 1; }; } _ACEOF -# VPATH may cause trouble with some makes, so we remove sole $(srcdir), -# ${srcdir} and @srcdir@ entries from VPATH if srcdir is ".", strip leading and +# VPATH may cause trouble with some makes, so we remove $(srcdir), +# ${srcdir} and @srcdir@ from VPATH if srcdir is ".", strip leading and # trailing colons and then remove the whole line if VPATH becomes empty # (actually we leave an empty line to preserve line numbers). if test "x$srcdir" = x.; then - ac_vpsub='/^[ ]*VPATH[ ]*=[ ]*/{ -h -s/// -s/^/:/ -s/[ ]*$/:/ -s/:\$(srcdir):/:/g -s/:\${srcdir}:/:/g -s/:@srcdir@:/:/g -s/^:*// + ac_vpsub='/^[ ]*VPATH[ ]*=/{ +s/:*\$(srcdir):*/:/ +s/:*\${srcdir}:*/:/ +s/:*@srcdir@:*/:/ +s/^\([^=]*=[ ]*\):*/\1/ s/:*$// -x -s/\(=[ ]*\).*/\1/ -G -s/\n// s/^[^=]*=[ ]*$// }' fi @@ -6066,7 +6921,9 @@ for ac_last_try in false false :; do if test -z "$ac_t"; then break elif $ac_last_try; then - as_fn_error $? "could not make $CONFIG_HEADERS" "$LINENO" 5 + { { $as_echo "$as_me:$LINENO: error: could not make $CONFIG_HEADERS" >&5 +$as_echo "$as_me: error: could not make $CONFIG_HEADERS" >&2;} + { (exit 1); exit 1; }; } else ac_delim="$ac_delim!$ac_delim _$ac_delim!! " fi @@ -6151,7 +7008,9 @@ cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 _ACAWK _ACEOF cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 - as_fn_error $? "could not setup config headers machinery" "$LINENO" 5 + { { $as_echo "$as_me:$LINENO: error: could not setup config headers machinery" >&5 +$as_echo "$as_me: error: could not setup config headers machinery" >&2;} + { (exit 1); exit 1; }; } fi # test -n "$CONFIG_HEADERS" @@ -6164,7 +7023,9 @@ do esac case $ac_mode$ac_tag in :[FHL]*:*);; - :L* | :C*:*) as_fn_error $? "invalid tag \`$ac_tag'" "$LINENO" 5 ;; + :L* | :C*:*) { { $as_echo "$as_me:$LINENO: error: invalid tag $ac_tag" >&5 +$as_echo "$as_me: error: invalid tag $ac_tag" >&2;} + { (exit 1); exit 1; }; };; :[FH]-) ac_tag=-:-;; :[FH]*) ac_tag=$ac_tag:$ac_tag.in;; esac @@ -6192,10 +7053,12 @@ do [\\/$]*) false;; *) test -f "$srcdir/$ac_f" && ac_f="$srcdir/$ac_f";; esac || - as_fn_error 1 "cannot find input file: \`$ac_f'" "$LINENO" 5 ;; + { { $as_echo "$as_me:$LINENO: error: cannot find input file: $ac_f" >&5 +$as_echo "$as_me: error: cannot find input file: $ac_f" >&2;} + { (exit 1); exit 1; }; };; esac case $ac_f in *\'*) ac_f=`$as_echo "$ac_f" | sed "s/'/'\\\\\\\\''/g"`;; esac - as_fn_append ac_file_inputs " '$ac_f'" + ac_file_inputs="$ac_file_inputs '$ac_f'" done # Let's still pretend it is `configure' which instantiates (i.e., don't @@ -6206,7 +7069,7 @@ do `' by configure.' if test x"$ac_file" != x-; then configure_input="$ac_file. $configure_input" - { $as_echo "$as_me:${as_lineno-$LINENO}: creating $ac_file" >&5 + { $as_echo "$as_me:$LINENO: creating $ac_file" >&5 $as_echo "$as_me: creating $ac_file" >&6;} fi # Neutralize special characters interpreted by sed in replacement strings. @@ -6219,7 +7082,9 @@ $as_echo "$as_me: creating $ac_file" >&6;} case $ac_tag in *:-:* | *:-) cat >"$tmp/stdin" \ - || as_fn_error $? "could not create $ac_file" "$LINENO" 5 ;; + || { { $as_echo "$as_me:$LINENO: error: could not create $ac_file" >&5 +$as_echo "$as_me: error: could not create $ac_file" >&2;} + { (exit 1); exit 1; }; } ;; esac ;; esac @@ -6247,7 +7112,47 @@ $as_echo X"$ac_file" | q } s/.*/./; q'` - as_dir="$ac_dir"; as_fn_mkdir_p + { as_dir="$ac_dir" + case $as_dir in #( + -*) as_dir=./$as_dir;; + esac + test -d "$as_dir" || { $as_mkdir_p && mkdir -p "$as_dir"; } || { + as_dirs= + while :; do + case $as_dir in #( + *\'*) as_qdir=`$as_echo "$as_dir" | sed "s/'/'\\\\\\\\''/g"`;; #'( + *) as_qdir=$as_dir;; + esac + as_dirs="'$as_qdir' $as_dirs" + as_dir=`$as_dirname -- "$as_dir" || +$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \ + X"$as_dir" : 'X\(//\)[^/]' \| \ + X"$as_dir" : 'X\(//\)$' \| \ + X"$as_dir" : 'X\(/\)' \| . 2>/dev/null || +$as_echo X"$as_dir" | + sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ + s//\1/ + q + } + /^X\(\/\/\)[^/].*/{ + s//\1/ + q + } + /^X\(\/\/\)$/{ + s//\1/ + q + } + /^X\(\/\).*/{ + s//\1/ + q + } + s/.*/./; q'` + test -d "$as_dir" && break + done + test -z "$as_dirs" || eval "mkdir $as_dirs" + } || test -d "$as_dir" || { { $as_echo "$as_me:$LINENO: error: cannot create directory $as_dir" >&5 +$as_echo "$as_me: error: cannot create directory $as_dir" >&2;} + { (exit 1); exit 1; }; }; } ac_builddir=. case "$ac_dir" in @@ -6304,6 +7209,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 # If the template does not know about datarootdir, expand it. # FIXME: This hack should be removed a few years after 2.60. ac_datarootdir_hack=; ac_datarootdir_seen= + ac_sed_dataroot=' /datarootdir/ { p @@ -6313,11 +7219,12 @@ ac_sed_dataroot=' /@docdir@/p /@infodir@/p /@localedir@/p -/@mandir@/p' +/@mandir@/p +' case `eval "sed -n \"\$ac_sed_dataroot\" $ac_file_inputs"` in *datarootdir*) ac_datarootdir_seen=yes;; *@datadir@*|*@docdir@*|*@infodir@*|*@localedir@*|*@mandir@*) - { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $ac_file_inputs seems to ignore the --datarootdir setting" >&5 + { $as_echo "$as_me:$LINENO: WARNING: $ac_file_inputs seems to ignore the --datarootdir setting" >&5 $as_echo "$as_me: WARNING: $ac_file_inputs seems to ignore the --datarootdir setting" >&2;} _ACEOF cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 @@ -6327,7 +7234,7 @@ cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 s&@infodir@&$infodir&g s&@localedir@&$localedir&g s&@mandir@&$mandir&g - s&\\\${datarootdir}&$datarootdir&g' ;; + s&\\\${datarootdir}&$datarootdir&g' ;; esac _ACEOF @@ -6356,22 +7263,26 @@ s&@MKDIR_P@&$ac_MKDIR_P&;t t $ac_datarootdir_hack " eval sed \"\$ac_sed_extra\" "$ac_file_inputs" | $AWK -f "$tmp/subs.awk" >$tmp/out \ - || as_fn_error $? "could not create $ac_file" "$LINENO" 5 + || { { $as_echo "$as_me:$LINENO: error: could not create $ac_file" >&5 +$as_echo "$as_me: error: could not create $ac_file" >&2;} + { (exit 1); exit 1; }; } test -z "$ac_datarootdir_hack$ac_datarootdir_seen" && { ac_out=`sed -n '/\${datarootdir}/p' "$tmp/out"`; test -n "$ac_out"; } && { ac_out=`sed -n '/^[ ]*datarootdir[ ]*:*=/p' "$tmp/out"`; test -z "$ac_out"; } && - { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $ac_file contains a reference to the variable \`datarootdir' -which seems to be undefined. Please make sure it is defined" >&5 + { $as_echo "$as_me:$LINENO: WARNING: $ac_file contains a reference to the variable \`datarootdir' +which seems to be undefined. Please make sure it is defined." >&5 $as_echo "$as_me: WARNING: $ac_file contains a reference to the variable \`datarootdir' -which seems to be undefined. Please make sure it is defined" >&2;} +which seems to be undefined. Please make sure it is defined." >&2;} rm -f "$tmp/stdin" case $ac_file in -) cat "$tmp/out" && rm -f "$tmp/out";; *) rm -f "$ac_file" && mv "$tmp/out" "$ac_file";; esac \ - || as_fn_error $? "could not create $ac_file" "$LINENO" 5 + || { { $as_echo "$as_me:$LINENO: error: could not create $ac_file" >&5 +$as_echo "$as_me: error: could not create $ac_file" >&2;} + { (exit 1); exit 1; }; } ;; :H) # @@ -6382,19 +7293,25 @@ which seems to be undefined. Please make sure it is defined" >&2;} $as_echo "/* $configure_input */" \ && eval '$AWK -f "$tmp/defines.awk"' "$ac_file_inputs" } >"$tmp/config.h" \ - || as_fn_error $? "could not create $ac_file" "$LINENO" 5 + || { { $as_echo "$as_me:$LINENO: error: could not create $ac_file" >&5 +$as_echo "$as_me: error: could not create $ac_file" >&2;} + { (exit 1); exit 1; }; } if diff "$ac_file" "$tmp/config.h" >/dev/null 2>&1; then - { $as_echo "$as_me:${as_lineno-$LINENO}: $ac_file is unchanged" >&5 + { $as_echo "$as_me:$LINENO: $ac_file is unchanged" >&5 $as_echo "$as_me: $ac_file is unchanged" >&6;} else rm -f "$ac_file" mv "$tmp/config.h" "$ac_file" \ - || as_fn_error $? "could not create $ac_file" "$LINENO" 5 + || { { $as_echo "$as_me:$LINENO: error: could not create $ac_file" >&5 +$as_echo "$as_me: error: could not create $ac_file" >&2;} + { (exit 1); exit 1; }; } fi else $as_echo "/* $configure_input */" \ && eval '$AWK -f "$tmp/defines.awk"' "$ac_file_inputs" \ - || as_fn_error $? "could not create -" "$LINENO" 5 + || { { $as_echo "$as_me:$LINENO: error: could not create -" >&5 +$as_echo "$as_me: error: could not create -" >&2;} + { (exit 1); exit 1; }; } fi # Compute "$ac_file"'s index in $config_headers. _am_arg="$ac_file" @@ -6432,7 +7349,7 @@ $as_echo X"$_am_arg" | s/.*/./; q'`/stamp-h$_am_stamp_count ;; - :C) { $as_echo "$as_me:${as_lineno-$LINENO}: executing $ac_file commands" >&5 + :C) { $as_echo "$as_me:$LINENO: executing $ac_file commands" >&5 $as_echo "$as_me: executing $ac_file commands" >&6;} ;; esac @@ -6527,7 +7444,47 @@ $as_echo X"$file" | q } s/.*/./; q'` - as_dir=$dirpart/$fdir; as_fn_mkdir_p + { as_dir=$dirpart/$fdir + case $as_dir in #( + -*) as_dir=./$as_dir;; + esac + test -d "$as_dir" || { $as_mkdir_p && mkdir -p "$as_dir"; } || { + as_dirs= + while :; do + case $as_dir in #( + *\'*) as_qdir=`$as_echo "$as_dir" | sed "s/'/'\\\\\\\\''/g"`;; #'( + *) as_qdir=$as_dir;; + esac + as_dirs="'$as_qdir' $as_dirs" + as_dir=`$as_dirname -- "$as_dir" || +$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \ + X"$as_dir" : 'X\(//\)[^/]' \| \ + X"$as_dir" : 'X\(//\)$' \| \ + X"$as_dir" : 'X\(/\)' \| . 2>/dev/null || +$as_echo X"$as_dir" | + sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ + s//\1/ + q + } + /^X\(\/\/\)[^/].*/{ + s//\1/ + q + } + /^X\(\/\/\)$/{ + s//\1/ + q + } + /^X\(\/\).*/{ + s//\1/ + q + } + s/.*/./; q'` + test -d "$as_dir" && break + done + test -z "$as_dirs" || eval "mkdir $as_dirs" + } || test -d "$as_dir" || { { $as_echo "$as_me:$LINENO: error: cannot create directory $as_dir" >&5 +$as_echo "$as_me: error: cannot create directory $as_dir" >&2;} + { (exit 1); exit 1; }; }; } # echo "creating $dirpart/$file" echo '# dummy' > "$dirpart/$file" done @@ -6539,12 +7496,15 @@ $as_echo X"$file" | done # for ac_tag -as_fn_exit 0 +{ (exit 0); exit 0; } _ACEOF +chmod +x $CONFIG_STATUS ac_clean_files=$ac_clean_files_save test $ac_write_fail = 0 || - as_fn_error $? "write failure creating $CONFIG_STATUS" "$LINENO" 5 + { { $as_echo "$as_me:$LINENO: error: write failure creating $CONFIG_STATUS" >&5 +$as_echo "$as_me: error: write failure creating $CONFIG_STATUS" >&2;} + { (exit 1); exit 1; }; } # configure is writing to config.log, and then calls config.status. @@ -6565,10 +7525,10 @@ if test "$no_create" != yes; then exec 5>>config.log # Use ||, not &&, to avoid exiting from the if with $? = 1, which # would make configure fail if this is the last instruction. - $ac_cs_success || as_fn_exit 1 + $ac_cs_success || { (exit 1); exit 1; } fi if test -n "$ac_unrecognized_opts" && test "$enable_option_checking" != no; then - { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: unrecognized options: $ac_unrecognized_opts" >&5 + { $as_echo "$as_me:$LINENO: WARNING: unrecognized options: $ac_unrecognized_opts" >&5 $as_echo "$as_me: WARNING: unrecognized options: $ac_unrecognized_opts" >&2;} fi diff --git a/gtfold-mfe/configure.in b/gtfold-mfe/configure.in index b5b456b..0643019 100644 --- a/gtfold-mfe/configure.in +++ b/gtfold-mfe/configure.in @@ -1,22 +1,22 @@ dnl Process this file with autoconf to produce a configure script. -dnl AC_PREREQ(1.8) +dnl AC_PREREQ([2.67]) dnl AC 2.62 needed for OpenMP -AC_PREREQ(2.62) +AC_PREREQ([2.63]) dnl AC_INIT (package, version, [bug-report-email], [tarname]) -AC_INIT([gtfold],[1.18]) +AC_INIT([gtfold],[2.0]) dnl check for this file's existence to make sure that the directory dnl specified by --srcdir is the right one AC_CONFIG_SRCDIR([README]) dnl Specify a header configuration file -AM_CONFIG_HEADER(gtfold_config.h) +AC_CONFIG_HEADERS([gtfold_config.h]) dnl Compute the canonical host-system type variable, host, and its dnl three individual parts host_cpu, host_vendor, and host_os. -AC_CANONICAL_SYSTEM +AC_CANONICAL_TARGET dnl Initialize Automake AM_INIT_AUTOMAKE @@ -62,7 +62,7 @@ dnl Check for libraries AC_CHECK_LIB(m, log2, AC_DEFINE([HAVE_LOG2],[],[log2 function is present])) dnl Check for header files -AC_STDC_HEADERS +AC_HEADER_STDC #AC_CHECK_HEADERS(sys/resource.h) #AC_CHECK_HEADERS(getopt.h) AC_CHECK_HEADERS([stdlib.h string.h sys/time.h]) @@ -99,27 +99,23 @@ fi dnl This is an example how to check for compiler characteristics that dnl are not a part of the standard Autoconf tests: -If Sun cc is present, define appropriate compiler flags +#If Sun cc is present, define appropriate compiler flags AC_MSG_CHECKING(for Sun C compiler) -AC_TRY_COMPILE([], [#ifndef __SUNPRO_C +AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[]], [[#ifndef __SUNPRO_C #include "error: this is not a Sun C compiler." #endif - ], - [AC_MSG_RESULT(yes) - gtfold_cv_check_sunpro_cc=yes], - [AC_MSG_RESULT(no) + ]])],[AC_MSG_RESULT(yes) + gtfold_cv_check_sunpro_cc=yes],[AC_MSG_RESULT(no) gtfold_cv_check_sunpro_cc=no]) if test "$gtfold_cv_check_sunpro_cc" == "yes"; then AC_MSG_CHECKING(for Sun C compiler architecture target) - AC_TRY_COMPILE([], [#ifndef __sparc + AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[]], [[#ifndef __sparc #include "error: this is not a Sun Sparc processor." #endif - ], - [AC_MSG_RESULT(yes) - gtfold_cv_check_sun_sparc=yes], - [AC_MSG_RESULT(no) + ]])],[AC_MSG_RESULT(yes) + gtfold_cv_check_sun_sparc=yes],[AC_MSG_RESULT(no) gtfold_cv_check_sun_sparc=no]) fi @@ -128,13 +124,11 @@ then if test "$gtfold_cv_check_sun_sparc" == "yes"; then AC_MSG_CHECKING(for Sun sparc v9 architecture) - AC_TRY_COMPILE([], [#ifndef __sparcv9 + AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[]], [[#ifndef __sparcv9 #include "error: this is not a Sun Sparc V9 processor." #endif - ], - [AC_MSG_RESULT(yes) - gtfold_cv_check_sun_sparcv9=yes], - [AC_MSG_RESULT(no) + ]])],[AC_MSG_RESULT(yes) + gtfold_cv_check_sun_sparcv9=yes],[AC_MSG_RESULT(no) gtfold_cv_check_sun_sparcv9=no]) fi fi @@ -184,7 +178,7 @@ AM_CONDITIONAL(GTFOLD_DEBUG, test x$debug = xtrue) dnl Create makefiles and other configuration files AC_CONFIG_FILES([Makefile src/Makefile data/Makefile include/Makefile]) -AC_CONFIG_FILES([data/Turner99/Makefile data/Turner04/Makefile data/Andronescu/Makefile]) +AC_CONFIG_FILES([data/Turner99/Makefile data/Turner04/Makefile data/Andronescu/Makefile data/UNAParams/Makefile data/RNAParams/Makefile]) dnl Generate `config.status' and launch it AC_OUTPUT diff --git a/gtfold-mfe/createsymlinks.sh b/gtfold-mfe/createsymlinks.sh new file mode 100644 index 0000000..1427a56 --- /dev/null +++ b/gtfold-mfe/createsymlinks.sh @@ -0,0 +1,14 @@ +#!/bin/sh +if [ $# != 1 ] +then +echo "Usage: sh createsymlinks.sh " +exit -1 +fi + +BINDIR=$1 +echo 'creating symlinks under' $BINDIR +cd $BINDIR +ln -sf gtfold gtmfe +ln -sf gtfold gtsubopt +ln -sf gtfold gtboltzmann + diff --git a/gtfold-mfe/data/Makefile.am b/gtfold-mfe/data/Makefile.am index d9d1d43..001e73e 100644 --- a/gtfold-mfe/data/Makefile.am +++ b/gtfold-mfe/data/Makefile.am @@ -1,2 +1,2 @@ -SUBDIRS = Turner04 Turner99 Andronescu +SUBDIRS = UNAParams RNAParams Turner04 Turner99 Andronescu diff --git a/gtfold-mfe/data/Makefile.in b/gtfold-mfe/data/Makefile.in index 20b49f3..a245c3c 100644 --- a/gtfold-mfe/data/Makefile.in +++ b/gtfold-mfe/data/Makefile.in @@ -1,4 +1,4 @@ -# Makefile.in generated by automake 1.11.1 from Makefile.am. +# Makefile.in generated by automake 1.11 from Makefile.am. # @configure_input@ # Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, @@ -128,7 +128,6 @@ PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@ PACKAGE_NAME = @PACKAGE_NAME@ PACKAGE_STRING = @PACKAGE_STRING@ PACKAGE_TARNAME = @PACKAGE_TARNAME@ -PACKAGE_URL = @PACKAGE_URL@ PACKAGE_VERSION = @PACKAGE_VERSION@ PATH_SEPARATOR = @PATH_SEPARATOR@ SET_MAKE = @SET_MAKE@ @@ -190,7 +189,7 @@ target_vendor = @target_vendor@ top_build_prefix = @top_build_prefix@ top_builddir = @top_builddir@ top_srcdir = @top_srcdir@ -SUBDIRS = Turner04 Turner99 Andronescu +SUBDIRS = UNAParams RNAParams Turner04 Turner99 Andronescu all: all-recursive .SUFFIXES: @@ -232,7 +231,7 @@ $(am__aclocal_m4_deps): # (which will cause the Makefiles to be regenerated when you run `make'); # (2) otherwise, pass the desired values on the `make' command line. $(RECURSIVE_TARGETS): - @fail= failcom='exit 1'; \ + @failcom='exit 1'; \ for f in x $$MAKEFLAGS; do \ case $$f in \ *=* | --[!k]*);; \ @@ -257,7 +256,7 @@ $(RECURSIVE_TARGETS): fi; test -z "$$fail" $(RECURSIVE_CLEAN_TARGETS): - @fail= failcom='exit 1'; \ + @failcom='exit 1'; \ for f in x $$MAKEFLAGS; do \ case $$f in \ *=* | --[!k]*);; \ diff --git a/gtfold-mfe/data/RNAParams/Makefile.am b/gtfold-mfe/data/RNAParams/Makefile.am new file mode 100644 index 0000000..8655bda --- /dev/null +++ b/gtfold-mfe/data/RNAParams/Makefile.am @@ -0,0 +1,23 @@ +## Process this file with automake to produce Makefile.in + +gtfold_datadir = $(datadir)/@PACKAGE@/RNAParams + +gtfold_data_DATA = \ + stack.DAT\ + miscloop.DAT\ + dangle.DAT\ + loop.DAT\ + int11.DAT\ + int21.DAT\ + int22.DAT\ + tloop.DAT\ + tstackh.DAT\ + tstacki.DAT\ + tstacke.DAT\ + tstackm.DAT + + +EXTRA_DIST = $(gtfold_data_DATA) + 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2.50 2.00 2.50 2.50 2.00 2.70 1.30 2.00 2.50 2.30 1.70 + 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 + 3.10 2.20 2.20 2.00 2.30 2.20 2.00 2.20 2.20 2.00 2.40 1.00 2.00 2.20 2.00 1.40 + 1.70 1.50 0.50 2.00 1.60 2.40 2.00 2.40 0.50 2.00 1.00 1.10 2.00 2.40 2.10 2.40 + 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 + 2.10 1.90 0.90 2.00 2.00 2.40 2.00 2.40 0.90 2.00 1.40 0.70 2.00 2.40 1.70 2.00 + 2.20 1.00 1.80 2.00 1.10 1.90 2.00 1.90 1.80 2.00 1.50 -1.20 2.00 1.90 -0.20 1.90 + 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 + 3.40 2.50 2.50 2.00 2.60 2.50 2.00 2.50 2.50 2.00 2.70 1.30 2.00 2.50 2.30 1.70 + 1.00 -0.30 0.50 2.00 -0.20 0.70 2.00 0.70 0.50 2.00 0.30 -2.50 2.00 0.70 -1.50 0.70 + 2.90 1.70 2.50 2.00 1.80 1.60 2.00 1.60 2.50 2.00 2.20 1.30 2.00 1.60 2.30 0.80 diff --git a/gtfold-mfe/data/RNAParams/loop.DAT b/gtfold-mfe/data/RNAParams/loop.DAT new file mode 100644 index 0000000..98c1285 --- /dev/null +++ b/gtfold-mfe/data/RNAParams/loop.DAT @@ -0,0 +1,30 @@ +1 inf 3.80 inf +2 4.10 2.80 inf +3 5.10 3.20 5.70 +4 1.70 3.60 5.60 +5 1.80 4.00 5.60 +6 2.00 4.40 5.40 +7 2.20 4.59 5.90 +8 2.30 4.70 5.60 +9 2.40 4.80 6.40 +10 2.50 4.90 6.50 +11 2.60 5.00 6.60 +12 2.70 5.10 6.70 +13 2.78 5.19 6.78 +14 2.86 5.27 6.86 +15 2.94 5.34 6.94 +16 3.01 5.41 7.01 +17 3.07 5.48 7.07 +18 3.13 5.54 7.13 +19 3.19 5.60 7.19 +20 3.25 5.65 7.25 +21 3.30 5.71 7.30 +22 3.35 5.76 7.35 +23 3.40 5.80 7.40 +24 3.45 5.85 7.44 +25 3.49 5.89 7.49 +26 3.53 5.94 7.53 +27 3.57 5.98 7.57 +28 3.61 6.02 7.61 +29 3.65 6.05 7.65 +30 3.69 6.09 7.69 diff --git a/gtfold-mfe/data/RNAParams/miscloop.DAT b/gtfold-mfe/data/RNAParams/miscloop.DAT new file mode 100644 index 0000000..69847f3 --- /dev/null +++ b/gtfold-mfe/data/RNAParams/miscloop.DAT @@ -0,0 +1,12 @@ +1.079 +3.00 +.50 .50 .50 .50 +3.40 .00 .40 +10.10 -0.30 -0.30 +0.50 +0.0 +0.0 +0.0 +0.0 +4.10 +0 diff --git a/gtfold-mfe/data/RNAParams/sint2.DAT b/gtfold-mfe/data/RNAParams/sint2.DAT new file mode 100644 index 0000000..96eabfd --- /dev/null +++ b/gtfold-mfe/data/RNAParams/sint2.DAT @@ -0,0 +1,24 @@ +1.70 1.70 1.70 1.70 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 +1.70 1.70 1.70 1.70 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 +1.70 1.70 -0.40 1.70 1.10 1.10 -1.00 1.10 1.10 1.10 -1.00 1.10 1.70 1.70 -0.40 1.70 1.70 1.70 -0.40 1.70 1.70 1.70 -0.40 1.70 +1.70 1.70 1.70 1.50 1.10 1.10 1.10 1.00 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.20 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 +1.10 1.10 1.10 1.10 0.40 -0.40 0.40 0.40 1.10 0.40 0.40 0.40 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 +1.10 1.10 1.10 1.10 0.30 0.50 0.40 0.50 0.40 0.40 0.40 0.40 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 +1.10 1.10 -1.00 1.10 -0.10 0.40 -1.70 0.40 0.40 0.40 -1.40 0.40 1.10 1.10 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1.70 -0.40 1.70 1.70 1.70 -0.40 1.70 +1.70 1.70 1.70 1.80 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.50 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 +1.70 1.70 1.70 1.70 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 +1.70 1.70 1.70 1.70 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 +1.70 1.70 -0.40 1.70 1.10 1.10 -1.00 1.10 1.10 1.10 -1.00 1.10 1.70 1.70 -0.40 1.70 1.70 1.70 -0.40 1.70 1.70 1.70 -0.40 1.70 +1.70 1.70 1.70 1.70 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 +1.70 1.70 1.70 1.70 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 +1.70 1.70 1.70 1.70 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 +1.70 1.70 -0.40 1.70 1.10 1.10 -1.00 1.10 1.10 1.10 -1.00 1.10 1.70 1.70 -0.40 1.70 1.70 1.70 -0.40 1.70 1.70 1.70 -0.40 1.70 +1.70 1.70 1.70 1.70 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 diff --git a/gtfold-mfe/data/RNAParams/sint4.DAT b/gtfold-mfe/data/RNAParams/sint4.DAT new file mode 100644 index 0000000..c878345 --- /dev/null +++ b/gtfold-mfe/data/RNAParams/sint4.DAT @@ -0,0 +1,576 @@ +2.80 2.30 1.70 2.00 2.80 3.40 2.00 3.40 1.70 2.00 2.10 1.00 2.00 3.10 2.20 2.90 +2.60 2.20 1.60 2.00 2.60 2.60 2.00 2.60 1.60 2.00 2.00 -0.20 2.00 2.30 1.10 1.80 +1.50 1.10 0.50 2.00 1.50 2.50 2.00 2.50 0.50 2.00 0.90 0.50 2.00 2.20 1.80 2.50 +2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 +2.50 2.10 1.50 2.00 2.50 2.50 2.00 2.50 1.50 2.00 1.90 -0.30 2.00 2.20 1.00 1.70 +3.10 2.00 2.40 2.00 2.50 2.50 2.00 2.50 2.40 2.00 2.40 0.70 2.00 2.20 1.90 1.60 +2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 +3.10 2.00 2.40 2.00 2.50 2.50 2.00 2.50 2.40 2.00 2.40 0.70 2.00 2.20 1.90 1.60 +1.50 1.10 0.50 2.00 1.50 2.50 2.00 2.50 0.50 2.00 0.90 0.50 2.00 2.20 1.80 2.50 +2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 +2.10 1.60 1.00 2.00 2.10 2.70 2.00 2.70 1.00 2.00 1.40 0.30 2.00 2.40 1.50 2.20 +2.30 0.90 2.10 2.00 1.30 2.30 2.00 2.30 2.10 2.00 1.70 -1.50 2.00 2.00 -0.20 2.30 +2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 +3.10 2.00 2.40 2.00 2.50 2.50 2.00 2.50 2.40 2.00 2.40 0.70 2.00 2.20 1.90 1.60 +1.30 -0.10 1.10 2.00 0.30 1.30 2.00 1.30 1.10 2.00 0.70 -2.50 2.00 1.00 -1.20 1.30 +2.70 1.20 2.40 2.00 1.70 1.70 2.00 1.70 2.40 2.00 2.00 0.70 2.00 1.40 1.90 0.80 +2.10 1.90 0.10 2.00 1.80 2.50 2.00 1.50 0.70 2.00 1.80 0.00 2.00 2.50 0.40 2.10 +2.00 1.70 0.00 2.00 1.70 1.70 2.00 0.70 0.60 2.00 1.60 -1.20 2.00 1.80 -0.80 1.00 +0.90 0.60 -1.10 2.00 0.60 1.60 2.00 0.70 -0.50 2.00 0.50 -0.50 2.00 1.70 -0.10 1.70 +2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 +1.90 1.60 -0.10 2.00 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html html-am info info-am \ + install install-am install-data install-data-am install-dvi \ + install-dvi-am install-exec install-exec-am \ + install-gtfold_dataDATA install-html install-html-am \ + install-info install-info-am install-man install-pdf \ + install-pdf-am install-ps install-ps-am install-strip \ + installcheck installcheck-am installdirs maintainer-clean \ + maintainer-clean-generic mostlyclean mostlyclean-generic pdf \ + pdf-am ps ps-am uninstall uninstall-am \ + uninstall-gtfold_dataDATA + + +# Tell versions [3.59,3.63) of GNU make to not export all variables. +# Otherwise a system limit (for SysV at least) may be exceeded. +.NOEXPORT: diff --git a/gtfold-mfe/data/Turner04-errors/Turner04-errors/Makefile.am b/gtfold-mfe/data/Turner04-errors/Turner04-errors/Makefile.am new file mode 100644 index 0000000..302a135 --- /dev/null +++ b/gtfold-mfe/data/Turner04-errors/Turner04-errors/Makefile.am @@ -0,0 +1,27 @@ +## Process this file with automake to produce Makefile.in + +gtfold_datadir = $(datadir)/@PACKAGE@/Turner04 + +gtfold_data_DATA = \ + stack.dat\ + miscloop.dat\ + dangle.dat\ + loop.dat\ + coaxial.dat\ + coaxstack.dat\ + hexaloop.dat\ + int11.dat\ + int21.dat\ + int22.dat\ + tloop.dat\ + triloop.dat\ + tstack.dat\ + tstackcoax.dat\ + tstackh.dat\ + tstacki.dat\ + tstackm.dat + +EXTRA_DIST = $(gtfold_data_DATA) + +CLEANFILES = *~ + diff --git a/gtfold-mfe/data/Turner04-errors/Turner04-errors/coaxial.dat b/gtfold-mfe/data/Turner04-errors/Turner04-errors/coaxial.dat new file mode 100644 index 0000000..1fb3051 --- /dev/null +++ b/gtfold-mfe/data/Turner04-errors/Turner04-errors/coaxial.dat @@ -0,0 +1,63 @@ +Data Arangement: + Y + ------------------ + (X) A C G U + ------------------ + 5' ==> 3' + AX + AY + 3' <== 5' + (A) . . . . + (C) . . . . + (G) . . . . + (U) -0.7 -0.1 -0.7 -0.1 +-------------------------------- +ERRORS IN STACKING ENERGIES : + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + AX AX AX AX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + CX CX CX CX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + GX GX GX GX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + UX UX UX UX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \ No newline at end of file diff --git a/gtfold-mfe/data/Turner04-errors/Turner04-errors/coaxstack.dat b/gtfold-mfe/data/Turner04-errors/Turner04-errors/coaxstack.dat new file mode 100644 index 0000000..cef509d --- /dev/null +++ b/gtfold-mfe/data/Turner04-errors/Turner04-errors/coaxstack.dat @@ -0,0 +1,63 @@ +Data Arangement: + Y + ------------------ + (X) A C G U + ------------------ + 5' ==> 3' + AX + AY + 3' <== 5' + (A) . . . . + (C) . . . . + (G) . . . . + (U) -0.7 -0.1 -0.7 -0.1 +-------------------------------- +ERRORS IN STACKING ENERGIES : TERMINAL MISMATCHES AND BASE-PAIRS. + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + AX AX AX AX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + CX CX CX CX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + GX GX GX GX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + UX UX UX UX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \ No newline at end of file diff --git a/gtfold-mfe/data/Turner04-errors/Turner04-errors/dangle.dat b/gtfold-mfe/data/Turner04-errors/Turner04-errors/dangle.dat new file mode 100644 index 0000000..7c9161b --- /dev/null +++ b/gtfold-mfe/data/Turner04-errors/Turner04-errors/dangle.dat @@ -0,0 +1,72 @@ + X X X X +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + AX AX AX AX + A C G U + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + X X X X +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + CX CX CX CX + A C G U + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + X X X X +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + GX GX GX GX + A C G U + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + X X X X +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + UX UX UX UX + A C G U + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + X X X X +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + A A A A + AX CX GX UX + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + X X X X +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + C C C C + AX CX GX UX + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + X X X X +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + G G G G + AX CX GX UX + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + X X X X +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + U U U U + AX CX GX UX + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 diff --git a/gtfold-mfe/data/Turner04-errors/Turner04-errors/hexaloop.dat b/gtfold-mfe/data/Turner04-errors/Turner04-errors/hexaloop.dat new file mode 100644 index 0000000..66eb771 --- /dev/null +++ b/gtfold-mfe/data/Turner04-errors/Turner04-errors/hexaloop.dat @@ -0,0 +1,6 @@ + Seq Energy + ------------- + ACAGUGCU 0 + ACAGUGAU 0 + ACAGUUCU 0 + ACAGUACU 0 \ No newline at end of file diff --git a/gtfold-mfe/data/Turner04-errors/Turner04-errors/int11.dat b/gtfold-mfe/data/Turner04-errors/Turner04-errors/int11.dat new file mode 100644 index 0000000..67aa76a --- /dev/null +++ b/gtfold-mfe/data/Turner04-errors/Turner04-errors/int11.dat @@ -0,0 +1,101 @@ +Data table for symetric interior loops of size 2 +Free energies at 37 degrees for RNA +Data Arrangement: + Y + ------------------ +(X) A C G U + ------------------ + 5' --> 3' + X + A A + U U + Y + 3' <-- 5' +(A) . . . . +(C) . . . . +(G) . . . . +(U) . . . . + Y Y Y Y Y Y + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + X X X X X X + A A A C A G A U A G A U + U U U G U C U A U U U G + Y Y Y Y Y Y + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 + 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 + Y Y Y Y Y Y + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + X X X X X X + C A C C C G C U C G C U + G U G G G C G A G U G G + Y Y Y Y Y Y + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 0.00 0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 + 0.00 0.00 -0.00 0.00 -0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 + Y Y Y Y Y Y + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + X X X X X X + G A G C G G G U G G G U + C U C G C C C A C U C G + Y Y Y Y Y Y + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 + 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 + Y Y Y Y Y Y + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + X X X X X X + U A U C U G U U U G U U + A U A G A C A A A U A G + Y Y Y Y Y Y + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 + 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 + Y Y Y Y Y Y + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + X X X X X X + G A G C G G G U G G G U + U U U G U C U A U U U G + Y Y Y Y Y Y + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 + 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 + Y Y Y Y Y Y + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + X X X X X X + U A U C U G U U U G U U + G U G G G C G A G U G G + Y Y Y Y Y Y + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 + 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 diff --git a/gtfold-mfe/data/Turner04-errors/Turner04-errors/int21.dat b/gtfold-mfe/data/Turner04-errors/Turner04-errors/int21.dat new file mode 100644 index 0000000..9966877 --- /dev/null +++ b/gtfold-mfe/data/Turner04-errors/Turner04-errors/int21.dat @@ -0,0 +1,353 @@ +Data tables for asymmetric interior loops of size 3 +Free energies at 37 degrees for RNA +Data arrangement: + Y + ------------------ +(X) A C G U + ------------------ + 5' --> 3' + X + A A + U U + YA + 3' <-- 5' +(A) . . . . +(C) . . . . +(G) . . . . +(U) . . . . + Y Y Y Y Y Y + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + X X X X X X + A A A C A G A U A G A U + U U U G U C U A U U U G + YA YA YA YA YA YA + 3' <-- 5' 3' <-- 5' 3' <-- 5' 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(INTERPOLATE WHERE NEEDED) +hp3 ave calc no tmm;hp4 ave calc with tmm; ave all bulges +SIZE INTERNAL BULGE HAIRPIN +------------------------------------------------------- +1 0 0.08 0 +2 0 1.3 0 +3 0 1.9 0.2 +4 0.1 0 0.1 +5 0.1 0 0.2 +6 0.1 0 0.1 +7 0.1 0 0.2 +8 0 0 0.2 +9 0 0 0.2 +10 0 0 0 +11 0 0 0 +12 0 0 0 +13 0 0 0 +14 0 0 0 +15 0 0 0 +16 0 0 0 +17 0 0 0 +18 0 0 0 +19 0 0 0 +20 0 0 0 +21 0 0 0 +22 0 0 0 +23 0 0 0 +24 0 0 0 +25 0 0 0 +26 0 0 0 +27 0 0 0 +28 0 0 0 +29 0 0 0 +30 0 0 0 diff --git a/gtfold-mfe/data/Turner04-errors/Turner04-errors/miscloop.dat b/gtfold-mfe/data/Turner04-errors/Turner04-errors/miscloop.dat new file mode 100644 index 0000000..c9b76e9 --- /dev/null +++ b/gtfold-mfe/data/Turner04-errors/Turner04-errors/miscloop.dat @@ -0,0 +1,48 @@ +Miscellaneous free energy rules +------------------------------- +Extrapolation for large loops based on polymer theory +internal, bulge or hairpin loops > 30: dS(T)=dS(30)+param*ln(n/30) +--> +1.079 +asymmetric internal loops: the ninio equation +the maximum correction +--> +3.0 +the f(m) array (see Ninio for details) +--> + .6 .6 .6 .6 +multibranched loops + offset, per nuc penalty, helix penalty +--> + 9.3 -.0 -.9 +efn2 multibranched loops + offset, per nuc penalty, helix penalty +--> + 9.3 0.0 -0.9 +miscloop asym +--> +0.9 +multiloop strain +--> +0.44 +terminal AU penalty +--> + 0.5 +bonus for GGG hairpin +--> +-2.2 +c hairpin slope +--> +0.3 +c hairpin intercept +--> +0.24 +c hairpin of 3 +--> +1.5 +Intermolecular initiation free energy +--> +4.1 +Bonus for Single C bulges adjacent to C +--> +0.3 diff --git a/gtfold-mfe/data/Turner04-errors/Turner04-errors/stack.dat b/gtfold-mfe/data/Turner04-errors/Turner04-errors/stack.dat new file mode 100644 index 0000000..81fa1e6 --- /dev/null +++ b/gtfold-mfe/data/Turner04-errors/Turner04-errors/stack.dat @@ -0,0 +1,63 @@ +Data Arangement: + Y + ------------------ + (X) A C G U + ------------------ + 5' ==> 3' + AX + AY + 3' <== 5' + (A) 0 0 0 0 + (C) 0 0 0 0 + (G) 0 0 0 0 + (U) -0.7 -0.1 -0.7 -0.1 +-------------------------------- +STACKING ENERGIES : + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + AX AX AX AX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.03 + 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.06 0 + 0 0 0 0 0 0 0 0 0 0 0 0 0 0.07 0 0.32 + 0 0 0 0 0 0 0 0 0 0 0 0 0.08 0 0.24 0 + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + CX CX CX CX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 0 0 0 0 0 0 0 0 0 0 0 0.07 0 0 0 0 + 0 0 0 0 0 0 0 0 0 0 0.07 0 0 0 0 0 + 0 0 0 0 0 0 0 0 0 0.09 0 0.27 0 0 0 0 + 0 0 0 0 0 0 0 0 0.06 0 0.24 0 0 0 0 0 + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + GX GX GX GX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 0 0 0 0 0 0 0 0.06 0 0 0 0 0 0 0 0.28 + 0 0 0 0 0 0 0.08 0 0 0 0 0 0 0 0.25 0 + 0 0 0 0 0 0.07 0 0.27 0 0 0 0 0 0.25 0 0.96 + 0 0 0 0 0.06 0 0.25 0 0 0 0 0 0.24 0 0.56 0 + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + UX UX UX UX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 0 0 0 0.09 0 0 0 0 0 0 0 0.30 0 0 0 0 + 0 0 0.06 0 0 0 0 0 0 0 0.27 0 0 0 0 0 + 0 0.07 0 0.30 0 0 0 0 0 0.24 0 0.48 0 0 0 0 +0.03 0 0.28 0 0 0 0 0 0.32 0 0.96 0 0 0 0 0 diff --git a/gtfold-mfe/data/Turner04-errors/Turner04-errors/tloop.dat b/gtfold-mfe/data/Turner04-errors/Turner04-errors/tloop.dat new file mode 100644 index 0000000..3a63c62 --- /dev/null +++ b/gtfold-mfe/data/Turner04-errors/Turner04-errors/tloop.dat @@ -0,0 +1,17 @@ + Seq Energy + ------------- +CUACGG 0 +CUCCGG 0 +CUUCGG 0 +CCAAGG 0 +CCCAGG 0 +CCGAGG 0 +CCUAGG 0 +CCACGG 0 +CCGCGG 0 +CCUCGG 0 +CUAAGG 0 +CUCAGG 0 +CUUAGG 0 +CUGCGG 0 +CAACGG 0 diff --git a/gtfold-mfe/data/Turner04-errors/Turner04-errors/triloop.dat b/gtfold-mfe/data/Turner04-errors/Turner04-errors/triloop.dat new file mode 100644 index 0000000..e66a4b6 --- /dev/null +++ b/gtfold-mfe/data/Turner04-errors/Turner04-errors/triloop.dat @@ -0,0 +1,4 @@ + Seq Energy + ------------- +CAACG 0 +GUUAC 0 \ No newline at end of file diff --git a/gtfold-mfe/data/Turner04-errors/Turner04-errors/tstack.dat b/gtfold-mfe/data/Turner04-errors/Turner04-errors/tstack.dat new file mode 100644 index 0000000..6ab5d45 --- /dev/null +++ b/gtfold-mfe/data/Turner04-errors/Turner04-errors/tstack.dat @@ -0,0 +1,63 @@ +Data Arangement: + Y + ------------------ + (X) A C G U + ------------------ + 5' ==> 3' + AX + AY + 3' <== 5' + (A) . . . . + (C) . . . . + (G) . . . . + (U) -0.7 -0.1 -0.7 -0.1 +-------------------------------- +STACKING ENERGIES : TERMINAL MISMATCHES AND BASE-PAIRS. + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + AX AX AX AX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + CX CX CX CX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + GX GX GX GX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + UX UX UX UX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 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Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + UX UX UX UX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 diff --git a/gtfold-mfe/data/Turner04-errors/Turner04-errors/tstackh.dat b/gtfold-mfe/data/Turner04-errors/Turner04-errors/tstackh.dat new file mode 100644 index 0000000..6ab5d45 --- /dev/null +++ b/gtfold-mfe/data/Turner04-errors/Turner04-errors/tstackh.dat @@ -0,0 +1,63 @@ +Data Arangement: + Y + ------------------ + (X) A C G U + ------------------ + 5' ==> 3' + AX + AY + 3' <== 5' + (A) . . . . + (C) . . . . + (G) . . . . + (U) -0.7 -0.1 -0.7 -0.1 +-------------------------------- +STACKING ENERGIES : TERMINAL MISMATCHES AND BASE-PAIRS. + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + AX AX AX AX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + CX CX CX CX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + GX GX GX GX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + UX UX UX UX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 diff --git a/gtfold-mfe/data/Turner04-errors/Turner04-errors/tstacki.dat b/gtfold-mfe/data/Turner04-errors/Turner04-errors/tstacki.dat new file mode 100644 index 0000000..6ab5d45 --- /dev/null +++ b/gtfold-mfe/data/Turner04-errors/Turner04-errors/tstacki.dat @@ -0,0 +1,63 @@ +Data Arangement: + Y + ------------------ + (X) A C G U + ------------------ + 5' ==> 3' + AX + AY + 3' <== 5' + (A) . . . . + (C) . . . . + (G) . . . . + (U) -0.7 -0.1 -0.7 -0.1 +-------------------------------- +STACKING ENERGIES : TERMINAL MISMATCHES AND BASE-PAIRS. + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + AX AX AX AX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + CX CX CX CX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + GX GX GX GX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + UX UX UX UX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 diff --git a/gtfold-mfe/data/Turner04-errors/Turner04-errors/tstackm.dat b/gtfold-mfe/data/Turner04-errors/Turner04-errors/tstackm.dat new file mode 100644 index 0000000..6ab5d45 --- /dev/null +++ b/gtfold-mfe/data/Turner04-errors/Turner04-errors/tstackm.dat @@ -0,0 +1,63 @@ +Data Arangement: + Y + ------------------ + (X) A C G U + ------------------ + 5' ==> 3' + AX + AY + 3' <== 5' + (A) . . . . + (C) . . . . + (G) . . . . + (U) -0.7 -0.1 -0.7 -0.1 +-------------------------------- +STACKING ENERGIES : TERMINAL MISMATCHES AND BASE-PAIRS. + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + AX AX AX AX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + CX CX CX CX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + GX GX GX GX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + UX UX UX UX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 diff --git a/gtfold-mfe/data/Turner99/Makefile.am b/gtfold-mfe/data/Turner99/Makefile.am index 4cf8fa7..4390f87 100644 --- a/gtfold-mfe/data/Turner99/Makefile.am +++ b/gtfold-mfe/data/Turner99/Makefile.am @@ -3,25 +3,19 @@ gtfold_datadir = $(datadir)/@PACKAGE@/Turner99 gtfold_data_DATA = \ - stack.dat\ - miscloop.dat\ - dangle.dat\ - loop.dat\ - asint1x2.dat\ - coaxial.dat\ - coaxstack.dat\ - int11.dat\ - int21.dat\ - int22.dat\ - sint2.dat\ - sint4.dat\ - tloop.dat\ - triloop.dat\ - tstack.dat\ - tstackcoax.dat\ - tstackh.dat\ - tstacki.dat\ - tstackm.dat + stack.DAT\ + miscloop.DAT\ + dangle.DAT\ + loop.DAT\ + int11.DAT\ + int21.DAT\ + int22.DAT\ + tloop.DAT\ + tstackh.DAT\ + tstacki.DAT\ + tstacke.DAT\ + tstackm.DAT + EXTRA_DIST = $(gtfold_data_DATA) diff --git a/gtfold-mfe/data/Turner99/Makefile.in b/gtfold-mfe/data/Turner99/Makefile.in index d9a1eb3..d21f2af 100644 --- a/gtfold-mfe/data/Turner99/Makefile.in +++ b/gtfold-mfe/data/Turner99/Makefile.in @@ -1,4 +1,4 @@ -# Makefile.in generated by automake 1.11.1 from Makefile.am. +# Makefile.in generated by automake 1.11 from Makefile.am. # @configure_input@ # Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, @@ -112,7 +112,6 @@ PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@ PACKAGE_NAME = @PACKAGE_NAME@ PACKAGE_STRING = @PACKAGE_STRING@ PACKAGE_TARNAME = @PACKAGE_TARNAME@ -PACKAGE_URL = @PACKAGE_URL@ PACKAGE_VERSION = @PACKAGE_VERSION@ PATH_SEPARATOR = @PATH_SEPARATOR@ SET_MAKE = @SET_MAKE@ @@ -176,25 +175,18 @@ top_builddir = @top_builddir@ top_srcdir = @top_srcdir@ gtfold_datadir = $(datadir)/@PACKAGE@/Turner99 gtfold_data_DATA = \ - stack.dat\ - miscloop.dat\ - dangle.dat\ - loop.dat\ - asint1x2.dat\ - coaxial.dat\ - coaxstack.dat\ - int11.dat\ - int21.dat\ - int22.dat\ - sint2.dat\ - sint4.dat\ - tloop.dat\ - triloop.dat\ - tstack.dat\ - tstackcoax.dat\ - tstackh.dat\ - tstacki.dat\ - tstackm.dat + stack.DAT\ + miscloop.DAT\ + dangle.DAT\ + loop.DAT\ + int11.DAT\ + int21.DAT\ + int22.DAT\ + tloop.DAT\ + tstackh.DAT\ + tstacki.DAT\ + tstacke.DAT\ + tstackm.DAT EXTRA_DIST = $(gtfold_data_DATA) CLEANFILES = *~ diff --git a/gtfold-mfe/data/Turner99/asint1x2.dat b/gtfold-mfe/data/Turner99/base_data/asint1x2.dat similarity index 100% rename from gtfold-mfe/data/Turner99/asint1x2.dat rename to gtfold-mfe/data/Turner99/base_data/asint1x2.dat diff --git a/gtfold-mfe/data/Turner99/coaxial.dat b/gtfold-mfe/data/Turner99/base_data/coaxial.dat similarity index 100% rename from gtfold-mfe/data/Turner99/coaxial.dat rename to gtfold-mfe/data/Turner99/base_data/coaxial.dat diff --git a/gtfold-mfe/data/Turner99/coaxstack.dat b/gtfold-mfe/data/Turner99/base_data/coaxstack.dat similarity index 100% rename from gtfold-mfe/data/Turner99/coaxstack.dat rename to gtfold-mfe/data/Turner99/base_data/coaxstack.dat diff --git a/gtfold-mfe/data/Turner99/dangle.dat b/gtfold-mfe/data/Turner99/base_data/dangle.dat similarity index 100% rename from gtfold-mfe/data/Turner99/dangle.dat rename to gtfold-mfe/data/Turner99/base_data/dangle.dat diff --git a/gtfold-mfe/data/Turner99/int11.dat b/gtfold-mfe/data/Turner99/base_data/int11.dat similarity index 100% rename from gtfold-mfe/data/Turner99/int11.dat rename to gtfold-mfe/data/Turner99/base_data/int11.dat diff --git a/gtfold-mfe/data/Turner99/int21.dat b/gtfold-mfe/data/Turner99/base_data/int21.dat similarity index 100% rename from gtfold-mfe/data/Turner99/int21.dat rename to gtfold-mfe/data/Turner99/base_data/int21.dat diff --git a/gtfold-mfe/data/Turner99/int22.dat b/gtfold-mfe/data/Turner99/base_data/int22.dat similarity index 100% rename from gtfold-mfe/data/Turner99/int22.dat rename to gtfold-mfe/data/Turner99/base_data/int22.dat diff --git a/gtfold-mfe/data/Turner99/loop.dat b/gtfold-mfe/data/Turner99/base_data/loop.dat similarity index 100% rename from gtfold-mfe/data/Turner99/loop.dat rename to gtfold-mfe/data/Turner99/base_data/loop.dat diff --git a/gtfold-mfe/data/Turner99/miscloop.dat b/gtfold-mfe/data/Turner99/base_data/miscloop.dat similarity index 100% rename from gtfold-mfe/data/Turner99/miscloop.dat rename to gtfold-mfe/data/Turner99/base_data/miscloop.dat diff --git a/gtfold-mfe/data/Turner99/sint2.dat b/gtfold-mfe/data/Turner99/base_data/sint2.dat similarity index 100% rename from gtfold-mfe/data/Turner99/sint2.dat rename to gtfold-mfe/data/Turner99/base_data/sint2.dat diff --git a/gtfold-mfe/data/Turner99/sint4.dat b/gtfold-mfe/data/Turner99/base_data/sint4.dat similarity index 100% rename from gtfold-mfe/data/Turner99/sint4.dat rename to gtfold-mfe/data/Turner99/base_data/sint4.dat diff --git a/gtfold-mfe/data/Turner99/stack.dat b/gtfold-mfe/data/Turner99/base_data/stack.dat similarity index 100% rename from gtfold-mfe/data/Turner99/stack.dat rename to gtfold-mfe/data/Turner99/base_data/stack.dat diff --git a/gtfold-mfe/data/Turner99/tloop.dat b/gtfold-mfe/data/Turner99/base_data/tloop.dat similarity index 100% rename from gtfold-mfe/data/Turner99/tloop.dat rename to gtfold-mfe/data/Turner99/base_data/tloop.dat diff --git a/gtfold-mfe/data/Turner99/triloop.dat b/gtfold-mfe/data/Turner99/base_data/triloop.dat similarity index 100% rename from gtfold-mfe/data/Turner99/triloop.dat rename to gtfold-mfe/data/Turner99/base_data/triloop.dat diff --git a/gtfold-mfe/data/Turner99/tstack.dat b/gtfold-mfe/data/Turner99/base_data/tstack.dat similarity index 100% rename from gtfold-mfe/data/Turner99/tstack.dat rename to gtfold-mfe/data/Turner99/base_data/tstack.dat diff --git a/gtfold-mfe/data/Turner99/tstackcoax.dat b/gtfold-mfe/data/Turner99/base_data/tstackcoax.dat similarity index 100% rename from gtfold-mfe/data/Turner99/tstackcoax.dat rename to gtfold-mfe/data/Turner99/base_data/tstackcoax.dat diff --git a/gtfold-mfe/data/Turner99/tstackh.dat b/gtfold-mfe/data/Turner99/base_data/tstackh.dat similarity index 100% rename from gtfold-mfe/data/Turner99/tstackh.dat rename to gtfold-mfe/data/Turner99/base_data/tstackh.dat diff --git a/gtfold-mfe/data/Turner99/tstacki.dat b/gtfold-mfe/data/Turner99/base_data/tstacki.dat similarity index 100% rename from gtfold-mfe/data/Turner99/tstacki.dat rename to gtfold-mfe/data/Turner99/base_data/tstacki.dat diff --git a/gtfold-mfe/data/Turner99/tstackm.dat b/gtfold-mfe/data/Turner99/base_data/tstackm.dat similarity index 100% rename from gtfold-mfe/data/Turner99/tstackm.dat rename to gtfold-mfe/data/Turner99/base_data/tstackm.dat diff --git a/gtfold-mfe/data/Turner99/dangle.DAT b/gtfold-mfe/data/Turner99/dangle.DAT new file mode 100644 index 0000000..9fb7c28 --- /dev/null +++ b/gtfold-mfe/data/Turner99/dangle.DAT @@ -0,0 +1,8 @@ +inf inf inf inf inf inf inf inf inf inf inf inf -0.80 -0.50 -0.80 -0.60 +inf inf inf inf inf inf inf inf -1.70 -0.80 -1.70 -1.20 inf inf inf inf +inf inf inf inf -1.10 -0.40 -1.30 -0.60 inf inf inf inf -0.80 -0.50 -0.80 -0.60 +-0.70 -0.10 -0.70 -0.10 inf inf inf inf -0.70 -0.10 -0.70 -0.10 inf inf inf inf +inf inf inf inf inf inf inf inf inf inf inf inf -0.30 -0.10 -0.20 -0.20 +inf inf inf inf inf inf inf inf -0.20 -0.30 -0.0 -0.0 inf inf inf inf +inf inf inf inf -0.50 -0.30 -0.20 -0.10 inf inf inf inf -0.30 -0.10 -0.20 -0.20 +-0.30 -0.30 -0.40 -0.20 inf inf inf inf -0.30 -0.30 -0.40 -0.20 inf inf inf inf diff --git a/gtfold-mfe/data/Turner99/int11.DAT b/gtfold-mfe/data/Turner99/int11.DAT new file mode 100644 index 0000000..96eabfd --- /dev/null +++ b/gtfold-mfe/data/Turner99/int11.DAT @@ -0,0 +1,24 @@ +1.70 1.70 1.70 1.70 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 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b/gtfold-mfe/data/Turner99/int21.DAT @@ -0,0 +1,96 @@ +3.90 3.70 3.10 5.50 3.20 3.00 2.40 4.80 3.20 3.00 2.40 4.80 3.90 3.70 3.10 5.50 3.90 3.70 3.10 5.50 3.90 3.70 3.10 5.50 +3.80 3.70 5.50 3.70 3.10 3.00 4.80 3.00 3.10 3.00 4.80 3.00 3.80 3.70 5.50 3.70 3.80 3.70 5.50 3.70 3.80 3.70 5.50 3.70 +3.20 5.50 2.30 5.50 2.50 4.80 1.60 4.80 2.50 4.80 1.60 4.80 3.20 5.50 2.30 5.50 3.20 5.50 2.30 5.50 3.20 5.50 2.30 5.50 +5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 +3.60 3.20 3.10 5.50 2.90 2.50 2.40 4.80 2.90 2.50 2.40 4.80 3.60 3.20 3.10 5.50 3.60 3.20 3.10 5.50 3.60 3.20 3.10 5.50 +3.70 4.00 5.50 3.70 3.00 3.30 4.80 3.00 3.00 3.30 4.80 3.00 3.70 4.00 5.50 3.70 3.70 4.00 5.50 3.70 3.70 4.00 5.50 3.70 +5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 +5.50 3.70 5.50 2.80 4.80 3.00 4.80 2.10 4.80 3.00 4.80 2.10 5.50 3.70 5.50 2.80 5.50 3.70 5.50 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inf +1.85 1.85 1.85 1.15 inf inf inf inf 1.85 1.85 1.85 1.15 inf inf inf inf diff --git a/gtfold-mfe/data/UNAParams/tstackm.DAT b/gtfold-mfe/data/UNAParams/tstackm.DAT new file mode 100644 index 0000000..ee473db --- /dev/null +++ b/gtfold-mfe/data/UNAParams/tstackm.DAT @@ -0,0 +1,16 @@ +inf inf inf inf inf inf inf inf inf inf inf inf -0.80 -1.00 -0.80 -0.90 +inf inf inf inf inf inf inf inf inf inf inf inf -0.60 -0.70 -2.20 -0.70 +inf inf inf inf inf inf inf inf inf inf inf inf -0.80 -2.10 -0.80 -0.80 +inf inf inf inf inf inf inf inf inf inf inf inf -1.10 -0.80 -1.10 -0.80 +inf inf inf inf inf inf inf inf -1.70 -1.70 -1.70 -1.70 inf inf inf inf +inf inf inf inf inf inf inf inf -1.00 -1.10 -3.30 -0.80 inf inf inf inf +inf inf inf inf inf inf inf inf -1.70 -2.40 -1.70 -1.70 inf inf inf inf +inf inf inf inf inf inf inf inf -1.60 -1.40 -1.60 -1.20 inf inf inf inf +inf inf inf inf -1.10 -1.50 -1.30 -1.90 inf inf inf inf -0.80 -1.00 -0.80 -1.30 +inf inf inf inf -1.10 -0.70 -3.40 -0.50 inf inf inf inf -0.60 -0.70 -2.50 -0.70 +inf inf inf inf -1.60 -3.30 -1.40 -1.30 inf inf inf inf -0.80 -2.10 -0.80 -0.80 +inf inf inf inf -1.70 -1.00 -2.00 -0.70 inf inf inf inf -1.40 -0.80 1.30 -0.80 +-1.00 -0.80 -1.10 -1.30 inf inf inf inf -1.00 -0.80 -1.10 -1.00 inf inf inf inf +-0.70 -0.60 -2.40 -0.50 inf inf inf inf -0.70 -0.60 -1.50 -0.50 inf inf inf inf +-1.10 -2.10 -1.20 -1.00 inf inf inf inf -0.70 -1.40 -0.80 0.30 inf inf inf inf +-0.90 -0.60 -1.40 -0.50 inf inf inf inf -0.50 -0.60 -0.50 -0.50 inf inf inf inf diff --git a/gtfold-mfe/depcomp b/gtfold-mfe/depcomp old mode 100644 new mode 100755 index e5f9736..df8eea7 --- a/gtfold-mfe/depcomp +++ b/gtfold-mfe/depcomp @@ -1,10 +1,10 @@ #! /bin/sh # depcomp - compile a program generating dependencies as side-effects -scriptversion=2007-03-29.01 +scriptversion=2009-04-28.21; # UTC -# Copyright (C) 1999, 2000, 2003, 2004, 2005, 2006, 2007 Free Software -# Foundation, Inc. +# Copyright (C) 1999, 2000, 2003, 2004, 2005, 2006, 2007, 2009 Free +# Software Foundation, Inc. # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by @@ -17,9 +17,7 @@ scriptversion=2007-03-29.01 # GNU General Public License for more details. # You should have received a copy of the GNU General Public License -# along with this program; if not, write to the Free Software -# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA -# 02110-1301, USA. +# along with this program. If not, see . # As a special exception to the GNU General Public License, if you # distribute this file as part of a program that contains a @@ -87,6 +85,15 @@ if test "$depmode" = dashXmstdout; then depmode=dashmstdout fi +cygpath_u="cygpath -u -f -" +if test "$depmode" = msvcmsys; then + # This is just like msvisualcpp but w/o cygpath translation. + # Just convert the backslash-escaped backslashes to single forward + # slashes to satisfy depend.m4 + cygpath_u="sed s,\\\\\\\\,/,g" + depmode=msvisualcpp +fi + case "$depmode" in gcc3) ## gcc 3 implements dependency tracking that does exactly what @@ -192,14 +199,14 @@ sgi) ' < "$tmpdepfile" \ | sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' | \ tr ' -' ' ' >> $depfile - echo >> $depfile +' ' ' >> "$depfile" + echo >> "$depfile" # The second pass generates a dummy entry for each header file. tr ' ' ' ' < "$tmpdepfile" \ | sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' -e 's/$/:/' \ - >> $depfile + >> "$depfile" else # The sourcefile does not contain any dependencies, so just # store a dummy comment line, to avoid errors with the Makefile @@ -328,7 +335,12 @@ hp2) if test -f "$tmpdepfile"; then sed -e "s,^.*\.[a-z]*:,$object:," "$tmpdepfile" > "$depfile" # Add `dependent.h:' lines. - sed -ne '2,${; s/^ *//; s/ \\*$//; s/$/:/; p;}' "$tmpdepfile" >> "$depfile" + sed -ne '2,${ + s/^ *// + s/ \\*$// + s/$/:/ + p + }' "$tmpdepfile" >> "$depfile" else echo "#dummy" > "$depfile" fi @@ -404,7 +416,7 @@ dashmstdout) # Remove the call to Libtool. if test "$libtool" = yes; then - while test $1 != '--mode=compile'; do + while test "X$1" != 'X--mode=compile'; do shift done shift @@ -455,32 +467,39 @@ makedepend) "$@" || exit $? # Remove any Libtool call if test "$libtool" = yes; then - while test $1 != '--mode=compile'; do + while test "X$1" != 'X--mode=compile'; do shift done shift fi # X makedepend shift - cleared=no - for arg in "$@"; do + cleared=no eat=no + for arg + do case $cleared in no) set ""; shift cleared=yes ;; esac + if test $eat = yes; then + eat=no + continue + fi case "$arg" in -D*|-I*) set fnord "$@" "$arg"; shift ;; # Strip any option that makedepend may not understand. Remove # the object too, otherwise makedepend will parse it as a source file. + -arch) + eat=yes ;; -*|$object) ;; *) set fnord "$@" "$arg"; shift ;; esac done - obj_suffix="`echo $object | sed 's/^.*\././'`" + obj_suffix=`echo "$object" | sed 's/^.*\././'` touch "$tmpdepfile" ${MAKEDEPEND-makedepend} -o"$obj_suffix" -f"$tmpdepfile" "$@" rm -f "$depfile" @@ -500,7 +519,7 @@ cpp) # Remove the call to Libtool. if test "$libtool" = yes; then - while test $1 != '--mode=compile'; do + while test "X$1" != 'X--mode=compile'; do shift done shift @@ -538,13 +557,27 @@ cpp) msvisualcpp) # Important note: in order to support this mode, a compiler *must* - # always write the preprocessed file to stdout, regardless of -o, - # because we must use -o when running libtool. + # always write the preprocessed file to stdout. "$@" || exit $? + + # Remove the call to Libtool. + if test "$libtool" = yes; then + while test "X$1" != 'X--mode=compile'; do + shift + done + shift + fi + IFS=" " for arg do case "$arg" in + -o) + shift + ;; + $object) + shift + ;; "-Gm"|"/Gm"|"-Gi"|"/Gi"|"-ZI"|"/ZI") set fnord "$@" shift @@ -557,16 +590,23 @@ msvisualcpp) ;; esac done - "$@" -E | - sed -n '/^#line [0-9][0-9]* "\([^"]*\)"/ s::echo "`cygpath -u \\"\1\\"`":p' | sort | uniq > "$tmpdepfile" + "$@" -E 2>/dev/null | + sed -n '/^#line [0-9][0-9]* "\([^"]*\)"/ s::\1:p' | $cygpath_u | sort -u > "$tmpdepfile" rm -f "$depfile" echo "$object : \\" > "$depfile" - . "$tmpdepfile" | sed 's% %\\ %g' | sed -n '/^\(.*\)$/ s:: \1 \\:p' >> "$depfile" + sed < "$tmpdepfile" -n -e 's% %\\ %g' -e '/^\(.*\)$/ s:: \1 \\:p' >> "$depfile" echo " " >> "$depfile" - . "$tmpdepfile" | sed 's% %\\ %g' | sed -n '/^\(.*\)$/ s::\1\::p' >> "$depfile" + sed < "$tmpdepfile" -n -e 's% %\\ %g' -e '/^\(.*\)$/ s::\1\::p' >> "$depfile" rm -f "$tmpdepfile" ;; +msvcmsys) + # This case exists only to let depend.m4 do its work. It works by + # looking at the text of this script. This case will never be run, + # since it is checked for above. + exit 1 + ;; + none) exec "$@" ;; @@ -585,5 +625,6 @@ exit 0 # eval: (add-hook 'write-file-hooks 'time-stamp) # time-stamp-start: "scriptversion=" # time-stamp-format: "%:y-%02m-%02d.%02H" -# time-stamp-end: "$" +# time-stamp-time-zone: "UTC" +# time-stamp-end: "; # UTC" # End: diff --git a/gtfold-mfe/gtfold_config.h b/gtfold-mfe/gtfold_config.h index 56549bc..b4a21e7 100644 --- a/gtfold-mfe/gtfold_config.h +++ b/gtfold-mfe/gtfold_config.h @@ -53,16 +53,16 @@ #define PACKAGE_NAME "gtfold" /* Define to the full name and version of this package. */ -#define PACKAGE_STRING "gtfold 1.18" +#define PACKAGE_STRING "gtfold 2.0" /* Define to the one symbol short name of this package. */ #define PACKAGE_TARNAME "gtfold" /* Define to the home page for this package. */ -#define PACKAGE_URL "" +/* #undef PACKAGE_URL */ /* Define to the version of this package. */ -#define PACKAGE_VERSION "1.18" +#define PACKAGE_VERSION "2.0" /* Define to 1 if you have the ANSI C header files. */ #define STDC_HEADERS 1 @@ -74,7 +74,7 @@ /* #undef TM_IN_SYS_TIME */ /* Version number of package */ -#define VERSION "1.18" +#define VERSION "2.0" /* Define to empty if `const' does not conform to ANSI C. */ /* #undef const */ diff --git a/gtfold-mfe/include/Makefile.am b/gtfold-mfe/include/Makefile.am index 545325a..5a61bdd 100644 --- a/gtfold-mfe/include/Makefile.am +++ b/gtfold-mfe/include/Makefile.am @@ -1,3 +1,2 @@ -noinst_HEADERS = algorithms.h constants.h data.h loader.h main.h traceback.h - +noinst_HEADERS = algorithms.h constants.h data.h loader.h main.h traceback.h partition-dangle.h random-sample.h algorithms-partition.h global.h options.h random-sample.h subopt_traceback.h constraints.h energy.h shapereader.h utils.h CLEANFILES = *~ diff --git a/gtfold-mfe/include/Makefile.in b/gtfold-mfe/include/Makefile.in index fd92471..607786e 100644 --- a/gtfold-mfe/include/Makefile.in +++ b/gtfold-mfe/include/Makefile.in @@ -1,4 +1,4 @@ -# Makefile.in generated by automake 1.11.1 from Makefile.am. +# Makefile.in generated by automake 1.11 from Makefile.am. # @configure_input@ # Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, @@ -93,7 +93,6 @@ PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@ PACKAGE_NAME = @PACKAGE_NAME@ PACKAGE_STRING = @PACKAGE_STRING@ PACKAGE_TARNAME = @PACKAGE_TARNAME@ -PACKAGE_URL = @PACKAGE_URL@ PACKAGE_VERSION = @PACKAGE_VERSION@ PATH_SEPARATOR = @PATH_SEPARATOR@ SET_MAKE = @SET_MAKE@ @@ -155,7 +154,7 @@ target_vendor = @target_vendor@ top_build_prefix = @top_build_prefix@ top_builddir = @top_builddir@ top_srcdir = @top_srcdir@ -noinst_HEADERS = algorithms.h constants.h data.h energy.h global.h loader.h main.h main-c.h subopt_traceback.h traceback.h +noinst_HEADERS = algorithms.h constants.h data.h loader.h main.h traceback.h partition-dangle.h random-sample.h algorithms-partition.h global.h options.h random-sample.h subopt_traceback.h constraints.h energy.h shapereader.h utils.h CLEANFILES = *~ all: all-am diff --git a/gtfold-mfe/include/algorithms-partition.h b/gtfold-mfe/include/algorithms-partition.h index b45d656..3bfb26d 100644 --- a/gtfold-mfe/include/algorithms-partition.h +++ b/gtfold-mfe/include/algorithms-partition.h @@ -5,25 +5,23 @@ #ifdef __cplusplus extern "C" { #endif - - +/* +typedef struct _pFuncData { + int len; + double** QB; + double** Q; + double** QM; +} p_func_data; +*/ void fill_partition_fn_arrays(int len, double** QB, double** Q, double** QM); -void fillBasePairProbabilities(int length, int *structure, double **Q, double **QB, double **QM, double**P); -void printBasePairProbabilities(int n, int *structure, double **P); +void fillBasePairProbabilities(int length, double **Q, double **QB, double **QM, double**P); +void printBasePairProbabilities(int n, int *structure, double **P, const char* bppfile); double probabilityUnpaired(int length, int i, double **P); double **mallocTwoD(int r, int c); void freeTwoD(double** arr, int r, int c); -typedef struct _pFuncData { - int len; - double** QB; - double** Q; - double** QM; - - // TODO: probability function stuff here -} pFuncData; #ifdef __cplusplus diff --git a/gtfold-mfe/include/algorithms.h b/gtfold-mfe/include/algorithms.h index 336e443..1f0f1df 100644 --- a/gtfold-mfe/include/algorithms.h +++ b/gtfold-mfe/include/algorithms.h @@ -23,7 +23,7 @@ #ifdef __cplusplus extern "C" { #endif - int calculate(int len, int nThreads); + int calculate(int len);//, int nThreads, int unamode ,int t_mismatch); #ifdef __cplusplus } #endif diff --git a/gtfold-mfe/include/boltzmann_main.h b/gtfold-mfe/include/boltzmann_main.h new file mode 100644 index 0000000..50841d4 --- /dev/null +++ b/gtfold-mfe/include/boltzmann_main.h @@ -0,0 +1,6 @@ +#ifndef _BPP_MAIN_H_ +#define _BPP_MAIN_H_ + +int boltzmann_main(int argc, char** argv); + +#endif diff --git a/gtfold-mfe/include/constraints.h b/gtfold-mfe/include/constraints.h index 508fb70..f21e115 100644 --- a/gtfold-mfe/include/constraints.h +++ b/gtfold-mfe/include/constraints.h @@ -4,29 +4,41 @@ extern int* BP; extern int** PBP; extern int** FBP; +extern int* ind; extern int nPBP; extern int nFBP; //static int load_constraints(const char* constr_file, int verbose=0); +#define BP(i,j) BP[ind[j]+i] + + int init_constraints(const char* constr_file, int length) ; void free_constraints(int length) ; void print_constraints(int length) ; - #ifdef __cplusplus extern "C" { #endif -int is_ss(int i, int j); -int prohibit_base(int i) ; -int check_base(int i) ; -int force_pair(int i, int j) ; -int force_pair1(int i, int j) ; -int check_iloop(int i, int j, int p, int q) ; -int check_pair(int i, int j) ; -int check_stack(int i, int j) ; -int check_hairpin(int i, int j) ; +int canStack(int i, int j); +int canSS(int i); +int canSSregion(int i, int j); +int canHairpin(int i, int j); +int canILoop(int i, int j, int p, int q); + +int forceSS(int i); +int forceSSregion(int i, int j); +int forcePair(int i, int j); + + +int withinCD(int i, int j); +int verify_structure(); + +void enable_constraints(int b); +void enable_limit_distance(int b); +void set_contact_distance(int dist); + #ifdef __cplusplus } #endif diff --git a/gtfold-mfe/include/data.h b/gtfold-mfe/include/data.h index d88382f..c0875eb 100644 --- a/gtfold-mfe/include/data.h +++ b/gtfold-mfe/include/data.h @@ -59,6 +59,11 @@ extern int init; extern int gail; /* It is either 0 or 1. It is used for grosely asymmetric internal loops */ extern float prelog; +extern int tstackm[5][5][6][6]; +extern int tstacke[5][5][6][6]; +extern int tstacki23[5][5][5][5]; + + #define fourBaseIndex(a, b, c, d) (((a) << 6) + ((b) << 4) + ((c) << 2) + (d)) #endif diff --git a/gtfold-mfe/include/energy.h b/gtfold-mfe/include/energy.h index c5fdb1f..30d3fd3 100644 --- a/gtfold-mfe/include/energy.h +++ b/gtfold-mfe/include/energy.h @@ -4,25 +4,24 @@ #include "data.h" extern int *V; -extern int *VV; -extern int *VV1; extern int *W; extern int *VBI; extern int *VM; extern int **WM; -extern int *WMu; -extern int *WMl; +extern int **WMPrime; extern int *indx; - +extern int **PP; #define V(i,j) V[indx[j]+i] #define VM(i,j) VM[indx[j]+i] #define WM(i,j) WM[i][j] +#define WMPrime(i,j) WMPrime[i][j] #define WMU(i,j) WM[i][j] #define WML(i,j) WM[j][i] -//#define WMU(i,j) WMu[indx[j]+i] -//#define WML(i,j) WMl[indx[j]+i] #define VBI(i,j) VBI[indx[j]+i] +//#define RT ((0.00198721 * 310.15) * 100.00) +extern const float RT; +extern const float RT_; #define auPen(i, j) ((( (i)==BASE_U || (j)==BASE_U ) && ( (i)==BASE_A || (i)==BASE_G || (j)==BASE_A || (j)==BASE_G )) ? auend : 0) @@ -40,6 +39,9 @@ int auPenalty(int i, int j); int eS(int i, int j); int eH(int i, int j); int eL(int i, int j, int ip, int jp); +int eL1(int i, int j, int ip, int jp); +int Estackm(int i, int j); +int Estacke(int i, int j); void create_tables(int len); void init_tables(int len); diff --git a/gtfold-mfe/include/global.h b/gtfold-mfe/include/global.h index fe2d9df..23ec167 100644 --- a/gtfold-mfe/include/global.h +++ b/gtfold-mfe/include/global.h @@ -3,16 +3,30 @@ #include "constants.h" +#ifdef __cplusplus +#include +using namespace std; +#endif + extern unsigned char *RNA; extern int *structure; extern int* constraints; +extern int g_nthreads; +extern int g_unamode; +extern int g_dangles; +extern int g_mismatch; +extern int g_verbose; +extern int g_prefilter_mode; +extern int g_prefilter1; +extern int g_prefilter2; + extern unsigned int chPairKey; -// The possible base pairs are (A,U), (U,A), (C,G), (G,C), (G,U) and (U,G). +// The possible base pairs are (A,U), (U,A), (C,G), (G,C), (G,U) +// and (U,G). #define checkPair(i, j) (((((i)-(j)) % 2) == 1 || (((i)-(j)) % 2)== -1) && (!( ((i)==BASE_A && (j)==BASE_C) || ((i)==BASE_C && (j)==BASE_A) ))) - #ifdef __cplusplus extern "C" { #endif @@ -21,10 +35,17 @@ void init_global_params(int len); void free_global_params(); void print_sequence(int len); void print_structure(int len); +void print_header() ; #ifdef __cplusplus } #endif +#ifdef __cplusplus +int read_sequence_file(const char* filename, std::string& seq); +bool encodeSequence(string seq); +void save_ct_file(string outputFile, string seq, int energy) ; +#endif + void init_checkPair(); int update_checkPair(int i, int j); diff --git a/gtfold-mfe/include/loader.h b/gtfold-mfe/include/loader.h index 20a0708..1bac05c 100644 --- a/gtfold-mfe/include/loader.h +++ b/gtfold-mfe/include/loader.h @@ -25,18 +25,21 @@ #include "constants.h" #include "data.h" -void readThermodynamicParameters(const char *userdatadir,bool userdatalogic); - -int initStackValues(std::string fileName); -int initMiscloopValues(std::string fileName); -int initDangleValues(std::string fileName); -int initLoopValues(std::string fileName); -int initTstkhValues(std::string fileName); -int initTstkiValues(std::string fileName); -int initTloopValues(std::string fileName); -int initInt21Values(std::string fileName); -int initInt22Values(std::string fileName); -int initInt11Values(std::string fileName); +void readThermodynamicParameters(const char *userdatadir,bool userdatalogic, int unamode, int rnamode, int t_mismatch); + +int initStackValues(const std::string& fileName, const std::string& dirPath); +int initMiscloopValues(const std::string& fileName, const std::string& dirPath); +int initDangleValues(const std::string& fileName, const std::string& dirPath); +int initLoopValues(const std::string& fileName, const std::string& dirPath); +int initTstkhValues(const std::string& fileName, const std::string& dirPath); +int initTstkiValues(const std::string& fileName, const std::string& dirPath); +int initTloopValues(const std::string& fileName, const std::string& dirPath); +int initInt21Values(const std::string& fileName, const std::string& dirPath); +int initInt22Values(const std::string& fileName, const std::string& dirPath); +int initInt11Values(const std::string& fileName, const std::string& dirPath); +int initTstkmValues(const std::string& fileName, const std::string& dirPath); +int initTstkeValues(const std::string& fileName, const std::string& dirPath); +int initTstk23Values(const std::string& fileName, const std::string& dirPath); extern std::string EN_DATADIR; diff --git a/gtfold-mfe/include/main.h b/gtfold-mfe/include/main.h index 7faf980..8fe342e 100644 --- a/gtfold-mfe/include/main.h +++ b/gtfold-mfe/include/main.h @@ -27,20 +27,13 @@ using namespace std; -void init_fold(string seq); -void free_fold(int len); +//void init_fold(string seq); +//void free_fold(int len); -bool encodeSequence(string seq); +//bool encodeSequence(string seq); void limit_contact_distance(int lCD, int length); -bool is_valid_base(char c) -{ - return ( (c-'A' == 0) || (c-'a' == 0) || - (c-'C' == 0) || (c-'c' == 0) || - (c-'G' == 0) || (c-'g' == 0) || - (c-'U' == 0) || (c-'u' == 0)); -} - +/* void trim_spaces(std::string& str) { // Trim Both leading and trailing spaces @@ -73,5 +66,5 @@ void tokenize(const std::string& str, std::vector& tokens, const st pos = str.find_first_of(delimiters, lastPos); } } - + */ #endif diff --git a/gtfold-mfe/include/mfe_main.h b/gtfold-mfe/include/mfe_main.h new file mode 100644 index 0000000..683be07 --- /dev/null +++ b/gtfold-mfe/include/mfe_main.h @@ -0,0 +1,8 @@ +#ifndef _MFE_MAIN_H_ +#define _MFE_MAIN_H_ + +int mfe_main(int argc, char** argv); +void init_fold(const char* seq); +void free_fold(int len); + +#endif diff --git a/gtfold-mfe/include/options.h b/gtfold-mfe/include/options.h index 7772be1..a1ecd7a 100644 --- a/gtfold-mfe/include/options.h +++ b/gtfold-mfe/include/options.h @@ -8,26 +8,49 @@ using namespace std; -extern bool ILSA; -extern bool NOISOLATE; -extern bool USERDATA; -extern bool PARAMS; +//extern bool ILSA; +//extern bool NOISOLATE; +//extern bool USERDATA; +//extern bool PARAMS; +/* extern bool LIMIT_DISTANCE; extern bool BPP_ENABLED; extern bool SUBOPT_ENABLED; extern bool CONS_ENABLED; extern bool VERBOSE; +extern bool SHAPE_ENABLED; +extern bool PARAM_DIR; +extern bool T_MISMATCH; +extern bool UNAMODE; +extern bool RNAMODE; +extern bool CALC_PART_FUNC; +extern bool RND_SAMPLE; +extern bool PF_COUNT_MODE; extern string seqfile; extern string constraintsFile; +extern string shapeFile; +extern string outputDir; extern string outputFile; +extern string bppOutFile; +extern string suboptFile; +extern string paramDir; -extern int suboptDelta; +extern float suboptDelta; extern int nThreads; +extern bool b_prefilter; +extern int prefilter1; +extern int prefilter2; +extern int dangles; +extern int num_rnd; + +extern bool LIMIT_DISTANCE; extern int contactDistance; +*/ + +//void help(); +//void parse_options(int argc, char** argv); +//void printRunConfiguration(string seq); -void help(); -void parse_options(int argc, char** argv); -void printRunConfiguration(string seq); #endif diff --git a/gtfold-mfe/include/partition-dangle.h b/gtfold-mfe/include/partition-dangle.h new file mode 100644 index 0000000..2843a60 --- /dev/null +++ b/gtfold-mfe/include/partition-dangle.h @@ -0,0 +1,27 @@ +#ifndef _PARTITION_DANGLE_H +#define _PARTITION_DANGLE_H + +#ifdef __cplusplus +extern "C" { +#endif + +typedef struct partition_d{ + double ** u; + double ** up; + double ** upm; + double ** s1; + double ** s2; + double ** s3; + double ** u1; + int length; +}dangle_struct; + +double cond_dangle(int j, int h, int l); +dangle_struct malloc_partition_arrays_d(int len); +void fill_partition_arrays_d(dangle_struct part_struct); + +#ifdef __cplusplus +} +#endif + +#endif diff --git a/gtfold-mfe/include/partition-func.h b/gtfold-mfe/include/partition-func.h new file mode 100644 index 0000000..e9bdffa --- /dev/null +++ b/gtfold-mfe/include/partition-func.h @@ -0,0 +1,40 @@ +#ifndef _PARTITION_DANGLE_H +#define _PARTITION_DANGLE_H + + +#include + +#ifdef __cplusplus +extern "C" { +#endif + +extern double ** u; +extern double ** up; +extern double ** upm; +extern double ** ud; +extern double ** u1d; + +extern double ** s1; +extern double ** s2; +extern double ** s3; +extern double ** u1; + +extern int part_len; +double ED3_new(int i, int j, int k); +double ED5_new(int i, int j, int k); +double EA_new(); +double EB_new(); +double EC_new(); +double eS_new(int i, int j); +double eL_new(int i, int j, int p, int q); +double eH_new(int i, int j); +double auPenalty_new(int i, int j); +double f(int j, int h, int l); +double calculate_partition(int len, int pf_count_mode); +void free_partition(); + +#ifdef __cplusplus +} +#endif + +#endif diff --git a/gtfold-mfe/include/random-sample.h b/gtfold-mfe/include/random-sample.h new file mode 100644 index 0000000..4a68889 --- /dev/null +++ b/gtfold-mfe/include/random-sample.h @@ -0,0 +1,15 @@ +#ifndef _RANDOM_SAMPLE_H +#define _RANDOM_SAMPLE_H + +#include + +using namespace std; + +typedef struct sub_seq_t{ + int start; + int end; + int paired; +}sub_seq; + +void multi_loop_strand(int i, int j, dangle_struct d_struct, int * structure, list * stack); +#endif diff --git a/gtfold-mfe/include/shapereader.h b/gtfold-mfe/include/shapereader.h new file mode 100644 index 0000000..02c3a2b --- /dev/null +++ b/gtfold-mfe/include/shapereader.h @@ -0,0 +1,23 @@ +#ifndef _SHAPEREADER_H_ +#define _SHAPEREADER_H_ + +extern double* SHAPEarray; +extern int* SHAPEenergies; + +void readSHAPEarray(const char* filename, int seqlength); +void free_shapeArray(int len); +void print_shapeArray(int len); +int calcShapeEnergy(double shapeNumber); +double shapeModel(double SHAPE_value); + +#ifdef __cplusplus +extern "C"{ +#endif + +int getShapeEnergy(int position); + +#ifdef __cplusplus +} +#endif + +#endif diff --git a/gtfold-mfe/include/stochastic-sampling.h b/gtfold-mfe/include/stochastic-sampling.h new file mode 100644 index 0000000..38f037f --- /dev/null +++ b/gtfold-mfe/include/stochastic-sampling.h @@ -0,0 +1,88 @@ +#ifndef __STOCHASTIC_SAMPLING__ +#define __STOCHASTIC_SAMPLING__ + +#include +#include +#include "partition-func.h" +#include "energy.h" + +enum {U=0,UP,UD,U1,U1D}; + +double randdouble(); +double U_0(int i, int j); +double U_ij(int i, int j); +double U_hj(int i, int h, int j); +double U_il(int i, int j); +double U_s1h(int i, int h, int j); +double U_ihlj_case1(int i, int h, int l, int j); +double U_ihlj_case2(int i, int h, int l, int j); +double U_ihlj_case3(int i, int h, int l, int j); +double UD_il_case1(int i, int l, int j); +double UD_il_case2(int i, int l, int j); +double UD_il_case3(int i, int l, int j); +double Q_ijH(int i, int j); +double Q_ijS(int i, int j); +double Q_ijM(int i, int j); +double UPM_ip1l_case1(int i, int l, int j); +double UPM_ip1l_case2(int i, int l, int j); +double UPM_ip2l_case1(int i, int l , int j); +double UPM_ip2l_case2(int i, int l , int j); +double UPM_ijs2h(int i, int h , int j); +double UPM_ijhl_case1(int i, int h, int l, int j); +double UPM_ijhl_case2(int i, int h, int l, int j); +double U1D_ij_il_case1(int i, int l, int j); +double U1D_ij_il_case2(int i, int l, int j); +double U1D_ij_il_case3(int i, int l, int j); +double U1_ij(int i, int j); +double U1_ij_s3h(int i, int h, int j); +double U1_j_hl_case1(int h, int l, int j); +double U1_j_hl_case2(int h, int l, int j); +double U1_j_hl_case3(int h, int l, int j); + +struct base_pair +{ + int i; + int j; + int t; + + base_pair(int i_, int j_, int t_) : i(i_), j(j_), t(t_) {} + base_pair(const base_pair& bp) :i(bp.i), j(bp.j), t(bp.t) { } + base_pair& operator = (const base_pair& bp) + { + if (this != &bp) + { + i = bp.i; + j = bp.j; + t = bp.t; + } + return *this; + } + + int type() const { return t ;} + + bool isPaired() const + { + return t == UP; + } + + friend std::ostream& operator << (std::ostream& out, const base_pair& bp) + { + out << '(' << bp.i << '-' << bp.j << ')' << ' ' << bp.t << std::endl; + return out; + } +}; + +void set_single_stranded(int i, int j, int* structure); +void set_base_pair(int i, int j, int* structure); + +void rnd_upm(int i, int j, int* structure); +void rnd_u1d(int i, int j, int* structure) ; +void rnd_u1(int i, int j, int* structure); +void rnd_up(int i, int j, int* structure); +void rnd_ud(int i, int j, int* structure); +void rnd_u(int i, int j, int* structure); + +double rnd_structure(int* structure, int len); +void batch_sample(int num_rnd, int length, double U); + +#endif diff --git a/gtfold-mfe/include/subopt_main.h b/gtfold-mfe/include/subopt_main.h new file mode 100644 index 0000000..1f26e43 --- /dev/null +++ b/gtfold-mfe/include/subopt_main.h @@ -0,0 +1,6 @@ +#ifndef _SUBOPT_MAIN_H_ +#define _SUBOPT_MAIN_H_ + +int subopt_main(int argc, char** argv); + +#endif diff --git a/gtfold-mfe/include/subopt_traceback.h b/gtfold-mfe/include/subopt_traceback.h index a02839e..2ab2241 100644 --- a/gtfold-mfe/include/subopt_traceback.h +++ b/gtfold-mfe/include/subopt_traceback.h @@ -30,7 +30,9 @@ #include #include -enum label {lW=0, lV, lVBI, lVM, lWM}; +#define UNIQUE_MULTILOOP_DECOMPOSITION + +enum label {lW=0, lV, lVBI, lVM, lWM, lWMPrime, lM, lM1}; extern const char* lstr[]; struct segment @@ -177,7 +179,7 @@ struct pstruct return st_v.empty(); } - void print() + void print() const { SEGSTACK st = st_segment; std::cout <<'[' << ' ' ; @@ -217,10 +219,17 @@ void push_to_gstack(ps_stack_t & gs, const ps_t& v); ss_map_t subopt_traceback(int len, int gap); -void traceV(int i, int j, ps_t & ps, ps_stack_t & gs, int energy); -void traceVBI(int i, int j, ps_t & ps, ps_stack_t & gs, int energy); -void traceW(int i, int j, ps_t & ps, ps_stack_t & gs, int energy); -void traceVM(int i, int j, ps_t & ps, ps_stack_t & gs, int energy); -void traceWM(ps_t& ps, ps_map_t& filter); +void traceV(int i, int j, ps_t & ps, ps_stack_t & gs); +void traceVBI(int i, int j, ps_t & ps, ps_stack_t & gs); +void traceW(int i, int j, ps_t & ps, ps_stack_t & gs); +void traceVM(int i, int j, ps_t & ps, ps_stack_t & gs); +void traceWM(int i, int j, ps_t & ps, ps_stack_t & gs); +void traceWMPrime(int i, int j, ps_t & ps, ps_stack_t & gs); +//void traceWM(ps_t& ps, ps_map_t& filter); + +#ifdef UNIQUE_MULTILOOP_DECOMPOSITION +void traceM(int i, int j, ps_t & ps, ps_stack_t & gs); +void traceM1(int i, int j, ps_t & ps, ps_stack_t & gs); +#endif #endif diff --git a/gtfold-mfe/include/traceback.h b/gtfold-mfe/include/traceback.h index a8bd6c4..ff654f4 100644 --- a/gtfold-mfe/include/traceback.h +++ b/gtfold-mfe/include/traceback.h @@ -26,7 +26,7 @@ #ifdef __cplusplus extern "C" { #endif - void trace(int len, int vbose); + void trace(int len); //, int vv, int mode, int mismatch); #ifdef __cplusplus } #endif @@ -36,5 +36,6 @@ int traceV(int i, int j); int traceVM(int i, int j); int traceVBI(int i, int j); int traceWM(int i, int j); +int traceWMPrime(int i, int j); #endif diff --git a/gtfold-mfe/include/utils.h b/gtfold-mfe/include/utils.h index dbe0fa7..a8e5c28 100644 --- a/gtfold-mfe/include/utils.h +++ b/gtfold-mfe/include/utils.h @@ -3,13 +3,19 @@ #include "constants.h" - #define MIN(X,Y) ((X) < (Y) ? (X) : (Y)) #define MAX(X,Y) ((X) > (Y) ? (X) : (Y)) #define MIN4(W,X,Y,Z) MIN(MIN(W,X),MIN(Y,Z)) +#define MIN3(W,X,Y) MIN(MIN(W,X),Y) char baseToDigit(const char* base) ; unsigned char encode(char base); int isWatsonCrickBase(char base); +double get_seconds(); + +#ifdef __cplusplus +extern "C" +#endif +int is_valid_base(char c); #endif diff --git a/gtfold-mfe/install-sh b/gtfold-mfe/install-sh index a5897de..6781b98 100755 --- a/gtfold-mfe/install-sh +++ b/gtfold-mfe/install-sh @@ -1,7 +1,7 @@ #!/bin/sh # install - install a program, script, or datafile -scriptversion=2006-12-25.00 +scriptversion=2009-04-28.21; # UTC # This originates from X11R5 (mit/util/scripts/install.sh), which was # later released in X11R6 (xc/config/util/install.sh) with the @@ -515,5 +515,6 @@ done # eval: (add-hook 'write-file-hooks 'time-stamp) # time-stamp-start: "scriptversion=" # time-stamp-format: "%:y-%02m-%02d.%02H" -# time-stamp-end: "$" +# time-stamp-time-zone: "UTC" +# time-stamp-end: "; # UTC" # End: diff --git a/gtfold-mfe/missing b/gtfold-mfe/missing old mode 100644 new mode 100755 index 1c8ff70..28055d2 --- a/gtfold-mfe/missing +++ b/gtfold-mfe/missing @@ -1,10 +1,10 @@ #! /bin/sh # Common stub for a few missing GNU programs while installing. -scriptversion=2006-05-10.23 +scriptversion=2009-04-28.21; # UTC -# Copyright (C) 1996, 1997, 1999, 2000, 2002, 2003, 2004, 2005, 2006 -# Free Software Foundation, Inc. +# Copyright (C) 1996, 1997, 1999, 2000, 2002, 2003, 2004, 2005, 2006, +# 2008, 2009 Free Software Foundation, Inc. # Originally by Fran,cois Pinard , 1996. # This program is free software; you can redistribute it and/or modify @@ -18,9 +18,7 @@ scriptversion=2006-05-10.23 # GNU General Public License for more details. # You should have received a copy of the GNU General Public License -# along with this program; if not, write to the Free Software -# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA -# 02110-1301, USA. +# along with this program. If not, see . # As a special exception to the GNU General Public License, if you # distribute this file as part of a program that contains a @@ -89,6 +87,9 @@ Supported PROGRAM values: tar try tar, gnutar, gtar, then tar without non-portable flags yacc create \`y.tab.[ch]', if possible, from existing .[ch] +Version suffixes to PROGRAM as well as the prefixes \`gnu-', \`gnu', and +\`g' are ignored when checking the name. + Send bug reports to ." exit $? ;; @@ -106,15 +107,22 @@ Send bug reports to ." esac +# normalize program name to check for. +program=`echo "$1" | sed ' + s/^gnu-//; t + s/^gnu//; t + s/^g//; t'` + # Now exit if we have it, but it failed. Also exit now if we # don't have it and --version was passed (most likely to detect -# the program). +# the program). This is about non-GNU programs, so use $1 not +# $program. case $1 in - lex|yacc) + lex*|yacc*) # Not GNU programs, they don't have --version. ;; - tar) + tar*) if test -n "$run"; then echo 1>&2 "ERROR: \`tar' requires --run" exit 1 @@ -138,7 +146,7 @@ esac # If it does not exist, or fails to run (possibly an outdated version), # try to emulate it. -case $1 in +case $program in aclocal*) echo 1>&2 "\ WARNING: \`$1' is $msg. You should only need it if @@ -148,7 +156,7 @@ WARNING: \`$1' is $msg. You should only need it if touch aclocal.m4 ;; - autoconf) + autoconf*) echo 1>&2 "\ WARNING: \`$1' is $msg. You should only need it if you modified \`${configure_ac}'. You might want to install the @@ -157,7 +165,7 @@ WARNING: \`$1' is $msg. You should only need it if touch configure ;; - autoheader) + autoheader*) echo 1>&2 "\ WARNING: \`$1' is $msg. You should only need it if you modified \`acconfig.h' or \`${configure_ac}'. You might want @@ -187,7 +195,7 @@ WARNING: \`$1' is $msg. You should only need it if while read f; do touch "$f"; done ;; - autom4te) + autom4te*) echo 1>&2 "\ WARNING: \`$1' is needed, but is $msg. You might have modified some files without having the @@ -210,7 +218,7 @@ WARNING: \`$1' is needed, but is $msg. fi ;; - bison|yacc) + bison*|yacc*) echo 1>&2 "\ WARNING: \`$1' $msg. You should only need it if you modified a \`.y' file. You may need the \`Bison' package @@ -240,7 +248,7 @@ WARNING: \`$1' $msg. You should only need it if fi ;; - lex|flex) + lex*|flex*) echo 1>&2 "\ WARNING: \`$1' is $msg. You should only need it if you modified a \`.l' file. You may need the \`Flex' package @@ -263,7 +271,7 @@ WARNING: \`$1' is $msg. You should only need it if fi ;; - help2man) + help2man*) echo 1>&2 "\ WARNING: \`$1' is $msg. You should only need it if you modified a dependency of a manual page. You may need the @@ -277,11 +285,11 @@ WARNING: \`$1' is $msg. You should only need it if else test -z "$file" || exec >$file echo ".ab help2man is required to generate this page" - exit 1 + exit $? fi ;; - makeinfo) + makeinfo*) echo 1>&2 "\ WARNING: \`$1' is $msg. You should only need it if you modified a \`.texi' or \`.texinfo' file, or any other file @@ -310,7 +318,7 @@ WARNING: \`$1' is $msg. You should only need it if touch $file ;; - tar) + tar*) shift # We have already tried tar in the generic part. @@ -363,5 +371,6 @@ exit 0 # eval: (add-hook 'write-file-hooks 'time-stamp) # time-stamp-start: "scriptversion=" # time-stamp-format: "%:y-%02m-%02d.%02H" -# time-stamp-end: "$" +# time-stamp-time-zone: "UTC" +# time-stamp-end: "; # UTC" # End: diff --git a/gtfold-mfe/scripts/dats2DATs.py b/gtfold-mfe/scripts/dats2DATs.py new file mode 100755 index 0000000..e488b84 --- /dev/null +++ b/gtfold-mfe/scripts/dats2DATs.py @@ -0,0 +1,53 @@ +import os, sys, re + +# read in arguments from command line +if len(sys.argv) != 3: + print "need directory names" + print "Usage: dats2DATs.py " +source_dir_name = sys.argv[1] +target_dir_name = sys.argv[2] + +# this function opens a .dat formatted file and returns a string with .DAT file format +def dat2DAT(file_name, num_cols, num_rows): + num_data_rows_seen = 0 + DAT_content = "" + file = open(file_name,'r') + + for line in file.readlines() : + if re.match('[\d\-\.\s]+\n', line) and not re.match('[\s\-]*\n', line): + # If the line contains only digits, negative signs, dots, and white space + # and does not contain ony dashes and whitespace convert the line to .DAT format + DAT_line = re.sub('\s+\.(\s)',r'\tinf\1', line) + DAT_line = re.sub('\s+\-','\t-', DAT_line) + DAT_line = re.sub('\s+(\d)',r'\t\1', DAT_line) + DAT_line = re.sub('\s+(\.\d)',r'\t\1', DAT_line) + DAT_line = DAT_line.lstrip().rstrip()+"\n" + DAT_content += DAT_line + + return DAT_content + +for file_prefix in ["dangle", "int11", "int21", "int22", "loop", "miscloop", "sint2", "sint4", "stack", "tstackh", "tstacki", "tstackm"]: + file_name = source_dir_name+"/"+file_prefix+".dat" + output_file_path = target_dir_name+"/"+file_prefix+".DAT" + output_file = open(output_file_path, 'w') + output_file.write(dat2DAT(file_name, 16, 16)) + #print dat2DAT(file_name, 16, 16) + +file_name = source_dir_name+"/tloop.dat" +output_file_path = target_dir_name+"/tloop.DAT" +DAT_content = "" +file = open(file_name,'r') + +for line in file.readlines() : + if re.match('[\d\-\.\sACGU]+\n', line) and not re.match('[\s\-]*\n', line): + # If the line contains only digits, negative signs, dots, and white space or ACGU + # and does not contain ony dashes and whitespace convert the line to .DAT format + DAT_line = re.sub('\s+\.(\s)',r'\tinf\1', line) + DAT_line = re.sub('\s+\-','\t-', DAT_line) + DAT_line = re.sub('\s+(\d)',r'\t\1', DAT_line) + DAT_line = re.sub('\s+(\.\d)',r'\t\1', DAT_line) + DAT_line = DAT_line.lstrip().rstrip()+"\n" + DAT_content += DAT_line +output_file = open(output_file_path, 'w') +output_file.write(DAT_content) + diff --git a/gtfold-mfe/src/Makefile.am b/gtfold-mfe/src/Makefile.am index 728863b..8a1ba22 100644 --- a/gtfold-mfe/src/Makefile.am +++ b/gtfold-mfe/src/Makefile.am @@ -7,16 +7,23 @@ bin_PROGRAMS = gtfold gtfold_SOURCES = \ main.cc\ - loader.cc\ + mfe_main.cc\ + loader.cc\ utils.cc\ options.cc\ constraints.cc\ - global.c\ + global.cc\ energy.c\ - algorithms.c \ - traceback.c \ - subopt_traceback.cc - + algorithms.c\ + traceback.c\ + subopt_main.cc\ + subopt_traceback.cc\ + stochastic-sampling.cc\ + algorithms-partition.c\ + boltzmann_main.cc\ + partition-dangle.c\ + partition-func.c\ + shapereader.cc gtfold_LDFLAGS = diff --git a/gtfold-mfe/src/Makefile.in b/gtfold-mfe/src/Makefile.in index a94f890..86a7787 100644 --- a/gtfold-mfe/src/Makefile.in +++ b/gtfold-mfe/src/Makefile.in @@ -1,4 +1,4 @@ -# Makefile.in generated by automake 1.11.1 from Makefile.am. +# Makefile.in generated by automake 1.11 from Makefile.am. # @configure_input@ # Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, @@ -31,7 +31,7 @@ PRE_INSTALL = : POST_INSTALL = : NORMAL_UNINSTALL = : PRE_UNINSTALL = : -POST_UNINSTALL = : +POST_UNINSTALL = : build_triplet = @build@ host_triplet = @host@ target_triplet = @target@ @@ -48,10 +48,13 @@ CONFIG_CLEAN_FILES = CONFIG_CLEAN_VPATH_FILES = am__installdirs = "$(DESTDIR)$(bindir)" PROGRAMS = $(bin_PROGRAMS) -am_gtfold_OBJECTS = main.$(OBJEXT) loader.$(OBJEXT) utils.$(OBJEXT) \ - options.$(OBJEXT) global.$(OBJEXT) energy.$(OBJEXT) \ - algorithms.$(OBJEXT) traceback.$(OBJEXT) constraints.$(OBJEXT) \ - subopt_traceback.$(OBJEXT) +am_gtfold_OBJECTS = main.$(OBJEXT) mfe_main.$(OBJEXT) loader.$(OBJEXT) \ + utils.$(OBJEXT) options.$(OBJEXT) constraints.$(OBJEXT) \ + global.$(OBJEXT) energy.$(OBJEXT) algorithms.$(OBJEXT) \ + traceback.$(OBJEXT) subopt_main.$(OBJEXT) \ + subopt_traceback.$(OBJEXT) stochastic-sampling.$(OBJEXT) \ + algorithms-partition.$(OBJEXT) boltzmann_main.$(OBJEXT) partition-dangle.$(OBJEXT) \ + partition-func.$(OBJEXT) shapereader.$(OBJEXT) gtfold_OBJECTS = $(am_gtfold_OBJECTS) gtfold_DEPENDENCIES = gtfold_LINK = $(CXXLD) $(AM_CXXFLAGS) $(CXXFLAGS) $(gtfold_LDFLAGS) \ @@ -115,7 +118,6 @@ PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@ PACKAGE_NAME = @PACKAGE_NAME@ PACKAGE_STRING = @PACKAGE_STRING@ PACKAGE_TARNAME = @PACKAGE_TARNAME@ -PACKAGE_URL = @PACKAGE_URL@ PACKAGE_VERSION = @PACKAGE_VERSION@ PATH_SEPARATOR = @PATH_SEPARATOR@ SET_MAKE = @SET_MAKE@ @@ -182,15 +184,23 @@ AM_CFLAGS = $(OPENMP_CFLAGS) -DDATADIR='$(datadir)/@PACKAGE@' AM_CXXFLAGS = -DDATADIR='$(datadir)/@PACKAGE@' gtfold_SOURCES = \ main.cc\ - loader.cc\ + mfe_main.cc\ + loader.cc\ utils.cc\ options.cc\ constraints.cc\ - global.c\ + global.cc\ energy.c\ - algorithms.c \ - traceback.c \ - subopt_traceback.cc + algorithms.c\ + traceback.c\ + subopt_main.cc\ + subopt_traceback.cc\ + stochastic-sampling.cc\ + algorithms-partition.c\ + boltzmann_main.cc\ + partition-dangle.c\ + partition-func.c\ + shapereader.cc gtfold_LDFLAGS = gtfold_LDADD = -lm @@ -249,8 +259,11 @@ install-binPROGRAMS: $(bin_PROGRAMS) while read type dir files; do \ if test "$$dir" = .; then dir=; else dir=/$$dir; fi; \ test -z "$$files" || { \ - echo " $(INSTALL_PROGRAM_ENV) $(INSTALL_PROGRAM) $$files '$(DESTDIR)$(bindir)$$dir'"; \ + echo "$(INSTALL_PROGRAM_ENV) $(INSTALL_PROGRAM) $$files '$(DESTDIR)$(bindir)$$dir'"; \ $(INSTALL_PROGRAM_ENV) $(INSTALL_PROGRAM) $$files "$(DESTDIR)$(bindir)$$dir" || exit $$?; \ + ln -sf $$files $(DESTDIR)$(bindir)$$dir/gtmfe || exit $$?;\ + ln -sf $$files $(DESTDIR)$(bindir)$$dir/gtsubopt || exit $$?;\ + ln -sf $$files $(DESTDIR)$(bindir)$$dir/gtboltzmann || exit $$?;\ } \ ; done @@ -276,13 +289,21 @@ mostlyclean-compile: distclean-compile: -rm -f *.tab.c +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/algorithms-partition.Po@am__quote@ +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/boltzmann_main.Po@am__quote@ @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/algorithms.Po@am__quote@ @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/constraints.Po@am__quote@ @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/energy.Po@am__quote@ @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/global.Po@am__quote@ @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/loader.Po@am__quote@ @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/main.Po@am__quote@ +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/mfe_main.Po@am__quote@ @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/options.Po@am__quote@ +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/partition-dangle.Po@am__quote@ +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/partition-func.Po@am__quote@ +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/shapereader.Po@am__quote@ +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/stochastic-sampling.Po@am__quote@ +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/subopt_main.Po@am__quote@ @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/subopt_traceback.Po@am__quote@ @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/traceback.Po@am__quote@ @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/utils.Po@am__quote@ diff --git a/gtfold-mfe/src/algorithms-partition.c b/gtfold-mfe/src/algorithms-partition.c index f87e190..fa3b9b8 100644 --- a/gtfold-mfe/src/algorithms-partition.c +++ b/gtfold-mfe/src/algorithms-partition.c @@ -10,13 +10,19 @@ #include "algorithms-partition.h" #include "data.h" +#ifdef _OPENMP +#include "omp.h" +#endif + + +#define MAX_LOOP 30 + // double[][] QB; // double[][] Q; // double[][] QM; // Boltzmann constant (R) * Standard 37C temperature (T in Kelvin) -double RT = 0.00198721 * 310.15; // Based on pseudocode in figure 6 in // @@ -31,7 +37,9 @@ double RT = 0.00198721 * 310.15; * @param QM Matrix * */ -void fill_partition_fn_arrays(int len, double** QB, double** Q, double** QM) { + + +void fill_partition_fn_arrays(int len, double** Q, double** QB, double** QM) { // multiConst[3] is a global variable with 3 values: a, b, c for the // experimental constants @@ -57,28 +65,45 @@ void fill_partition_fn_arrays(int len, double** QB, double** Q, double** QM) { // fill in values in the array for(l=1; l<=len; ++l) { - for(i=1; i<= len-l+1; ++i) { + //Parrallelize + //#ifdef _OPENMP + //#pragma omp parallel for private (i,j) schedule(guided) + //#endif + for(i=1; i<= len - l + 1; i++) { - int j = i+l-1; + int j = i + l - 1; // QB recursion // Only calculate if i and j actually pair - if(checkPair(i,j)) { + if(canPair(RNA[i],RNA[j])) { // NOTE: eH returns an integer encoded as fixed point. So a // return value of 115 represents raw value 115/100 = 1.15 - QB[i][j] = exp(-eH(i,j)/100.0/RT); - + QB[i][j] = exp(-eH(i,j)/RT); + for(d=i+1; d<=j-4; ++d) { + //if(d - i - 1 > MAX_LOOP) + // break; for(e=d+4; e<=j-1; ++e) { - - if(d == i + 1 && e == j -1) - QB[i][j] += exp(-eS(i,j)/100.0/RT)*QB[d][e]; - else - QB[i][j] += exp(-eL(i,j,d,e)/100.0/RT)*QB[d][e]; - - QB[i][j] += QM[i+1][d-1]*QB[d][e] * - exp(-(a + b + c*(j-e-1))/100.0/RT); + + // if(d - i - 1 + j - e - 1 > MAX_LOOP) + // break; + + if(QB[d][e] != 0){ + //more general than chkpair + //if we cant pair, move on + + if(d == i + 1 && e == j -1){ + QB[i][j] += exp(-eS(i,j)/RT)*QB[d][e]; + } + else{ + //printf("i: %d j: %d d: %d e: %d\n", i,j,d,e); + QB[i][j] += exp(-eL(i,j,d,e)/RT)*QB[d][e]; + } + + QB[i][j] += QM[i+1][d-1]*QB[d][e] * + exp(-(a + b + c*(j-e-1))/RT); + } } } } @@ -88,12 +113,13 @@ void fill_partition_fn_arrays(int len, double** QB, double** Q, double** QM) { for(d=i; d<=j-4; ++d) { for(e=d+4; e<=j; ++e) { Q[i][j] += Q[i][d-1]*QB[d][e]; - QM[i][j] += exp(-(b+c*(d-i)+c*(j-e))/100.0) * QB[d][e]; - QM[i][j] += QM[i][d-1] * QB[d][e] * exp(-(b+c*(j-e))/100.0/RT); + QM[i][j] += exp(-(b+c*(d-i)+c*(j-e))/RT) * QB[d][e]; + QM[i][j] += QM[i][d-1] * QB[d][e] * exp(-(b+c*(j-e))/RT); } } } } + printf("Total partition number: %f\n", Q[1][len]); } /** @@ -103,7 +129,7 @@ void fill_partition_fn_arrays(int len, double** QB, double** Q, double** QM) { * index j. structure[i] = 0 means the nucleotide is * unpaired. */ -void fillBasePairProbabilities(int length, int *structure, double **Q, double **QB, double **QM, double**P) { +void fillBasePairProbabilities(int length, double **Q, double **QB, double **QM, double**P) { int d, l, h, i, j; double tempBuffer; @@ -137,22 +163,22 @@ void fillBasePairProbabilities(int length, int *structure, double **Q, double ** tempBuffer = P[i][j]*QB[h][l]/QB[i][j]; if(i == h-1 && j == l+1) //of which stacked pairs are a special case - tempBuffer *= exp(-eS(i,j)/100.0/RT); + tempBuffer *= exp(-eS(i,j)/RT); else - tempBuffer *= exp(-eL(i,j,h,l)/100.0/RT); + tempBuffer *= exp(-eL(i,j,h,l)/RT); P[h][l] += tempBuffer; // third term tempBuffer = 0; // Start over for multiloops if(j - l > 3) - tempBuffer += exp(-((h-i-1)*c/100.0/RT)) * QM[l+1][j-1]; + tempBuffer += exp(-((h-i-1)*c/RT)) * QM[l+1][j-1]; if(h - i > 3) - tempBuffer += exp(-((j-l-1)*c/100.0/RT)) * QM[i+1][h-1]; + tempBuffer += exp(-((j-l-1)*c/RT)) * QM[i+1][h-1]; if(j - l > 3 && h - i > 3) tempBuffer += QM[i+1][h-1] * QM[l+1][j-1]; - tempBuffer *= P[i][j] * QB[h][l] / QB[i][j] * exp(-(a+b)/100.0/RT); + tempBuffer *= P[i][j] * QB[h][l] / QB[i][j] * exp(-(a+b)/RT); P[h][l] += tempBuffer; } @@ -173,16 +199,21 @@ void fillBasePairProbabilities(int length, int *structure, double **Q, double ** * unpaired. * @param P Partition function array */ -void printBasePairProbabilities(int n, int *structure, double **P) { +void printBasePairProbabilities(int n, int *structure, double **P, const char* outfile) { + FILE* outp = fopen(outfile,"w"); + if (outp == NULL) { + fprintf(stderr, "printBasePairProbabilities() : Cannot open %s",outfile); + } int i; for(i=1; i<=n; ++i) { int j = structure[i]; if(j) - printf("%d-%d pair\tPr: %f\n", i, j, P[MIN(i,j)][MAX(i,j)]); + fprintf(outp, "%d-%d pair\tPr: %f\n", i, j, P[MIN(i,j)][MAX(i,j)]); else - printf("%d unpaired\tPr: %f\n", i, probabilityUnpaired(n, i, P)); + fprintf(outp, "%d unpaired\tPr: %f\n", i, probabilityUnpaired(n, i, P)); } + fclose(outp); } /** @@ -217,7 +248,6 @@ double **mallocTwoD(int r, int c) { return NULL; } } - return arr; } diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c index a10f0f7..07f987f 100644 --- a/gtfold-mfe/src/algorithms.c +++ b/gtfold-mfe/src/algorithms.c @@ -1,155 +1,320 @@ /* - GTfold: compute minimum free energy of RNA secondary structure - Copyright (C) 2008 David A. Bader - http://www.cc.gatech.edu/~bader - - This program is free software: you can redistribute it and/or modify - it under the terms of the GNU General Public License as published by - the Free Software Foundation, either version 3 of the License, or - (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - GNU General Public License for more details. - - You should have received a copy of the GNU General Public License - along with this program. If not, see . -*/ - +GTfold: compute minimum free energy of RNA secondary structure +Copyright (C) 2008 David A. Bader +http://www.cc.gatech.edu/~bader +This program is free software: you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation, either version 3 of the License, or +(at your option) any later version. +This program is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +GNU General Public License for more details. +You should have received a copy of the GNU General Public License +along with this program. If not, see . + */ #include #include #include #include #include #include - #include "constants.h" #include "utils.h" #include "energy.h" #include "global.h" #include "algorithms.h" #include "constraints.h" - -#ifdef _OPENMP +#include "shapereader.h" +#ifdef _OPENMP #include "omp.h" #endif -int calculate(int len, int nThreads) { - int b, i, j; +//#define DEBUG 1 + +void initializeMatrix(int len) { + int i, j; + + for (i = 1; i <= len; ++i) + for (j = len; j >= i; --j) + if (canPair(RNA[i],RNA[j]) && j-i > TURN) + PP[i][j] = 1; +} + +void prefilter(int len, int prefilter1, int prefilter2) { + char** in; + int i, j, k, count; + + in = (char**)malloc(len*sizeof(char*)); + for (i = 1; i <= len; ++i) in[i - 1] = (char*)malloc(len*sizeof(char)); + + for (i = 1; i <= len - prefilter2 + 1; ++i) + for (j = len; j >= prefilter2 && j >= i; --j) { + count = 0; + for (k = 0; k < prefilter2 && k <= (j - i) / 2; ++k) + if (PP[i + k][j - k] == 1) ++count; + if (count >= prefilter1) + for (k = 0; k < prefilter2 && k <= (j - i) / 2; ++k) + ++in[i + k - 1][j - k - 1]; + } + + for (i = 1; i <= len; ++i) { + for (j = len; j >= i; --j) + if (!in[i - 1][j - 1]) PP[i][j] = 0; + free(in[i - 1]); + } + + free(in); +} + +int calcVBI(int i, int j) { + int p=0, q=0; + int VBIij = INFINITY_; + + for (p = i+1; p <= MIN(j-2-TURN,i+MAXLOOP+1) ; p++) { + int minq = j-i+p-MAXLOOP-2; + if (minq < p+1+TURN) minq = p+1+TURN; + int maxq = (p==(i+1))?(j-2):(j-1); + + for (q = minq; q <= maxq; q++) { + if (PP[p][q]==0) continue; + if (!canILoop(i,j,p,q)) continue; + VBIij = MIN(eL(i, j, p, q) + V(p,q), VBIij); + } + } + + return VBIij; +} + +int calcVBI1(int i, int j) { + int p=0, q=0; + int VBIij = INFINITY_; + + for (p = i+1; p <= MIN(j-2-TURN,i+MAXLOOP+1) ; p++) { + int minq = j-i+p-MAXLOOP-2; + if (minq < p+1+TURN) minq = p+1+TURN; + int maxq = (p==(i+1))?(j-2):(j-1); + + for (q = minq; q <= maxq; q++) { + if (PP[p][q]==0) continue; + if (!canILoop(i,j,p,q)) continue; + VBIij = MIN(eL1(i, j, p, q) + V(p,q), VBIij); + } + } + + return VBIij; +} + +int calcVBI2(int i, int j, int len) { + int d, ii, jj; + int energy = INFINITY_; + for (d = j-i-3; d >= TURN+1 && d >= j-i-2-MAXLOOP; --d) + for (ii = i + 1; ii < j - d && ii <= len; ++ii) + { + jj = d + ii; + if (PP[ii][jj]==1) + energy = MIN(energy, eL1(i, j, ii, jj) + V(ii, jj)); + } + + return energy; +} + +int calculate(int len) { + int b, i, j; #ifdef _OPENMP - if (nThreads>0) omp_set_num_threads(nThreads); + if (g_nthreads > 0) omp_set_num_threads(g_nthreads); #endif #ifdef _OPENMP #pragma omp parallel #pragma omp master - fprintf(stdout,"Thread count: %3d \n",omp_get_num_threads()); + if (g_verbose) fprintf(stdout,"Thread count: %3d \n",omp_get_num_threads()); #endif - for (b = TURN+1; b <= len-1; b++) { + initializeMatrix(len); + if (g_unamode || g_prefilter_mode) { + prefilter(len,g_prefilter1,g_prefilter2); + } + + for (b = TURN+1; b <= len-1; b++) { #ifdef _OPENMP #pragma omp parallel for private (i,j) schedule(guided) #endif - for (i = 1; i <= len - b; i++) { - j = i + b; - int flag = 0, newWM = INFINITY_; - - if (canPair(RNA[i], RNA[j])) { - flag = 1; - int eh = check_hairpin(i,j)?INFINITY_:eH(i, j); //hair pin - int es = check_stack(i,j)?INFINITY_:(eS(i, j) + V(i+1,j-1)); // stack - if (j-i > 6) { // Internal Loop BEGIN - int p=0, q=0; - int VBIij = INFINITY_; - - for (p = i+1; p <= MIN(j-2-TURN,i+MAXLOOP+1) ; p++) { - int minq = j-i+p-MAXLOOP-2; - if (minq < p+1+TURN) minq = p+1+TURN; - for (q = minq; q < j; q++) { - if (!canPair(RNA[p], RNA[q])) continue; - if (check_iloop(i,j,p,q)) continue; - VBIij = MIN(eL(i, j, p, q) + V(p,q), VBIij); - } - } - VBI(i,j) = check_pair(i,j)?INFINITY_:VBIij; - } // Internal Loop END - - if (j-i > 10) { // Multi Loop BEGIN - int h; - int VMij, VMijd, VMidj, VMidjd; - VMij = VMijd = VMidj = VMidjd = INFINITY_; - - for (h = i+TURN+1; h <= j-1-TURN; h++) { - VMij = MIN(VMij, WMU(i+1,h-1) + WML(h,j-1)); - VMidj = MIN(VMidj, WMU(i+2,h-1) + WML(h,j-1)); - VMijd = MIN(VMijd, WMU(i+1,h-1) + WML(h,j-2)); - VMidjd = MIN(VMidjd, WMU(i+2,h-1) + WML(h,j-2)); - newWM = MIN(newWM, VMij); - } - - int d3 = Ed3(i,j,j-1); - int d5 = Ed5(i,j,i+1); - - VMij = MIN(VMij, check_base(i+1)?(VMidj + d5 +Ec):INFINITY_) ; - VMij = MIN(VMij, check_base(j-1)?(VMijd + d3 +Ec):INFINITY_); - VMij = MIN(VMij, (check_base(i+1)&&check_base(j-1))?(VMidjd + d5 + d3+ 2*Ec):INFINITY_); - VMij = VMij + Ea + Eb + auPenalty(i,j); - VM(i,j) = check_pair(i,j)?INFINITY_:VMij; - } // Multi Loop END - - V(i,j) = check_pair(i,j)?INFINITY_:MIN4(eh,es,VBI(i,j),VM(i,j)); - } - else - V(i,j) = INFINITY_; - - if (j-i > 4) { // WM BEGIN - int h; - if (!flag) { - for (h = i+TURN+1 ; h <= j-TURN-1; h++) { - newWM = MIN(newWM, WMU(i,h-1) + WML(h,j)); - } - } - - newWM = MIN(V(i,j) + auPenalty(i,j) + Eb, newWM); - newWM = check_base(i)?MIN(V(i+1,j) + Ed3(j,i+1,i) + auPenalty(i+1,j) + Eb + Ec, newWM): INFINITY_; - newWM = check_base(j)?MIN(V(i,j-1) + Ed5(j-1,i,j) + auPenalty(i,j-1) + Eb + Ec, newWM) : INFINITY_; - newWM = (check_base(i)&&check_base(j))?MIN(V(i+1,j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j) + auPenalty(i+1,j-1) + Eb + 2*Ec, newWM): INFINITY_; - - newWM = check_base(i)?MIN(WMU(i+1,j) + Ec, newWM):INFINITY_; - newWM = check_base(j)?MIN(WML(i,j-1) + Ec, newWM):INFINITY_; - - WMU(i,j) = WML(i,j) = newWM; - } // WM END - } - } - - for (j = TURN+2; j <= len; j++) { - int i, branch=0, Wj, Widjd, Wijd, Widj, Wij, Wim1; - Wj = INFINITY_; - for (i = 1; i < j-TURN; i++) { - Wij = Widjd = Wijd = Widj = INFINITY_; - Wim1 = MIN(0, W[i-1]); - Wij = V(i, j) + auPenalty(i, j) + Wim1; - Widjd = (check_base(i)&&check_base(j))?(V(i+1,j-1) + auPenalty(i+1,j-1) + Ed3(j-1,i + 1,i) + Ed5(j-1,i+1,j) + Wim1):INFINITY_; - Wijd = check_base(j)?(V(i,j-1) + auPenalty(i,j-1) + Ed5(j-1,i,j) + Wim1):INFINITY_; - Widj = (check_base(i))?(V(i+1, j) + auPenalty(i+1,j) + Ed3(j,i + 1,i) + Wim1):INFINITY_; - Wj = MIN(MIN4(Wij, Widjd, Wijd, Widj), Wj); - - if (Wj1) energy += Ed3(j,i,i-1); + if (j ii; --jj) { + fprintf(file, "%d %d %d\n",ii,jj,VBI(ii,jj)); + } + } + fclose(file); + + file = fopen("Eh.txt", "w"); + for (ii = 1; ii <= len; ++ii) { + for (jj = len; jj > ii; --jj) { + int eh = INFINITY_; + if (PP[ii][jj]) eh = eH(ii,jj); + fprintf(file, "%d %d %d\n",ii,jj,eh>=INFINITY_?INFINITY_:eh); + } + } + fclose(file); + + file = fopen("Es.txt", "w"); + for (ii = 1; ii <= len; ++ii) { + for (jj = len; jj > ii; --jj) { + int es = INFINITY_; + if (PP[ii][jj] && PP[ii+1][jj-1]) es = eS(ii,jj); + fprintf(file, "%d %d %d\n",ii,jj,es>=INFINITY_?INFINITY_:es); + } + } + fclose(file); + + file = fopen("BP.txt", "w"); + for (ii = 1; ii <= len; ++ii) { + for (jj = len; jj > ii; --jj) { + fprintf(file, "%d %d %d\n",ii,jj,PP[ii][jj]); + } + } + fclose(file); + + file = fopen("VM.txt", "w"); + for (ii = 1; ii <= len; ++ii) { + for (jj = len; jj > ii; --jj) { + fprintf(file, "%d %d %d\n",ii,jj,VM(ii,jj)); + } + } + fclose(file); + + file = fopen("WM.txt", "w"); + for (ii = 1; ii <= len; ++ii) { + for (jj = len; jj > ii; --jj) { + fprintf(file, "%d %d %d\n",ii,jj,WM(ii,jj)); + } + } + fclose(file); +#endif + + return W[len]; } diff --git a/gtfold-mfe/src/boltzmann_main.cc b/gtfold-mfe/src/boltzmann_main.cc new file mode 100644 index 0000000..b423c0e --- /dev/null +++ b/gtfold-mfe/src/boltzmann_main.cc @@ -0,0 +1,225 @@ +#include +#include +#include +#include +#include + +#include "global.h" +#include "loader.h" +#include "algorithms-partition.h" +#include "boltzmann_main.h" +#include "partition-func.h" +#include "mfe_main.h" +#include "stochastic-sampling.h" +#include "algorithms.h" +#include "traceback.h" + +using namespace std; + +static bool CALC_PART_FUNC = false; +static bool PF_COUNT_MODE = false; +static bool BPP_ENABLED = false; +static bool PARAM_DIR = false; +static bool RND_SAMPLE = false; +static bool CALC_PF_DO = false; +static bool CALC_PF_DS = false; + +static string seqfile = ""; +static string outputPrefix = ""; +static string outputDir = ""; +static string outputFile = ""; +static string paramDir; // default value +static string bppOutFile = ""; +static int num_rnd = 0; + +static void help() { + printf("Usage: gtboltzmann [OPTION]... FILE\n\n"); + + printf(" FILE is an RNA sequence file containing only the sequence or in FASTA format.\n\n"); + + printf("OPTIONS\n"); + + printf(" --partition Calculate the partition function (default is using sfold reccurences).\n"); + printf(" --partition -dS Calculate the partition function using sfold reccurences.\n"); + printf(" --partition -d0 Calculate the partition function using -d0 reccurences.\n"); + printf(" --partition -d2 Calculate the partition function using -d2 reccurences (Under implementation).\n"); + + printf(" --sample INT Sample number of structures equal to INT\n"); + printf(" --pfcount Calculate the structure count using partition function and zero energy value.\n"); + printf(" --bpp Calculate base pair probabilities.\n"); + printf("\n"); + printf(" -o, --output NAME Write output files with prefix given in NAME\n"); + printf(" -p --paramdir DIR Path to directory from which parameters are to be read\n"); + printf(" -h, --help Output help (this message) and exit.\n"); + printf(" -w, --workdir DIR Path of directory where output files will be written.\n"); + exit(-1); +} + +static void parse_options(int argc, char** argv) { + int i; + + for(i=1; i 0) { + outputPrefix = outputPrefix.substr(pos+1); + } + + // and if an extension exists, remove it ... + if(outputPrefix.find(".") != string::npos) + outputPrefix.erase(outputPrefix.rfind(".")); + } + + // If output dir specified + if (!outputDir.empty()) { + outputFile += outputDir; + outputFile += "/"; + bppOutFile += outputDir; + bppOutFile += "/"; + } + // ... and append the .ct + outputFile += outputPrefix; + outputFile += ".ct"; + + bppOutFile += outputPrefix; + bppOutFile += "_bpp.txt"; +} + + +int boltzmann_main(int argc, char** argv) { + std::string seq; + + parse_options(argc, argv); + + if (read_sequence_file(seqfile.c_str(), seq) == FAILURE) { + printf("Failed to open sequence file: %s.\n\n", seqfile.c_str()); + exit(-1); + } + + init_fold(seq.c_str()); + + readThermodynamicParameters(paramDir.c_str(), PARAM_DIR, 0, 0, 0); + + if (CALC_PART_FUNC == true && CALC_PF_DS == true) { + printf("\nComputing partition function in -dS mode ...\n"); + calculate_partition(seq.length(),0); + free_partition(); + } + else if (CALC_PART_FUNC == true && CALC_PF_DO == true) { + printf("\nCalculating partition function in -d0 mode ...\n"); + double ** Q, **QM, **QB, **P; + Q = mallocTwoD(seq.length() + 1, seq.length() + 1); + QM = mallocTwoD(seq.length() + 1, seq.length() + 1); + QB = mallocTwoD(seq.length() + 1, seq.length() + 1); + P = mallocTwoD(seq.length() + 1, seq.length() + 1); + + + fill_partition_fn_arrays(seq.length(), Q, QB, QM); + freeTwoD(Q, seq.length() + 1, seq.length() + 1); + freeTwoD(QM, seq.length() + 1, seq.length() + 1); + freeTwoD(QB, seq.length() + 1, seq.length() + 1); + freeTwoD(P, seq.length() + 1, seq.length() + 1); + } + else if (CALC_PART_FUNC == true) { + printf("\nComputing partition function...\n"); + int pf_count_mode = 0; + if(PF_COUNT_MODE) pf_count_mode=1; + + calculate_partition(seq.length(),pf_count_mode); + free_partition(); + } else if (RND_SAMPLE == true) { + printf("\nComputing partition function...\n"); + int pf_count_mode = 0; + if(PF_COUNT_MODE) pf_count_mode=1; + double U = calculate_partition(seq.length(),pf_count_mode); + + batch_sample(num_rnd, seq.length(), U); + + free_partition(); + } else if(BPP_ENABLED) { + printf("\n"); + printf("Calculating partition function\n"); + double ** Q, **QM, **QB, **P; + Q = mallocTwoD(seq.length() + 1, seq.length() + 1); + QM = mallocTwoD(seq.length() + 1, seq.length() + 1); + QB = mallocTwoD(seq.length() + 1, seq.length() + 1); + P = mallocTwoD(seq.length() + 1, seq.length() + 1); + + + fill_partition_fn_arrays(seq.length(), Q, QB, QM); + fillBasePairProbabilities(seq.length(), Q, QB, QM, P); + printBasePairProbabilities(seq.length(), structure, P, bppOutFile.c_str()); + printf("Saved BPP output in %s\n",bppOutFile.c_str()); + + freeTwoD(Q, seq.length() + 1, seq.length() + 1); + freeTwoD(QM, seq.length() + 1, seq.length() + 1); + freeTwoD(QB, seq.length() + 1, seq.length() + 1); + freeTwoD(P, seq.length() + 1, seq.length() + 1); + } else { + printf("No valid option specified !\n\n"); + help(); + } + + free_fold(seq.length()); + return EXIT_SUCCESS; +} diff --git a/gtfold-mfe/src/constraints.cc b/gtfold-mfe/src/constraints.cc index 97cbc5e..b1f2a1b 100644 --- a/gtfold-mfe/src/constraints.cc +++ b/gtfold-mfe/src/constraints.cc @@ -5,29 +5,56 @@ #include #include #include +#include +#include #include "global.h" #include "options.h" #include "constraints.h" int* BP; +int* ind; + +typedef pair basepair_t; + +/* +ZS: Explanation to BP array. + +BP(i,j) for i!=j can have one of the following values: +0: Nothing is required about a pair i,j in constraints +1: Force pairing between i and j. This implies also that + any non-nested pairings will be prohibited and any + other pairs i and j would be involved in are also prohibited. +2: Prohibit pairing between i and j. (Nothing else is done) + +BP(i,i) can have one of the following values: +0: Nothing is known about position i at all +3: Position i is forced to be single-stranded. This implies also that + any pairs with i will be prohibited. +4: Position i is NOT single-stranded, it is forced to be in a pair. +5: Position i is prohibited from pairing with at least one nucleotide. +*/ + int** PBP; int** FBP; int nPBP; int nFBP; -bool compare_bp(const std::pair& o1, - const std::pair& o2) { - return o1.first < o2.first; -} +static bool CONS_ENABLED = false; +static bool LIMIT_DISTANCE = false; +static int contactDistance = -1; +void enable_constraints(int b) {CONS_ENABLED = b;} +void enable_limit_distance(int b) {LIMIT_DISTANCE = b;} +void set_contact_distance(int dist) {contactDistance = dist;} -static int load_constraints(const char* constr_file, int verbose=0) { - std::ifstream cfcons; - fprintf(stdout, "- Running with constraints\n"); +static int load_constraints(const char* constr_file, int seq_length, int verbose=0) { + + fprintf(stdout, "- Running with constraints\n"); - cfcons.open(constr_file, std::ios::in); + std::ifstream cfcons; + cfcons.open(constr_file, std::ios::in); if (cfcons == 0) { fprintf(stderr, "Error opening constraint file\n\n"); cfcons.close(); @@ -84,71 +111,211 @@ static int load_constraints(const char* constr_file, int verbose=0) { } } - std::vector > v_fbp; + map all_bases; for(it=0; it< nFBP; it++) { - for(int k=1;k<= FBP[it][2];k++) - v_fbp.push_back(std::pair(FBP[it][0]+k-1, FBP[it][1]-k+1)); - } - std::sort(v_fbp.begin(), v_fbp.end(), compare_bp); - for (size_t ii = 0; ii < v_fbp.size() -1 ; ++ii) { - if (v_fbp[ii].second <= v_fbp[ii+1].second) { - fprintf(stderr, "\nConstraints create pseudoknots, exiting !!!\n"); - exit(-1); + for(int k=1;k<= FBP[it][2];k++) { + basepair_t base_pair(FBP[it][0]+k-1, FBP[it][1]-k+1); + pair::iterator, bool> retVal; + retVal = all_bases.insert(pair(base_pair.first, base_pair)); + if (base_pair.first < 1 || base_pair.first > seq_length) { + fprintf(stderr, "\nBase %d from constraint (%d,%d) is out of bounds of the sequence which has length %d \n", + base_pair.first, base_pair.first, base_pair.second, seq_length); + exit(1); + } + if (base_pair.second < 1 || base_pair.second > seq_length) { + fprintf(stderr, "\nBase %d from constraint (%d,%d) is out of bounds of the sequence which has length %d \n", + base_pair.second, base_pair.first, base_pair.second, seq_length); + exit(1); + } + if (base_pair.first >= base_pair.second - TURN) { + fprintf(stderr, "\nDistance between bases of base pair (%d,%d) is too small\n", + base_pair.first, base_pair.second); + exit(1); + } + if (retVal.second == false) { + fprintf(stderr, "\nDuplicate base %d encountered in Constraints. Base Pair %d,%d\n", + base_pair.first, base_pair.first, base_pair.second); + exit(1); + } + retVal = all_bases.insert(pair(base_pair.second, base_pair) ); + if (retVal.second == false) { + fprintf(stderr, "\nDuplicate base %d encountered in Constraints. Base Pair %d,%d\n", + base_pair.first, base_pair.first, base_pair.second); + exit(1); + } } - } + vector verify_stack; + for (map::iterator it = all_bases.begin(); it != all_bases.end(); ++it) { + + pair map_element = (*it); + int base = map_element.first; + basepair_t base_pair = map_element.second; + if (base_pair.first == base) { + verify_stack.push_back(base_pair); + } else { + basepair_t last_base_pair = verify_stack.back(); + if (last_base_pair.second == base) { + verify_stack.pop_back(); + } + else { + fprintf(stderr, "\nConstraints create pseudoknots, exiting !!!\n"); + exit(1); + } + } + } return 0; } int init_constraints(const char* constr_file,int length) { - load_constraints(constr_file); + enable_constraints(true); + load_constraints(constr_file, length); + + + int i,j,it,k; + ind = (int*) malloc((length+1) * sizeof(int)); + if (ind == NULL) { + perror("Cannot allocate variable 'ind'"); + exit(-1); + } + for(i = 1; i<=length; i++){ + ind[i] = (i*(i-1)) >> 1; //n(n-1)/2 + } - BP = (int*) malloc((length + 1) * sizeof(int)); - if (BP == NULL) { - perror("Cannot allocate variable 'constraints'"); - exit(-1); - } + + BP = (int*) malloc((((length+1)*(length))/2+1)*sizeof(int)); + if (BP == NULL) { + perror("Cannot allocate variable 'constraints'"); + exit(-1); + } - int i, it, k; + int LLL = length*(length+1)/2 + 1; - for(i = 1; i <= length; i++) - BP[i] = (RNA[i]=='N')?-1:0 ; - if (nPBP != 0) { - for (it = 0; it < nPBP; it++) { - if (PBP[it][2] < 1) { - printf("Invalid entry (%d %d %d)\n", PBP[it][0], PBP[it][1],PBP[it][2]); + //ZS: initialize all basepairing constraints to 0 (default is nothing known) + for(i = 0; i PBP[it][1] && PBP[it][1]!=0){ + temp = PBP[it][0]; + PBP[it][0] = PBP[it][1]; + PBP[it][1] = temp; + } + } + + for(it = 0; it < nPBP; it++){ + if(PBP[it][2] < 1){ + printf("Invalid entry (P: %d %d %d)\n", PBP[it][0], PBP[it][1], PBP[it][2]); continue; - } - for(k= 1; k <= PBP[it][2];k++) { - BP[PBP[it][0]+k-1] = -1; - if(PBP[it][1]!=0) { - BP[PBP[it][1]+1-k] = -1; + } + + for(k = 1; k <= PBP[it][2]; k++){ + + if(PBP[it][1] == 0){ + //force single-stranded + BP(PBP[it][0]+k-1, PBP[it][0]+k-1) = 3; + //prohibit all pairs with that base + for(i = 1; i<=length; i++){ + if(i FBP[it][1]){ + temp = FBP[it][0]; + FBP[it][0] = FBP[it][1]; + FBP[it][1] = temp; + } + } + for(it = 0; it 0 && BP[i] > i) - printf("("); - else if (BP[i] > 0 && BP[i] < i) - printf(")"); - else if (BP[i] < 0) - printf("x"); - else - printf("."); + switch(BP(i,i)){ + case 3: + //printf("%d: .\n", i);break; + printf("x");break; + case 4: + //printf("%d - ", i); + for(j = 1;j<=len;j++){ + if(i 0) return 1; - } - return 0; - } +int forcePair(int i, int j) { +//ZS: this function returns true if the pair i-j is forced. + if (CONS_ENABLED) + return BP(i,j)==1; else return 0; } -int prohibit_base(int i) { - return (BP[i] == -1); +int forceSS(int i){ +//ZS: this function returns true if base i is forced to be single-stranded + if(CONS_ENABLED) + return BP(i,i)==3; + else + return 0; } -int check_base(int i) { - if (CONS_ENABLED) - return (BP[i] <= 0); - else +int forceSSregion(int i, int j){ + //ZS: This returns 1 if all nucleotides between i and j are forced to be single-stranded, 0 if there is at least one that is not + if(CONS_ENABLED){ + for(int p = i; p 0 && j != BP[i]); +int canILoop(int i, int j, int p, int q) { +//ZS: This function returns 1 if internal loop with pairs i,j and p,q is allowed, 0 if not allowed + if (CONS_ENABLED){ + //Need to check that i,j and p,q pairs are allowed, + //and single-stranded regions between i,p and q,j are allowed + return canStack(i,j) && canStack(p,q) && canSSregion(i,p) && canSSregion(q,j); + } + else + return withinCD(i,j) && withinCD(p,q); } -int force_pair1(int i, int j) { - if (CONS_ENABLED) - return (BP[i]==j); - else - return 0; +int canHairpin(int i, int j) { + //ZS: Returns 1 if a hairpin between i,j is allowed, 0 if not allowed + if (CONS_ENABLED){ + //Need to check if pair is allowed and if anything pairs between them + return canStack(i,j) && canSSregion(i,j); + } + else return withinCD(i,j); } -int check_iloop(int i, int j, int p, int q) { - if (CONS_ENABLED) - return is_ss(i,p) || is_ss(q,j); - else - return 0; +int canSSregion(int i, int j){ +//ZS: This function returns 0 if any nucleotide between i and j is forced to pair with something +//(i and j are NOT included in the check) + if(CONS_ENABLED){ + for(int p = i+1; p 30) { + /* AM: Does not depend upon i and j and ip and jp - Stacking Energies */ + loginc = (int) floor(prelog * log((double) size / 30.0)); + energy = bulge[30] + eparam[2] + loginc + auPen(RNA[i], RNA[j]) + + auPen(RNA[ip], RNA[jp]); + } else if (size <= 30 && size != 1) { + /* Does not depend upon i and j and ip and jp - Stacking Energies */ + energy = bulge[size] + eparam[2]; + energy += auPen(RNA[i], RNA[j]) + auPen(RNA[ip], RNA[jp]); + } else if (size == 1) { + energy = stack[fourBaseIndex(RNA[i], RNA[j], RNA[ip], RNA[jp])] + + bulge[size] + eparam[2] + + + getShapeEnergy(i) + getShapeEnergy(j) + getShapeEnergy(ip) + getShapeEnergy(jp); + } + } else { + /* Internal loop */ + lopsided = abs(size1 - size2); + + if (size > 30) { + loginc = (int) floor(prelog * log((double) size / 30.0)); + + if (!((size1 == 1 || size2 == 1) && gail)) { /* normal internal loop with size > 30*/ + + energy = tstki[fourBaseIndex(RNA[i], RNA[j], RNA[i + 1], RNA[j - 1])] + + tstki[fourBaseIndex(RNA[jp], RNA[ip], RNA[jp + 1], RNA[ip - 1])] + inter[30] + loginc + + eparam[3] + MIN(maxpen, (lopsided * poppen[MIN(2, MIN(size1, size2))])); + } else { /* if size is more than 30 and it is a grossely asymmetric internal loop and gail is not zero*/ + energy = tstki[fourBaseIndex(RNA[i], RNA[j], BASE_A, BASE_A)] + tstki[fourBaseIndex(RNA[jp], RNA[ip], BASE_A, + BASE_A)] + inter[30] + loginc + eparam[3] + MIN(maxpen, (lopsided * poppen[MIN(2, MIN(size1, size2))])); + } + } + else if (size1 == 2 && size2 == 2) { /* 2x2 internal loop */ + energy = iloop22[RNA[i]][RNA[ip]][RNA[j]][RNA[jp]][RNA[i + 1]][RNA[i + 2]][RNA[j - 1]][RNA[j - 2]]; + } else if (size1 == 1 && size2 == 2) { + energy = iloop21[RNA[i]][RNA[j]][RNA[i + 1]][RNA[j - 1]][RNA[j - 2]][RNA[ip]][RNA[jp]]; + } else if (size1 == 2 && size2 == 1) { /* 1x2 internal loop */ + energy = iloop21[RNA[jp]][RNA[ip]][RNA[j - 1]][RNA[i + 2]][RNA[i + 1]][RNA[j]][RNA[i]]; + } else if (size == 2) { /* 1*1 internal loops */ + energy = iloop11[RNA[i]][RNA[i + 1]][RNA[ip]][RNA[j]][RNA[j - 1]][RNA[jp]]; + } else if ((size1 == 2 && size2 == 3) || (size1 == 3 && size2 == 2)) { + return tstacki23[RNA[i]][RNA[j]][RNA[i + 1]][RNA[j - 1]] + + tstacki23[RNA[jp]][RNA[ip]][RNA[jp + 1]][RNA[ip - 1]]; + } + else if ((size1 == 1 || size2 == 1) && gail) { /* gail = (Grossly Asymmetric Interior Loop Rule) (on/off <-> 1/0) */ + energy = tstki[fourBaseIndex(RNA[i], RNA[j], BASE_A, BASE_A)] + tstki[fourBaseIndex(RNA[jp], RNA[ip], BASE_A, BASE_A)] + + inter[size] + loginc + eparam[3] + MIN(maxpen, (lopsided * poppen[MIN(2, MIN(size1, size2))])); + } else { /* General Internal loops */ + energy = tstki[fourBaseIndex(RNA[i], RNA[j], RNA[i + 1], RNA[j - 1])] + tstki[fourBaseIndex(RNA[jp], RNA[ip], RNA[jp + 1], RNA[ip - 1])] + inter[size] + + loginc + eparam[3] + MIN(maxpen, (lopsided * poppen[MIN(2, MIN(size1, size2))])); + + } + } + + return energy; +} + inline int eL(int i, int j, int ip, int jp) { int energy; int size1, size2, size; @@ -153,7 +243,8 @@ inline int eL(int i, int j, int ip, int jp) { energy += auPen(RNA[i], RNA[j]) + auPen(RNA[ip], RNA[jp]); } else if (size == 1) { energy = stack[fourBaseIndex(RNA[i], RNA[j], RNA[ip], RNA[jp])] - + bulge[size] + eparam[2]; /* mans */ + + bulge[size] + eparam[2] + + + getShapeEnergy(i) + getShapeEnergy(j) + getShapeEnergy(ip) + getShapeEnergy(jp); } } else { /* Internal loop */ @@ -162,61 +253,43 @@ inline int eL(int i, int j, int ip, int jp) { if (size > 30) { loginc = (int) floor(prelog * log((double) size / 30.0)); - /* Please check what should be the difference in the following two options. Is it correct?*/ if (!((size1 == 1 || size2 == 1) && gail)) { /* normal internal loop with size > 30*/ - energy = tstki[fourBaseIndex(RNA[i], RNA[j], RNA[i + 1], RNA[j - - 1])] + tstki[fourBaseIndex(RNA[jp], RNA[ip], RNA[jp - + 1], RNA[ip - 1])] + inter[30] + loginc + eparam[3] - + MIN(maxpen, (lopsided * poppen[MIN(2, MIN(size1, - size2))])); + energy = tstki[fourBaseIndex(RNA[i], RNA[j], RNA[i + 1], RNA[j - 1])] + + tstki[fourBaseIndex(RNA[jp], RNA[ip], RNA[jp + 1], RNA[ip - 1])] + inter[30] + loginc + + eparam[3] + MIN(maxpen, (lopsided * poppen[MIN(2, MIN(size1, size2))])); } else { /* if size is more than 30 and it is a grossely asymmetric internal loop and gail is not zero*/ - energy - = tstki[fourBaseIndex(RNA[i], RNA[j], BASE_A, BASE_A)] - + tstki[fourBaseIndex(RNA[jp], RNA[ip], BASE_A, - BASE_A)] + inter[30] + loginc - + eparam[3] + MIN(maxpen, (lopsided - * poppen[MIN(2, MIN(size1, size2))])); + energy = tstki[fourBaseIndex(RNA[i], RNA[j], BASE_A, BASE_A)] + tstki[fourBaseIndex(RNA[jp], RNA[ip], BASE_A, + BASE_A)] + inter[30] + loginc + eparam[3] + MIN(maxpen, (lopsided * poppen[MIN(2, MIN(size1, size2))])); } } - /* if size is not > 30, we have a looooot of cases... */ - else if (size1 == 2 && size2 == 2) { - /* 2x2 internal loop */ - energy - = iloop22[RNA[i]][RNA[ip]][RNA[j]][RNA[jp]][RNA[i + 1]][RNA[i - + 2]][RNA[j - 1]][RNA[j - 2]]; + else if (size1 == 2 && size2 == 2) { /* 2x2 internal loop */ + energy = iloop22[RNA[i]][RNA[ip]][RNA[j]][RNA[jp]][RNA[i + 1]][RNA[i + 2]][RNA[j - 1]][RNA[j - 2]]; } else if (size1 == 1 && size2 == 2) { - energy - = iloop21[RNA[i]][RNA[j]][RNA[i + 1]][RNA[j - 1]][RNA[j - 2]][RNA[ip]][RNA[jp]]; - } else if (size1 == 2 && size2 == 1) { - /* 1x2 internal loop */ - energy = iloop21[RNA[jp]][RNA[ip]][RNA[j - 1]][RNA[i + 2]][RNA[i - + 1]][RNA[j]][RNA[i]]; - } else if (size == 2) { - /* 1*1 internal loops */ - energy - = iloop11[RNA[i]][RNA[i + 1]][RNA[ip]][RNA[j]][RNA[j - 1]][RNA[jp]]; - } else if ((size1 == 1 || size2 == 1) && gail) { /* gail = (Grossly Asymmetric Interior Loop Rule) (on/off <-> 1/0) */ - energy = tstki[fourBaseIndex(RNA[i], RNA[j], BASE_A, BASE_A)] - + tstki[fourBaseIndex(RNA[jp], RNA[ip], BASE_A, BASE_A)] - + inter[size] + loginc + eparam[3] + MIN(maxpen, (lopsided - * poppen[MIN(2, MIN(size1, size2))])); + energy = iloop21[RNA[i]][RNA[j]][RNA[i + 1]][RNA[j - 1]][RNA[j - 2]][RNA[ip]][RNA[jp]]; + } else if (size1 == 2 && size2 == 1) { /* 1x2 internal loop */ + energy = iloop21[RNA[jp]][RNA[ip]][RNA[j - 1]][RNA[i + 2]][RNA[i + 1]][RNA[j]][RNA[i]]; + } else if (size == 2) { /* 1*1 internal loops */ + energy = iloop11[RNA[i]][RNA[i + 1]][RNA[ip]][RNA[j]][RNA[j - 1]][RNA[jp]]; + } + //else if ((size1 == 2 && size2 == 3) || (size1 == 3 && size2 == 2)) { + // return tstacki23[RNA[i]][RNA[j]][RNA[i + 1]][RNA[j - 1]] + + // tstacki23[RNA[jp]][RNA[ip]][RNA[jp + 1]][RNA[ip - 1]]; + //} + else if ((size1 == 1 || size2 == 1) && gail) { /* gail = (Grossly Asymmetric Interior Loop Rule) (on/off <-> 1/0) */ + energy = tstki[fourBaseIndex(RNA[i], RNA[j], BASE_A, BASE_A)] + tstki[fourBaseIndex(RNA[jp], RNA[ip], BASE_A, BASE_A)] + + inter[size] + loginc + eparam[3] + MIN(maxpen, (lopsided * poppen[MIN(2, MIN(size1, size2))])); } else { /* General Internal loops */ - energy - = tstki[fourBaseIndex(RNA[i], RNA[j], RNA[i + 1], - RNA[j - 1])] + tstki[fourBaseIndex(RNA[jp], - RNA[ip], RNA[jp + 1], RNA[ip - 1])] + inter[size] - + loginc + eparam[3] /* AM: I don't understand this eparam value, I think they do not play any role currently. Please look in loader.cc file, for what value have been assinged to various elements of eparam array */ - + MIN(maxpen, - (lopsided * poppen[MIN(2, MIN(size1, size2))])); /* */ + energy = tstki[fourBaseIndex(RNA[i], RNA[j], RNA[i + 1], RNA[j - 1])] + tstki[fourBaseIndex(RNA[jp], RNA[ip], RNA[jp + 1], RNA[ip - 1])] + inter[size] + + loginc + eparam[3] + MIN(maxpen, (lopsided * poppen[MIN(2, MIN(size1, size2))])); + } } return energy; } -inline int eH(int i, int j) -{ +inline int eH(int i, int j) { /* Hairpin loop for all the bases between i and j */ /* size for size of the loop, energy is the result, loginc is for the extrapolation for loops bigger than 30 */ int size; @@ -321,11 +394,19 @@ inline int eH(int i, int j) return energy; } -inline int eS(int i, int j) -{ +inline int eS(int i, int j) { int energy; /* not sure about eparam[1], come from MFold.. = 0 */ - energy = stack[fourBaseIndex(RNA[i], RNA[j], RNA[i+1], RNA[j-1])] + eparam[1]; + energy = stack[fourBaseIndex(RNA[i], RNA[j], RNA[i+1], RNA[j-1])] + eparam[1] + + getShapeEnergy(i) + getShapeEnergy(j) + getShapeEnergy(i+1) + getShapeEnergy(j-1) ; return energy; } + +inline int Estackm(int i, int j) { + return tstackm[RNA[i]][RNA[j]][RNA[i + 1]][RNA[j - 1]]; +} + +inline int Estacke(int i, int j) { + return tstacke[RNA[i]][RNA[j]][RNA[i + 1]][RNA[j - 1]]; +} diff --git a/gtfold-mfe/src/global.c b/gtfold-mfe/src/global.c deleted file mode 100644 index a72088c..0000000 --- a/gtfold-mfe/src/global.c +++ /dev/null @@ -1,82 +0,0 @@ -#include -#include - -#include "global.h" - -unsigned char *RNA; -int *structure; -unsigned int chPairKey; - -void init_global_params(int len) { - RNA = (unsigned char *) malloc((len+1)* sizeof(unsigned char)); - if (RNA == NULL) { - perror("Cannot allocate variable 'RNA'"); - exit(-1); - } - structure = (int *) malloc((len+1) * sizeof(int)); - if (structure == NULL) { - perror("Cannot allocate variable 'structure'"); - exit(-1); - } - - init_checkPair(); -} - -void free_global_params() { - free(structure); - free(RNA); -} - -void print_sequence(int len) { - int i; - for (i = 1; i <= len; i++) { - if (RNA[i] == BASE_A) - printf("A"); - else if (RNA[i] == BASE_C) - printf("C"); - else if (RNA[i] == BASE_G) - printf("G"); - else if (RNA[i] == BASE_U) - printf("U"); - else - printf("N"); - } - printf("\n"); -} - -void print_structure(int len) { - int i = 1; - for (i = 1; i <= len; i++) - { - if (structure[i] > 0 && structure[i] > i) - printf("("); - else if (structure[i] > 0 && structure[i] < i) - printf(")"); - else - printf("."); - } - printf("\n"); -} - -void init_checkPair() { - int i, j; - chPairKey = 0; - for (i = 0; i < 4; i++) - for (j = 0; j < 4; j++) - chPairKey += checkPair(i, j) << ((i << 2) + j); -} - -int update_checkPair(int i, int j) { - int r = 0; - if (!((i >= 0 && i <=3 )&&(j >=0 && j <=3))) - return r; - if (!(chPairKey & (1 << ((i << 2) + j)))) { - chPairKey += 1 << ((i << 2) + j); - r = 1; - } - return r; -} - -inline int canPair(int a, int b) { - return (chPairKey & (1 << (((a)<<2) + (b)))); -} diff --git a/gtfold-mfe/src/global.cc b/gtfold-mfe/src/global.cc new file mode 100644 index 0000000..eb91d90 --- /dev/null +++ b/gtfold-mfe/src/global.cc @@ -0,0 +1,227 @@ +#include +#include +#include + +#include "utils.h" +#include "global.h" +#include "constraints.h" + +unsigned char *RNA; +int *structure; +unsigned int chPairKey; + +int g_nthreads; +int g_dangles; +int g_unamode; +int g_mismatch; +int g_verbose; +int g_prefilter_mode; +int g_prefilter1; +int g_prefilter2; + +void init_global_params(int len) { + RNA = (unsigned char *) malloc((len+1)* sizeof(unsigned char)); + if (RNA == NULL) { + perror("Cannot allocate variable 'RNA'"); + exit(-1); + } + structure = (int *) malloc((len+1) * sizeof(int)); + if (structure == NULL) { + perror("Cannot allocate variable 'structure'"); + exit(-1); + } + + init_checkPair(); +} + +void free_global_params() { + free(structure); + free(RNA); +} + +void print_sequence(int len) { + int i; + for (i = 1; i <= len; i++) { + if (RNA[i] == BASE_A) + printf("A"); + else if (RNA[i] == BASE_C) + printf("C"); + else if (RNA[i] == BASE_G) + printf("G"); + else if (RNA[i] == BASE_U) + printf("U"); + else + printf("N"); + } + printf("\n"); +} + +void print_structure(int len) { + int i = 1; + for (i = 1; i <= len; i++) + { + if (structure[i] > 0 && structure[i] > i) + printf("("); + else if (structure[i] > 0 && structure[i] < i) + printf(")"); + else + printf("."); + } + printf("\n"); +} + +int read_sequence_file(const char* filename, std::string& seq) { + seq = ""; + + ifstream fs; + fs.open(filename, ios::in); + if (!fs.good()) return FAILURE; + + string line; + while(fs.good()) { + getline(fs, line); + // exclude lines starting with FASTA comment characters + if(line[0] != ';' && line[0] != '>' && line.length() > 0) + seq += line; + } + + fs.close(); + + size_t loc; + while((loc = seq.find(" ")) != string::npos) + seq.erase(loc, 1); + + return SUCCESS; +} + +bool encodeSequence(string seq) { + unsigned int unspecifiedBaseCount=0; + unsigned int unspecifiedBases[seq.length()]; + + for(unsigned int i=1; i<=seq.length(); i++) { + RNA[i] = encode(seq[i-1]); + + // die on non-IUPAC codes + if (RNA[i]=='X') { + fprintf(stderr, "ERROR: Non-IUPAC nucleotide code at position: %d (%c)\n", i, seq[i-1]); + fprintf(stderr, "See http://www.bioinformatics.org/sms/iupac.html for valid codes.\n"); + return false; + } + + // add non-canonical IUPAC codes to the warning list + if(!isWatsonCrickBase(seq[i-1])) + unspecifiedBases[unspecifiedBaseCount++]=i; + } + + // just print a warning for non-canonical IUPAC codes + if(unspecifiedBaseCount > 0) { + printf("\nIncompletely-specified IUPAC codes have been detected at position%s: ", unspecifiedBaseCount == 1 ? "" : "s"); + + // put [0] first for nice comma separation + printf("%d (%c)", unspecifiedBases[0], seq.at(unspecifiedBases[0]-1)); + for(unsigned int i=1; i= 0 && i <=3 )&&(j >=0 && j <=3))) + return r; + if (!(chPairKey & (1 << ((i << 2) + j)))) { + chPairKey += 1 << ((i << 2) + j); + r = 1; + } + return r; +} + +int canPair(int a, int b) { + return (chPairKey & (1 << (((a)<<2) + (b)))); +} + +/* +void help() { + printf("Usage: gtfold [OPTION]... FILE\n\n"); + + printf(" FILE is an RNA sequence file containing only the sequence or in FASTA format.\n\n"); + + printf("OPTIONS\n"); + printf(" -c, --constraints FILE\n"); + printf(" Load constraints from FILE. See Constraint syntax below.\n"); + printf(" -d, --dangle INT Restricts treatment of dangling energies (INT=0,2),\n"); + printf(" see below for details.\n"); + printf(" -h, --help Output help (this message) and exit.\n"); + printf(" -l, --limitCD INT Set a maximum base pair contact distance to INT. If no\n"); + printf(" limit is given, base pairs can be over any distance.\n"); + printf(" -m --mismatch Enable terminal mismatch calculations\n"); +// printf(" -n, --noisolate Prevent isolated base pairs from forming.\n"); + printf(" -o, --output NAME Write output files with prefix given in NAME\n"); + printf(" -p --paramdir DIR Path to directory from which parameters are to be read\n"); + printf(" -t, --threads INT Limit number of threads used to INT.\n"); + printf(" -v, --verbose Run in verbose mode (includes loop-by-loop energy decomposition\n"); + printf(" and confirmation of constraints satisfied).\n"); + printf(" -w, --workdir DIR Path of directory where output files will be written.\n"); + printf(" --prefilter INT Prohibits any basepair which does not have appropriate\n"); + printf(" neighboring nucleotides such that it could be part of\n"); + printf(" a helix of length INT.\n"); + printf(" --rnafold Run as RNAfold default mode (ViennaPackage version 1.8.5).\n"); + printf(" --unafold Run as UNAfold default mode (version 3.8), subject to traceback\n"); + printf(" implementation.\n"); + + printf("\nBETA OPTIONS\n"); + printf(" --bpp Calculate base pair probabilities.\n"); + printf(" --partition Calculate the partition function.\n"); + printf(" --pf_count Calculate the structure count using partition function and zero energy value.\n"); + printf(" --subopt NUM Calculate suboptimal structures within NUM kcal/mol\n"); + printf(" of the MFE. (Uses -d 2 treatment of dangling energies.)\n"); + printf(" -s, --useSHAPE FILE Use SHAPE constraints from FILE.\n"); + + printf("\nConstraint syntax:\n"); + printf("\tF i j k # force (i,j)(i+1,j-1),.......,(i+k-1,j-k+1) pairs.\n"); + printf("\tP i j k # prohibit (i,j)(i+1,j-1),.......,(i+k-1,j-k+1) pairs.\n"); + printf("\tP i 0 k # make bases from i to i+k-1 single stranded bases.\n"); + + printf("\nDangle:\n"); + printf("\tINT=0 ignores dangling energies (mostly for debugging).\n"); + printf("\tINT=2 dangling energies are added for nucleotides on either\n"); + printf("\tside of each branch in multi-loops and external loops.\n"); + printf("\tAll other values for INT are ignored.\n"); + exit(-1); +} +*/ diff --git a/gtfold-mfe/src/loader.cc b/gtfold-mfe/src/loader.cc index f916f3c..1c39db9 100644 --- a/gtfold-mfe/src/loader.cc +++ b/gtfold-mfe/src/loader.cc @@ -20,11 +20,17 @@ #include #include #include +#include #include #include #include +#include +#include +#include +#include + #include "data.h" #include "utils.h" #include "constants.h" @@ -33,7 +39,6 @@ #define xstr(s) str(s) #define str(s) #s -//#define GENBIN 1 using namespace std; @@ -52,14 +57,20 @@ int tstkh[256]; /* Terminal mismatch energy used in the calculations of hairpin int tstki[256]; /* Terminal mismatch energy used in the calculations of internal loops */ int tloop[maxtloop + 1][2]; int numoftloops; -int iloop22[5][5][5][5][5][5][5][5]; /* 2*2 internal looops */ int iloop21[5][5][5][5][5][5][5]; /* 2*1 internal loops */ +int iloop22[5][5][5][5][5][5][5][5]; /* 2*2 internal looops */ int iloop11[5][5][5][5][5][5]; /* 1*1 internal loops */ -int coax[6][6][6][6]; -int tstackcoax[6][6][6][6]; -int coaxstack[6][6][6][6]; -int tstack[6][6][6][6]; -int tstkm[6][6][6][6]; + +//int coax[6][6][6][6]; +//int tstackcoax[6][6][6][6]; +//int coaxstack[6][6][6][6]; +//int tstack[6][6][6][6]; +//int tstkm[6][6][6][6]; + +int tstackm[5][5][6][6]; +int tstacke[5][5][6][6]; +int tstacki23[5][5][5][5]; + int auend; int gubonus; int cint; /* cint, cslope, c3 are used for poly C hairpin loops */ @@ -74,199 +85,180 @@ int init; int gail; /* It is either 0 or 1. It is used for grosely asymmetric internal loops */ float prelog; -void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) { - -#ifndef GENBIN - if (!userdatalogic) - { - EN_DATADIR.assign(xstr(DATADIR)); - EN_DATADIR += "/"; - EN_DATADIR += userdatadir; - } else - { - EN_DATADIR.assign(userdatadir); - } -#else - EN_DATADIR = "data"; -#endif - - //Handle the ending forward slash case - if (EN_DATADIR[EN_DATADIR.length() - 1] != '/') { - EN_DATADIR += "/"; - } - - initMiscloopValues("miscloop.dat"); - // miscloop.dat - Miscellaneous loop file - initStackValues("stack.dat"); - // stack.dat - free energies for base pair stacking - initDangleValues("dangle.dat"); - // dangle.dat - single base stacking free energies - initLoopValues("loop.dat"); - // loop.dat - entropic component for internal, bulge and hairpin loops. - initTstkhValues("tstackh.dat"); - // tstackh.dat - free energies for terminal mismatch stacking in hairpin loops - initTstkiValues("tstacki.dat"); - // tstacki.dat - free energies for terminal mismatch stacking in internal loops - initTloopValues("tloop.dat"); - // tloop.dat - free energies for distinguished tetraloops - initInt21Values("int21.dat"); - // int21.dat - free energies for 2 x 1 interior loops - initInt22Values("int22.dat"); - // int22.dat - free energies for 2 x 2 interior loops - initInt11Values("int11.dat"); - // int11.dat - free energies for 1 x 1 interior loops +void readThermodynamicParameters(const char *userdatadir,bool userdatalogic, int unamode = 0, int rnamode = 0, int mismatch = 0) { + struct stat buf; + + if (!userdatalogic) { + std::string opt1, opt2, opt3; + char cwd[1024]; + bool found = false; + + opt1.assign(xstr(DATADIR)); + if (getenv("GTFOLDDATADIR") != 0) + opt2.assign(getenv("GTFOLDDATADIR")); + if (getcwd(cwd, sizeof(cwd)) != 0) { + opt3.assign(cwd); + opt3 += "/data"; + } + + if (stat(opt2.c_str(), &buf) == 0) { + found = true; + EN_DATADIR.assign(opt2); + fprintf(stdout,"Checking for environ variable 'GTFOLDDATADIR', found \n"); + } else { + if (found == false) fprintf(stdout,"Checking for environ variable 'GTFOLDDATADIR', not found \n"); + } + + if (!found && stat(opt1.c_str(), &buf) == 0) { + found = true; + EN_DATADIR.assign(opt1); + fprintf(stdout,"Checking for default datadir '%s', found.\n", opt1.c_str()); + } else { + if (found == false) fprintf(stdout,"Checking for default datadir '%s', not found.\n", opt1.c_str()); + } + + if (!found && stat(opt3.c_str(), &buf) == 0){ + found = true; + EN_DATADIR.assign(opt3); + fprintf(stdout,"Checking under current dir '%s', found.\n", opt3.c_str()); + + } else { + if (found == false) fprintf(stdout,"Checking under current dir '%s', not found.\n", opt3.c_str()); + } + + EN_DATADIR += "/"; + if (found == false) { + exit(-1); + } + + if (unamode) { + EN_DATADIR += "UNAParams"; + }else if (rnamode) { + EN_DATADIR += "RNAParams"; + } else { + EN_DATADIR += "Turner99"; + } + } + else { + EN_DATADIR.assign(userdatadir); + if (stat(EN_DATADIR.c_str(), &buf) == -1){ + fprintf(stdout,"Checking for parameter files in dir '%s', not found.\n\n", EN_DATADIR.c_str()); + exit(-1); + } + } + + //Handle the ending forward slash case + if (EN_DATADIR[EN_DATADIR.length() - 1] != '/') { + EN_DATADIR += "/"; + } + + initMiscloopValues("miscloop.DAT", EN_DATADIR); + initDangleValues("dangle.DAT", EN_DATADIR); + initStackValues("stack.DAT", EN_DATADIR); + initLoopValues("loop.DAT", EN_DATADIR); + initTstkhValues("tstackh.DAT", EN_DATADIR); + initTstkiValues("tstacki.DAT", EN_DATADIR); + initTloopValues("tloop.DAT", EN_DATADIR); + + if (unamode) { + initInt21Values("asint1x2.DAT", EN_DATADIR); + initInt22Values("sint4.DAT", EN_DATADIR); + initInt11Values("sint2.DAT", EN_DATADIR); + initTstkmValues("tstackm.DAT", EN_DATADIR); + initTstkeValues("tstacke.DAT", EN_DATADIR); + initTstk23Values("tstacki23.DAT", EN_DATADIR); + } else if (mismatch) { + initTstkmValues("tstackm.DAT", EN_DATADIR); + initTstkeValues("tstacke.DAT", EN_DATADIR); + initInt21Values("int21.DAT", EN_DATADIR); + initInt22Values("int22.DAT", EN_DATADIR); + initInt11Values("int11.DAT", EN_DATADIR); + + } + else { + initInt21Values("int21.DAT", EN_DATADIR); + initInt22Values("int22.DAT", EN_DATADIR); + initInt11Values("int11.DAT", EN_DATADIR); + } } +int initStackValues(const string& fileName, const string& dirPath) { + std::string filePath; + std::ifstream cf; - int initStackValues(string fileName) { + filePath = dirPath + fileName; + cf.open(filePath.c_str(), ios::in); - ifstream cf; //cf = current file - int i, j, k, l; - int ii, jj, kk, ll; - int index; - char currentLine[256]; - string currentString; - string s; + if (!cf.good()) { + std::cerr << "File open failed - " << filePath << std::endl; + cf.close(); + exit(-1); + } - // Initialize the array with INFINITY - for (i = 0; i < 4; i++) { - for (j = 0; j < 4; j++) { - for (k = 0; k < 4; k++) { - for (l = 0; l < 4; l++) { + for (int i = 0; i < 4; i++) { + for (int j = 0; j < 4; j++) { + for (int k = 0; k < 4; k++) { + for (int l = 0; l < 4; l++) { stack[fourBaseIndex(i,j,k,l)] = INFINITY_; } } } } - - fileName = EN_DATADIR + fileName; - cf.open(fileName.c_str(), ios::in); - if (cf.fail()) { - cerr << "File open failed" << endl; - exit(-1); - } - - // Read the thermodynamic parameters. - // The 24 first lines are junk we don't need - for (index = 1; index <= 15; index++) { - cf.getline(currentLine, 256); - } - - i = 0; - kk = 0; - ii = 0; - jj = 0; - ll = 0; - - while (i < 16) { - - if (i % 4 == 0) - for (index = 1; index < 9; index++) - cf.getline(currentLine, 256); - - cf.getline(currentLine, 256); - s = currentLine; - j = 0; - - ll = 0; - jj = 0; - - int z = 0; - int r = 0; - - while (s[z] != '\0') { - - if (s[z] == ' ') - z++; - - else if (s[z] == '.') { - z++; - ll++; - if (ll == 4) - ll = 0; - r++; - if (r % 4 == 0) - jj++; - } else { - char value[10]; - int x = 0; - - while (s[z] != ' ' && s[z] != '\0') { - value[x++] = s[z++]; - } - - value[x] = '\0'; - - int temp = (int) floor(100.0 * atof(value) + .5); - stack[fourBaseIndex(ii,jj,kk,ll)] = temp; - r++; - z++; - if (r % 4 == 0) - jj++; - ll++; - if (ll == 4) - ll = 0; + + int count = 0; + + while (cf.good()) { + int i, j, k, l; + + std::string line; + std::stringstream ss; + + getline(cf, line); + ss << line; + if (line.empty()) continue; + + i = count/4; + k = count%4; + + for (int cols = 0; cols < 16; cols++) { + std::string val; + ss >> val; + j = cols/4; + l = cols%4; + if (!(val == "inf")) { + stack[fourBaseIndex(i,j,k,l)] = (int) floor(100.0 * atof(val.c_str()) + .5); } - } - i++; - if (!(i % 4)) - ii++; - - /* jj = 1; */ - kk = (i % 4); - + } + ++count; } - cf.close(); -#if 0 - cout << " Done!" << endl; -#endif + return 0; } - int initMiscloopValues(string fileName) { - /* - miscloop.dat - Miscellaneous loop file. Contains : - 1. Extrapolation for large loops based on polymer theory - 2. Asymmetric internal loop correction parameters. - 3. the f(m) array (see Ninio for details) - 4. Paremeters for multibranch loops - 5. Paremeters for multibranch loops (for efn2 only) - 6. Terminal AU or GU penalty - 7. Bonus for GGG hairpin - 8,9,10. C hairpin rules: a) slope b) intercept c) value for size 3 - 11. Intermolecular initiation free energy - 12. GAIL Rule (Grossly Asymmetric Interior Loop Rule) (on or off) - */ +int initMiscloopValues(const string& fileName, const string& dirpath) { + std::string filePath; + std::ifstream cf; - char currentWord[256]; - string s; - ifstream cf; //cf = current file + filePath = dirpath + fileName; + cf.open(filePath.c_str(), ios::in); - fileName = EN_DATADIR + fileName; -#if 0 - cout << "Getting miscloop values from " << fileName << endl; -#endif - cf.open(fileName.c_str(), ios::in); - if (cf.fail()) { - cerr << "File open failed" << endl; - exit(-1); + if (!cf.good()) { + std::cerr << "File open failed - " << filePath << std::endl; + cf.close(); + exit(-1); } - s = ""; - cf >> currentWord; + char currentWord[256]; + std::string s; + for (int index = 1; index < 13; index++) { // There are total 12 values to read in. - while (strcmp(currentWord, "-->")) { - cf >> currentWord; - } if (index == 1) { cf >> currentWord; prelog = 100 * atof(currentWord); - //cout << "prelog = " << prelog << endl; } if (index == 2) { cf >> currentWord; maxpen = int(atof(currentWord) * 100.0 + .5); - //cout << "maxpen = " << maxpen << endl; } if (index == 3) { for (int count = 1; count <= 4; count++) { @@ -292,7 +284,6 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) { s = currentWord; multConst[count - 1] = (int) (atof(s.c_str()) * 100 + 0.5); eparam[table[count]] = (int) (atof(s.c_str()) * 100 + 0.5); - //cout << "\n multi " << multConst[count-1]; } } if (index == 5) { @@ -336,150 +327,86 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) { } } - cf.close(); + cf.close(); + return 0; } - int initDangleValues(string fileName) { - ifstream cf; //cf = current file - char currentLine[256]; - string currentString; - string s; - int index; - int i, j, k, l; - int ii, jj, kk, ll; // ii = 1st base, jj = 2nd base, kk = 3rd base, ll = 1 up or 2 low - - for (i = 0; i < 4; i++) { - for (j = 0; j < 4; j++) { - for (k = 0; k < 4; k++) { - for (l = 0; l < 2; l++) { +int initDangleValues(const std::string& fileName, + const std::string& dirPath) { + std::string filePath; + std::ifstream cf; + + filePath = dirPath + fileName; + cf.open(filePath.c_str(), ios::in); + + for (int i = 0; i < 4; i++) { + for (int j = 0; j < 4; j++) { + for (int k = 0; k < 4; k++) { + for (int l = 0; l < 2; l++) { dangle[i][j][k][l] = INFINITY_; } } } } - - fileName = EN_DATADIR + fileName; - cf.open(fileName.c_str(), ios::in); - if (cf.fail()) { - cerr << "File open failed" << endl; - exit(-1); - } - - // The 8 first lines are junk - for (index = 1; index <= 8; index++) { - cf.getline(currentLine, 256); - } - - // 8 lines of useful data - i = 0; - ii = 0; - jj = 0; - kk = 0; - ll = 0; - - while (i < 8) { - - if (i != 0) - for (index = 1; index < 9; index++) - cf.getline(currentLine, 256); - - cf.getline(currentLine, 256); - s = currentLine; - j = 0; - - jj = 0; - - int z = 0; - int r = 0; - - while (s[z] != '\0') { - - if (s[z] == ' ') - z++; - - else if (s[z] == '.') { - z++; - kk++; - if (kk == 4) - kk = 0; - r++; - if (r % 4 == 0) - jj++; - } else { - char value[10]; - int x = 0; - - while (s[z] != ' ' && s[z] != '\0') { - value[x++] = s[z++]; - } - - value[x] = '\0'; - - int temp = (int) floor(100.0 * atof(value) + .5); - //if ( temp == 0 ) temp = -1; - dangle[ii][jj][kk][ll] = temp; - //cout<< "\n " << temp << " "<< ii <<" "<< jj << " "<< kk << " " << ll ; - r++; - z++; - if (r % 4 == 0) - jj++; - kk++; - if (kk == 4) - kk = 0; - + + int count = 0; + + while (cf.good()) { + int i, j, k, l; + + std::string line; + std::stringstream ss; + + getline(cf, line); + ss << line; + if (line.empty()) continue; + + i = count%4; + l = count/4; + + for (int cols = 0; cols < 16; cols++) { + std::string val; + + j = cols/4; + ss >> val; + k = cols%4; + if (!(val == "inf")) { + dangle[i][j][k][l] = (int) floor(100.0 * atof(val.c_str()) + .5); } - - } - - i++; - ii++; - if (ii == 4) - ii = 0; - - if (i == 4) - ll = 1; - + } + ++count; } - cf.close(); - -#if 0 - cout << " Done!" << endl; -#endif + return 0; } - int initLoopValues(string fileName) { +int initLoopValues( const string& fileName, const string& dirPath) { // algorithm.c, line 2996 ifstream cf; // current file - char currentLine[256]; + std::string filePath; + + filePath = dirPath + fileName; + cf.open(filePath.c_str(), ios::in); + + //char currentLine[256]; char currentWord[256]; string s; - int index; + int index= 0; int tempValue = 0; -#if 0 - cout << "Getting loop values..."; -#endif - fileName = EN_DATADIR + fileName; - cf.open(fileName.c_str(), ios::in); if (cf.fail()) { - cerr << "File open failed" << endl; + cerr << "File open failed " << filePath << endl; exit(-1); } - // The 4 first lines are junk we don't need - for (index = 1; index <= 4; index++) { - cf.getline(currentLine, 256); - //s = currentLine; - //cout << s << endl; - } + while (index < 30) { for (int j = 1; j <= 4; j++) { cf >> currentWord; if (j == 1) index = atoi(currentWord); if (j > 1) { - if (strcmp(currentWord, ".")) { + if (strcmp(currentWord, "inf")) { tempValue = (int) (100 * atof(currentWord) + 0.5); } else { tempValue = INFINITY_; @@ -500,228 +427,224 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) { } cf.close(); -#if 0 - cout << " Done!" << endl; -#endif return 0; } - int initTstkhValues(string fileName) { - ifstream cf; //cf = current file - int i, j, k, l; - int ii, jj, kk, ll; - int index; - char currentLine[256]; - string currentString; - string s; +int initTstk23Values(const std::string& fileName, const std::string& dirPath) { + int i1, j1, i2, j2; + std::string filePath; + std::ifstream cf; + std::string val; - for (i = 0; i < 4; i++) { - for (j = 0; j < 4; j++) { - for (k = 0; k < 4; k++) { - for (l = 0; l < 4; l++) { - tstkh[fourBaseIndex(i,j,k,l)] = INFINITY_; - } - } - } - } + filePath = dirPath + fileName; + cf.open(filePath.c_str(), ios::in); - fileName = EN_DATADIR + fileName; - cf.open(fileName.c_str(), ios::in); if (cf.fail()) { - cerr << "File open failed" << endl; + cerr << "File open failed " << filePath << endl; exit(-1); } - // The 27 first lines are junk we don't need - for (index = 1; index <= 15; index++) { - cf.getline(currentLine, 256); - } - - i = 0; - kk = 0; - ii = 0; - jj = 0; - ll = 0; - - while (i < 16) { - - if (i % 4 == 0) - for (index = 1; index < 9; index++) - cf.getline(currentLine, 256); + for (i1 = 0; i1 < 5; ++i1) + for (i2 = 0; i2 < 5; ++i2) + for (j1 = 0; j1 < 5; ++j1) + for (j2 = 0; j2 < 5; ++j2) + if (i1 == 4 || j1 == 4) + tstacki23[i1][j1][i2][j2] = INFINITY_; + else if (i2 == 4 || j2 == 4) + tstacki23[i1][j1][i2][j2] = 0; + else { + cf >> val; + tstacki23[i1][j1][i2][j2] = (val == "inf")? (INFINITY_): + ((int) floor(100.0 * atof(val.c_str()) + .5)); + } + cf.close(); - cf.getline(currentLine, 256); - s = currentLine; - j = 0; + return 0; +} - ll = 0; - jj = 0; - int z = 0; - int r = 0; - while (s[z] != '\0') { - if (s[z] == ' ') - z++; +int initTstkeValues(const std::string& fileName, const std::string& dirPath) { + int i1, j1, i2, j2; + std::string filePath; + std::ifstream cf; + std::string val; - else if (s[z] == '.') { - z++; - ll++; - if (ll == 4) - ll = 0; - r++; - if (r % 4 == 0) - jj++; - } + filePath = dirPath + fileName; + cf.open(filePath.c_str(), ios::in); - else { - char value[10]; - int x = 0; + if (cf.fail()) { + cerr << "File open failed " << filePath << endl; + exit(-1); + } - while (s[z] != ' ' && s[z] != '\0') { - value[x++] = s[z++]; + for (i1 = 0; i1 < 5; ++i1) { + for (i2 = 0; i2 < 6; ++i2) { + for (j1 = 0; j1 < 5; ++j1) { + for (j2 = 0; j2 < 6; ++j2) { + if (i1 == 4 || j1 == 4) + tstacke[i1][j1][i2][j2] = INFINITY_; + else if (i2 == 5 || j2 == 5) + tstacke[i1][j1][i2][j2] = INFINITY_; + else if (i2 == 4 || j2 == 4) + tstacke[i1][j1][i2][j2] = 0; + else { + cf >> val; + tstacke[i1][j1][i2][j2] = (val == "inf")? (INFINITY_): + ((int) floor(100.0 * atof(val.c_str()) + .5)); + } } - - value[x] = '\0'; - - int temp = (int) floor(100.0 * atof(value) + .5); - tstkh[fourBaseIndex(ii,jj,kk,ll)] = temp; - - r++; - z++; - if (r % 4 == 0) - jj++; - ll++; - if (ll == 4) - ll = 0; } - } - i++; - if (!(i % 4)) - ii++; - - jj = 0; - kk = (i % 4); - + } } cf.close(); -#if 0 - cout << " Done!" << endl; -#endif + return 0; } - int initTstkiValues(string fileName) { - ifstream cf; //cf = current file - int i, j, k, l; - int ii, jj, kk, ll; - int index; - char currentLine[256]; - string currentString; - string s; +int initTstkmValues(const std::string& fileName, const std::string& dirPath) { + int i1, j1, i2, j2; + std::string filePath; + std::ifstream cf; + std::string val; - for (i = 0; i < 4; i++) { - for (j = 0; j < 4; j++) { - for (k = 0; k < 4; k++) { - for (l = 0; l < 4; l++) { - tstki[fourBaseIndex(i,j,k,l)] = INFINITY_; - } - } - } - } - - fileName = EN_DATADIR + fileName; - cf.open(fileName.c_str(), ios::in); + filePath = dirPath + fileName; + cf.open(filePath.c_str(), ios::in); + if (cf.fail()) { - cerr << "File open failed" << endl; + cerr << "File open failed " << filePath << endl; exit(-1); } - // The 27 first lines are junk we don't need - for (index = 1; index <= 15; index++) { - cf.getline(currentLine, 256); + for (i1 = 0; i1 < 5; ++i1) { + for (i2 = 0; i2 < 6; ++i2) { + for (j1 = 0; j1 < 5; ++j1) { + for (j2 = 0; j2 < 6; ++j2) { + if (i1 == 4 || j1 == 4) + tstackm[i1][j1][i2][j2] = INFINITY_; + else if (i2 == 5 || j2 == 5) + tstackm[i1][j1][i2][j2] = INFINITY_; + else if (i2 == 4 || j2 == 4) + tstackm[i1][j1][i2][j2] = 0; + else { + cf >> val; + tstackm[i1][j1][i2][j2] = (val == "inf")? (INFINITY_): + ((int) floor(100.0 * atof(val.c_str()) + .5)); + } + } + } + } } - i = 0; - kk = 0; - ii = 0; - jj = 0; - ll = 0; + cf.close(); - while (i < 16) { + return 0; +} - if (i % 4 == 0) - for (index = 1; index < 9; index++) - cf.getline(currentLine, 256); +int initTstkhValues(const std::string& fileName, const std::string& dirPath) { + std::string filePath; + std::ifstream cf; - cf.getline(currentLine, 256); - s = currentLine; - j = 0; + filePath = dirPath + fileName; + cf.open(filePath.c_str(), ios::in); - ll = 0; - jj = 0; + for (int i = 0; i < 4; i++) { + for (int j = 0; j < 4; j++) { + for (int k = 0; k < 4; k++) { + for (int l = 0; l < 2; l++) { + tstkh[fourBaseIndex(i,j,k,l)] = INFINITY_; + } + } + } + } + + int count = 0; + + while (cf.good()) { + int i, j, k, l; + + std::string line; + std::stringstream ss; + + getline(cf, line); + ss << line; + if (line.empty()) continue; + + i = count/4; + k = count%4; + + for (int cols = 0; cols < 16; cols++) { + std::string val; + ss >> val; + j = cols/4; + l = cols%4; + if (!(val == "inf")) { + tstkh[fourBaseIndex(i,j,k,l)]= (int) floor(100.0 * atof(val.c_str()) + .5); + } + } + ++count; + } + + return 0; +} - int z = 0; - int r = 0; - while (s[z] != '\0') { +int initTstkiValues(const std::string& fileName, const std::string& dirPath) { + std::string filePath; + std::ifstream cf; - if (s[z] == ' ') - z++; + filePath = dirPath + fileName; + cf.open(filePath.c_str(), ios::in); - else if (s[z] == '.') { - z++; - ll++; - if (ll == 4) - ll = 0; - r++; - if (r % 4 == 0) - jj++; + for (int i = 0; i < 4; i++) { + for (int j = 0; j < 4; j++) { + for (int k = 0; k < 4; k++) { + for (int l = 0; l < 2; l++) { + tstki[fourBaseIndex(i,j,k,l)] = INFINITY_; + } } + } + } - else { - char value[10]; - int x = 0; + int count = 0; - while (s[z] != ' ' && s[z] != '\0') { - value[x++] = s[z++]; - } + while (cf.good()) { + int i, j, k, l; - value[x] = '\0'; + std::string line; + std::stringstream ss; - int temp = (int) floor(100.0 * atof(value) + .5); - tstki[fourBaseIndex(ii,jj,kk,ll)] = temp; - - //cout << "\n temp " << temp << " " <> val; + j = cols/4; + l = cols%4; + if (!(val == "inf")) { + tstki[fourBaseIndex(i,j,k,l)]= (int) floor(100.0 * atof(val.c_str()) + .5); + } + } + ++count; } - cf.close(); -#if 0 - cout << " Done!" << endl; -#endif return 0; } -//SH: Rewritten as an error was being generated by this function. - int initTloopValues(string fileName) { - ifstream cf; +int initTloopValues(const std::string& fileName, const std::string& dirPath) { + std::string filePath; + std::ifstream cf; + + filePath = dirPath + fileName; + cf.open(filePath.c_str(), ios::in); + int count; char currentLine[256]; char currentSeqNumbers[7]; @@ -732,20 +655,6 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) { string s, temp; -#if 0 - cout << "Getting tloop values..."; -#endif - - fileName = EN_DATADIR + fileName; - cf.open(fileName.c_str(), ios::in); - if (cf.fail()) { - cerr << "File open failed" << endl; - exit(-1); - } - // skip 2 lines - cf.getline(currentLine, 256); - cf.getline(currentLine, 256); - numoftloops = 0; while (!cf.eof() && (++(numoftloops) < maxtloop)) { @@ -759,33 +668,25 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) { for (count = 0; count < 6; count++) { temp = currentLine[count + clindex]; currentSeqNumbers[count] = baseToDigit(temp.c_str()); - //cout << currentSeqNumbers[count]; - //cout << currentLine[count+1]; } - //cout << endl; clindex=clindex+7; while(currentLine[clindex]== ' ') clindex++; count = 0; while(currentLine[clindex+count]!=' '&¤tLine[clindex+count]!='\0') { currentValue[count] = currentLine[count + clindex]; count++; - //cout << currentValue[count]; } - //cout << endl; - + tloop[numoftloops][0] = (int) atoi(currentSeqNumbers); - tloop[numoftloops][1] = (int) floor(100.0 * atof(currentValue) + 0.5); - //cout << " -- "<< tloop[numoftloops][0] << " | " << tloop[numoftloops][1] << endl; + + if (!(strcmp(currentValue,"inf")==0)) + tloop[numoftloops][1] = (int) floor(100.0 * atof(currentValue) + 0.5); } cf.close(); -#if 0 - cout << " Done!" << endl; -#endif return 0; } - int initInt22Values(string fileName) { - +int initInt22Values(const std::string& fileName, const std::string& dirPath) { //Read the 2x2 internal loops //key iloop22[a][b][c][d][j][l][k][m] = //a j l b @@ -803,66 +704,36 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) { iloop22[i][j][k][r][q][t][y][z] = INFINITY_; ifstream cf; - int index, flag; char currentLine[256], currentValue[6]; - string s, s1, s2, temp; - string sre; int base[4]; int l, m; -#if 0 - cout << "Getting Int22 values..."; -#endif - fileName = EN_DATADIR + fileName; - cf.open(fileName.c_str(), ios::in); - if (cf.fail()) { - cerr << "File open failed" << endl; + string filePath = dirPath + fileName; + cf.open(filePath.c_str(), ios::in); + if (!cf.good()) { + cerr << "File open failed " << filePath << endl; exit(-1); } - // Get rid of the 38 1st lines - for (index = 1; index < 28; index++) { - cf.getline(currentLine, 256); - } + const char* str[] = {"A-U","C-G","G-C","U-A","G-U","U-G"}; + - sre = "Y"; - flag = 0; - - for (index = 1; index <= 36; index++) { // 36 tables 16x16 - // Go to the beginning of the tables - while (!flag) { - cf.getline(currentLine, 256); + int outer, inner; - s = currentLine; + for (int index = 1; index <= 36; index++) { // 36 tables 16x16 + std::stringstream ss1; + std::string s ; - int z = 0; - while (s[z] != '\0') { - - if (s[z] == 'Y') - flag = 1; - - z++; - } - } - flag = 0; - - // We skip 5 lines - for (i = 0; i < 5; ++i) { - cf.getline(currentLine, 256); - } - - // get the closing bases - cf.getline(currentLine, 256); - s1 = currentLine; - cf.getline(currentLine, 256); - s2 = currentLine; - s = s1 + s2; - - int z = 0; + outer = (index-1)/6; + inner = (index-1)%6; + ss1 << str[outer][0] << '-' << str[inner][0] << '-' << str[outer][2] << '-' << + str[inner][2]; + ss1 >> s; + int k = 0; + int z = 0; while (s[z] != '\0') { - if (s[z] == 'A') base[k++] = BASE_A; else if (s[z] == 'C') @@ -871,22 +742,15 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) { base[k++] = BASE_G; else if (s[z] == 'U') base[k++] = BASE_U; - z++; } - cf.getline(currentLine, 256); - - //key iloop22[a][b][c][d][j][l][k][m] = - //a j l b - //c k m d - - for (int rowIndex = 1; rowIndex <= 16; rowIndex++) { + cf.getline(currentLine, 256); + std::stringstream ss; + ss << currentLine; for (int colIndex = 1; colIndex <= 16; colIndex++) { - cf >> currentValue; - // rowIndex = j*4+k - // colIndex = l*4+m + ss >> currentValue; j = ((rowIndex - 1) - (rowIndex - 1) % 4) / 4; k = (rowIndex - 1) % 4; @@ -894,23 +758,18 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) { l = ((colIndex - 1) - (colIndex - 1) % 4) / 4; m = (colIndex - 1) % 4; - iloop22[base[0]][base[1]][base[2]][base[3]][j][l][k][m] - = (int) floor(100.0 * atof(currentValue) + 0.5); - //int temp = (int) floor(100.0*atof(currentValue)+0.5); - //printf("\n temp is : %d %d %d %d %d %d %d %d %d", temp, base[0], base[2], base[1], base[3], j, k, l, m ); + if (!(strcmp(currentValue,"inf")==0)) + iloop22[base[0]][base[1]][base[2]][base[3]][j][l][k][m] + = (int) floor(100.0 * atof(currentValue) + 0.5); } } } cf.close(); -#if 0 - cout << " Done!" << endl; -#endif return 0; } - int initInt21Values(string fileName) { - +int initInt21Values(const std::string& fileName, const std::string& dirPath) { // 24x6 arrays of 4x4 values // c // a f @@ -921,7 +780,7 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) { char currentLine[256]; string sre; string s, s1, s2; - int a, b, c, d, e, f, g, index; + int a, b, c, d, e, f, g; int i, j, k, r, q, t, y; int z; @@ -958,87 +817,44 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) { base1[6] = BASE_U + 1; base2[6] = BASE_G + 1; - fileName = EN_DATADIR + fileName; - cf.open(fileName.c_str(), ios::in); + std::string filePath = dirPath + fileName; + cf.open(filePath.c_str(), ios::in); if (cf.fail()) { - cerr << "File open failed" << endl; + cerr << "File open failed" << filePath << endl; exit(-1); } - // Get rid of the 18 1st lines - for (index = 1; index <= 17; index++) { - cf.getline(currentLine, 256); - } - i = 1; - while (i <= 6) { - j = 1; - while (j <= 4) { - k = 1; - - for (index = 1; index <= 10; index++) - cf.getline(currentLine, 256); - - s = currentLine; - while (k <= 4) { - cf.getline(currentLine, 256); - - s = currentLine; - r = 0; - z = 0; int jj = 1; d = 1; - while (s[z] != '\0') { - - if (s[z] == ' ') - z++; - - else if (s[z] == '.') { - z++; - d++; - if (d == 5) - d = 1; - r++; - if (r % 4 == 0) - jj++; - } - else { - char value[10]; - int x = 0; - - while (s[z] != ' ' && s[z] != '\0') { - value[x++] = s[z++]; - } - - value[x] = '\0'; - - int temp = (int) floor(100.0 * atof(value) + .5); - a = base1[i]; - b = base2[i]; - f = base1[jj]; - g = base2[jj]; - c = k; - e = j; - - iloop21[a - 1][b - 1][c - 1][d - 1][e - 1][f - 1][g - 1] - = temp; - //printf("\n temp %d, a %d , b %d, c %d, d %d, e %d, f %d, g %d", temp, a, b, c, d, e, f, g); - r++; - z++; - if (r % 4 == 0) - jj++; - d++; - if (d == 5) - d = 1; - } + std::stringstream ss; + ss << currentLine; + + for (z = 1; z <=24 ; z++) { + char value[32]; + ss >> value; + int temp = (int) floor(100.0 * atof(value) + .5); + a = base1[i]; + b = base2[i]; + f = base1[jj]; + g = base2[jj]; + c = k; + e = j; + + if (!(strcmp(value,"inf")==0)) + iloop21[a - 1][b - 1][c - 1][d - 1][e - 1][f - 1][g - 1] = temp; + r++; + if (r % 4 == 0) jj++; + d++; + if (d == 5) d = 1; } k++; } @@ -1050,13 +866,8 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) { return 0; } - int initInt11Values(string fileName) { - - //Read the 1x1 internal loops - //key iloop11[a][b][c][d][j][l][k][m] = - //a b c - //d e f +int initInt11Values(const std::string& fileName, const std::string& dirPath) { int i, j, k, r, q, t; for (i = 0; i < 4; i++) @@ -1068,37 +879,20 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) { iloop11[i][j][k][r][q][t] = INFINITY_; ifstream cf; - int index; char currentLine[256]; string s; int base1[7]; int base2[7]; - //int j, k, l, m; int a, b, c, d, f; -#if 0 - cout << "Getting Int11 values..."; -#endif - fileName = EN_DATADIR + fileName; - cf.open(fileName.c_str(), ios::in); + std::string filePath = dirPath + fileName; + cf.open(filePath.c_str(), ios::in); if (cf.fail()) { - cerr << "File open failed" << endl; + cerr << "File open failed " << filePath << endl; exit(-1); } - // Get rid of the 19 1st lines - for (index = 1; index <= 17; index++) { - cf.getline(currentLine, 256); - } - - /* - Structure of the file: - array of 6x6 arrays - Order: - AU CG GC UA GU UG - */ - base1[1] = BASE_A + 1; base2[1] = BASE_U + 1; base1[2] = BASE_C + 1; @@ -1117,75 +911,42 @@ void readThermodynamicParameters(const char *userdatadir,bool userdatalogic) { while (k < 6) { k++; - index = 0; - for (index = 1; index <= 10; index++) { - cf.getline(currentLine, 256); - } - i = 0; b = 1; while (i < 4) { - int jj = 1; ++i; cf.getline(currentLine, 256); - s = currentLine; - j = 0; int r = 0; - int z = 0; int e = 1; - while (s[z] != '\0') { - - if (s[z] == ' ') - z++; - - else if (s[z] == '.') { - z++; - e++; - if (e == 5) - e = 1; - r++; - if (r % 4 == 0) - jj++; - } - - else { - char value[10]; - int x = 0; - - while (s[z] != ' ' && s[z] != '\0') { - value[x++] = s[z++]; - } + std::stringstream ss; + ss << currentLine; - value[x] = '\0'; - - int temp = (int) floor(100.0 * atof(value) + .5); - a = base1[k]; - d = base2[k]; - c = base1[jj]; - f = base2[jj]; + for (int z=1; z <= 24; ++z) { + char value[32]; + ss >> value; + int temp = (int) floor(100.0 * atof(value) + .5); + a = base1[k]; + d = base2[k]; + c = base1[jj]; + f = base2[jj]; + + if (!(strcmp(value,"inf")==0)) iloop11[a - 1][b - 1][c - 1][d - 1][e - 1][f - 1] = temp; - r++; - z++; - if (r % 4 == 0) - jj++; - e++; - if (e == 5) - e = 1; - } + + r++; + if (r % 4 == 0) jj++; + e++; + if (e == 5) e = 1; } b++; } } cf.close(); -#if 0 - cout << " Done!" << endl; -#endif + return 0; } - - diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc index 76e24d7..1689af9 100644 --- a/gtfold-mfe/src/main.cc +++ b/gtfold-mfe/src/main.cc @@ -1,6 +1,7 @@ /* GTfold: compute minimum free energy of RNA secondary structure - Copyright (C) 2008 David A. Bader + Copyright (C) 2007-2011 David A. Bader, Christine E. Heitsch, + and Steve C. Harvey http://www.cc.gatech.edu/~bader This program is free software: you can redistribute it and/or modify @@ -18,223 +19,170 @@ */ #include +#include #include #include #include #include -#include -#include #include #include #include #include #include "main.h" +#include "mfe_main.h" +#include "boltzmann_main.h" +#include "subopt_main.h" #include "utils.h" -#include "loader.h" -#include "options.h" #include "global.h" -#include "energy.h" -#include "algorithms.h" -#include "constraints.h" -#include "traceback.h" -#include "subopt_traceback.h" - -using namespace std; - -double get_seconds() { - struct timeval tv; - gettimeofday(&tv, NULL); - return (double) tv.tv_sec + (double) tv.tv_usec / 1000000.0; -} - -void init_fold(string seq) { - int len = seq.length(); - - init_global_params(len); - - if (!encodeSequence(seq)) { - free_fold(seq.length()); - exit(0); - } - - create_tables(len); - - if (CONS_ENABLED) { - init_constraints(constraintsFile.c_str(), len); - } -} - -void free_fold(int len) { - if (CONS_ENABLED) - free_constraints(len); - - free_tables(len); - free_global_params(); -} - -/** - * Read the sequence out of the given filename and store it in seq - * - * @param filename A c string with the file to open - * @param seq A C++ string object (passed by reference) to save to - * @return SUCCESS or FAILURE - */ -int read_sequence_file(const char* filename, std::string& seq) { - seq = ""; - - ifstream fs; - fs.open(filename, ios::in); - if (fs == NULL) - return FAILURE; - - string line; - getline(fs, line); - while(line.length() > 0) { - // exclude lines starting with FASTA comment characters - if(line[0] != ';' && line[0] != '>') - seq += line; - getline(fs, line); - } - - fs.close(); - - size_t loc; - while((loc = seq.find(" ")) != string::npos) - seq.erase(loc, 1); - - return SUCCESS; -} - -/** - * Encode the given string of letters into an RNA sequence. - * - * This handles IUPAC codes and places the results into the array RNA. - * - * @param seq The string to encode - * @return A boolean representing success or failure of the encoding. Failure - * can occur when seeing unknown IUPAC codes. - */ -bool encodeSequence(string seq) { - unsigned int unspecifiedBaseCount=0; - unsigned int unspecifiedBases[seq.length()]; - - for(unsigned int i=1; i<=seq.length(); i++) { - RNA[i] = encode(seq[i-1]); - - // die on non-IUPAC codes - if (RNA[i]=='X') { - fprintf(stderr, "ERROR: Non-IUPAC nucleotide code at position: %d (%c)\n", i, seq[i-1]); - fprintf(stderr, "See http://www.bioinformatics.org/sms/iupac.html for valid codes.\n"); - return false; - } - - // add non-canonical IUPAC codes to the warning list - if(!isWatsonCrickBase(seq[i-1])) - unspecifiedBases[unspecifiedBaseCount++]=i; - } - - // just print a warning for non-canonical IUPAC codes - if(unspecifiedBaseCount > 0) { - printf("\nIncompletely-specified IUPAC codes have been detected at position%s: ", unspecifiedBaseCount == 1 ? "" : "s"); - - // put [0] first for nice comma separation - printf("%d (%c)", unspecifiedBases[0], seq.at(unspecifiedBases[0]-1)); - for(unsigned int i=1; i= MAXENG) + printf("- Minimum Free Energy: %12.4f kcal/mol\n", 0.00); + else + printf("- Minimum Free Energy: %12.4f kcal/mol\n", energy/100.00); printf("- MFE runtime: %9.6f seconds\n", t1); - - + + if (SUBOPT_ENABLED) { t1 = get_seconds(); - subopt_traceback(seq.length(), suboptDelta); + ss_map_t subopt_data = subopt_traceback(seq.length(), 100.0*suboptDelta); t1 = get_seconds() - t1; - printf("Subopt traceback running time: %9.6f seconds\n\n", t1); - - free_fold(seq.length()); + printf("\n"); + printf("Subopt traceback running time: %9.6f seconds\n", t1); + + printf("Subopt structures saved in %s\n", suboptFile.c_str()); + save_subopt_file(suboptFile, subopt_data, seq, energy); + //free_fold(seq.length()); exit(0); } t1 = get_seconds(); - trace(seq.length(), VERBOSE); + trace(seq.length()); //, VERBOSE, UNAMODE, T_MISMATCH); t1 = get_seconds() - t1; - + printf("\n"); print_sequence(seq.length()); print_structure(seq.length()); if (CONS_ENABLED) print_constraints(seq.length()); + if (SHAPE_ENABLED && VERBOSE) + print_shapeArray(seq.length()); save_ct_file(outputFile, seq, energy); printf("\nMFE structure saved in .ct format to %s\n", outputFile.c_str()); - // release the malloc'd arrays - free_fold(seq.length()); - return EXIT_SUCCESS; -} + if(CONS_ENABLED && VERBOSE){ + printf("Verifying that structure fulfills constraint criteria... "); + if(verify_structure()){ + printf("OK\n"); + } + else{ + printf("ERROR: NOT OK!!\n"); + fprintf(stderr, "ERROR: Structure does not fulfill constraint criteria.\n"); + fprintf(stderr, "Structure file: %s\n", outputFile.c_str()); + fprintf(stderr, "Constraint file: %s\n", constraintsFile.c_str()); + } + } + */ +/* + if(BPP_ENABLED){ + printf("\n"); + printf("Calculating partition function\n"); + double ** Q, **QM, **QB, **P; + Q = mallocTwoD(seq.length() + 1, seq.length() + 1); + QM = mallocTwoD(seq.length() + 1, seq.length() + 1); + QB = mallocTwoD(seq.length() + 1, seq.length() + 1); + P = mallocTwoD(seq.length() + 1, seq.length() + 1); + + + fill_partition_fn_arrays(seq.length(), Q, QB, QM); + fillBasePairProbabilities(seq.length(), Q, QB, QM, P); + printBasePairProbabilities(seq.length(), structure, P, bppOutFile.c_str()); + printf("Saved BPP output in %s\n",bppOutFile.c_str()); + + freeTwoD(Q, seq.length() + 1, seq.length() + 1); + freeTwoD(QM, seq.length() + 1, seq.length() + 1); + freeTwoD(QB, seq.length() + 1, seq.length() + 1); + freeTwoD(P, seq.length() + 1, seq.length() + 1); + } +*/ + // release the malloc'd arrays + //free_fold(seq.length()); +/* + dangle_struct partition; + partition = malloc_partition_arrays_d(seq.length()); + fill_partition_arrays_d(partition); + printf("Done with the partition functioni.\n"); +*/ + //return EXIT_SUCCESS; +//} diff --git a/gtfold-mfe/src/mfe_main.cc b/gtfold-mfe/src/mfe_main.cc new file mode 100644 index 0000000..0525ea2 --- /dev/null +++ b/gtfold-mfe/src/mfe_main.cc @@ -0,0 +1,448 @@ +/* + GTfold: compute minimum free energy of RNA secondary structure + Copyright (C) 2007-2011 David A. Bader, Christine E. Heitsch, + and Steve C. Harvey + http://www.cc.gatech.edu/~bader + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program. If not, see . + */ + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +#include "main.h" +#include "mfe_main.h" +#include "utils.h" +#include "loader.h" +//#include "options.h" +#include "global.h" +#include "energy.h" +#include "algorithms.h" +#include "constraints.h" +#include "traceback.h" +#include "shapereader.h" + +using namespace std; + +static bool PARAM_DIR = false; +//static bool LIMIT_DISTANCE; +static bool CONS_ENABLED = false; +static bool VERBOSE = false; +static bool SHAPE_ENABLED = false; +static bool T_MISMATCH = false; +static bool UNAMODE = false; +static bool RNAMODE = false; +static bool b_prefilter = false; + +static string seqfile = ""; +static string constraintsFile = ""; +static string outputPrefix = ""; +static string outputFile = ""; +static string outputDir = ""; +static string shapeFile = ""; +static string paramDir; // default value + +static int dangles=-1; +static int prefilter1=2; +static int prefilter2=2; + +static int nThreads = -1; +static int contactDistance = -1; + +static void help(); +void printRunConfiguration(string seq); +void parse_mfe_options(int argc, char** argv); + +void init_fold(const char* seq) { + assert(seq != NULL); + int len = strlen(seq); + + init_global_params(len); + + if (!encodeSequence(seq)) { + free_fold(len); + exit(0); + } + + create_tables(len); + + if (CONS_ENABLED) { + init_constraints(constraintsFile.c_str(), len); + } + + if (SHAPE_ENABLED) { + readSHAPEarray(shapeFile.c_str(),len); + } + + if (UNAMODE) { + if (T_MISMATCH) printf("Ignoring -m option, using --unafold\n"); + if (PARAM_DIR) printf("Ignoring -p option, using --unafold\n"); + if (dangles == 0 || dangles == 2) + printf("Ignoring -d option, using --unafold\n"); + if (b_prefilter == 1) + printf("Ignoring --prefilter option, using --unafold\n"); + T_MISMATCH = false; + PARAM_DIR = false; + dangles = -1; + b_prefilter = false; + } + + if (RNAMODE) { + if (T_MISMATCH) printf("Ignoring -m option, using --rnafold\n"); + if (PARAM_DIR) printf("Ignoring -p option, using --rnafold\n"); + if (dangles == 0 || dangles == 2) + printf("Ignoring -d option, using --rnafold\n"); + if (b_prefilter == 1) + printf("Ignoring --prefilter option, using --rnafold\n"); + T_MISMATCH = false; + PARAM_DIR = false; + dangles = -1; + b_prefilter = false; + } + + if ((dangles == 0 || dangles == 2) && !UNAMODE && !RNAMODE) { + if (T_MISMATCH) printf("Ignoring -m option, using -d option\n"); + T_MISMATCH = false; + } else { + if (dangles != -1 && !UNAMODE && !RNAMODE) printf("Ignoring -d as it accept 0 or 2 only\n"); + dangles = -1; + } + + g_nthreads = nThreads; + g_unamode = UNAMODE; + g_mismatch = T_MISMATCH; + g_verbose = VERBOSE; + g_prefilter_mode = b_prefilter; + g_prefilter1 = prefilter1; + g_prefilter2 = prefilter2; + g_dangles = dangles; + +#ifdef DEBUG + printf("g_nthreads = %d\n", g_nthreads); + printf("g_unamode = %d\n", g_unamode); + printf("g_mismatch = %d\n", g_mismatch); + printf("g_prefilter_mode = %d\n", g_prefilter_mode); + printf("g_dangles = %d\n", g_dangles); + +#endif + +} + +void free_fold(int len) { + if (CONS_ENABLED) + free_constraints(len); + if (SHAPE_ENABLED){ + free_shapeArray(len); + } + + free_tables(len); + free_global_params(); +} + + +int mfe_main(int argc, char** argv) { + std::string seq; + int energy; + + parse_mfe_options(argc, argv); + + if (read_sequence_file(seqfile.c_str(), seq) == FAILURE) { + printf("Failed to open sequence file: %s.\n\n", seqfile.c_str()); + exit(-1); + } + + init_fold(seq.c_str()); + + // Read in thermodynamic parameters. Always use Turner99 data (for now) + readThermodynamicParameters(paramDir.c_str(), PARAM_DIR, UNAMODE, RNAMODE, T_MISMATCH); + printRunConfiguration(seq); + + printf("\nComputing minimum free energy structure...\n"); + fflush(stdout); + + double t1 = get_seconds(); + energy = calculate(seq.length()) ; + t1 = get_seconds() - t1; + + printf("Done.\n\n"); + printf("Results:\n"); + if (energy >= MAXENG) + printf("- Minimum Free Energy: %12.4f kcal/mol\n", 0.00); + else + printf("- Minimum Free Energy: %12.4f kcal/mol\n", energy/100.00); + printf("- MFE runtime: %9.6f seconds\n", t1); + + t1 = get_seconds(); + trace(seq.length()); + t1 = get_seconds() - t1; + + printf("\n"); + print_sequence(seq.length()); + print_structure(seq.length()); + + if (CONS_ENABLED) + print_constraints(seq.length()); + + if (SHAPE_ENABLED && VERBOSE) + print_shapeArray(seq.length()); + + save_ct_file(outputFile, seq, energy); + printf("\nMFE structure saved in .ct format to %s\n", outputFile.c_str()); + + if(CONS_ENABLED && VERBOSE){ + printf("Verifying that structure fulfills constraint criteria... "); + if(verify_structure()){ + printf("OK\n"); + } + else{ + printf("ERROR: NOT OK!!\n"); + fprintf(stderr, "ERROR: Structure does not fulfill constraint criteria.\n"); + fprintf(stderr, "Structure file: %s\n", outputFile.c_str()); + fprintf(stderr, "Constraint file: %s\n", constraintsFile.c_str()); + } + } + + free_fold(seq.length()); + + return EXIT_SUCCESS; +} + + +void parse_mfe_options(int argc, char** argv) { + int i; + + for(i=1; i= 0 && !strcmp(ss.str().c_str(),argv[i])) { + //LIMIT_DISTANCE = true; + enable_limit_distance(true); + set_contact_distance(contactDistance); + } + else + help(); + } + else + help(); + }else if(strcmp(argv[i], "--prefix") == 0 || strcmp(argv[i], "-o") == 0) { + if(i < argc) + outputPrefix = argv[++i]; + else + help(); + } else if (strcmp(argv[i], "--workdir") == 0 || strcmp(argv[i], "-w") == 0) { + if(i < argc) + outputDir = argv[++i]; + else + help(); + } else if (strcmp(argv[i], "--paramdir") == 0 || strcmp(argv[i], "-p") == 0) { + if(i < argc) { + paramDir = argv[++i]; + PARAM_DIR = true; + } + else + help(); + } else if (strcmp(argv[i], "--dangle") == 0 || strcmp(argv[i], "-d") == 0) { + std::string cmd = argv[i]; + if(i < argc) { + dangles = atoi(argv[++i]); + if (!(dangles == 0 || dangles == 2)) { + dangles = -1; + printf("Ignoring %s option as it accepts either 0 or 2\n", cmd.c_str()); + } + } else + help(); + } else if (strcmp(argv[i], "-m") == 0 || strcmp(argv[i], "--mismatch") == 0) { + T_MISMATCH = true; + } else if (strcmp(argv[i], "--unafold") == 0) { + UNAMODE = true; + } else if (strcmp(argv[i], "--rnafold") == 0) { + RNAMODE = true; + } else if (strcmp(argv[i], "--prefilter") == 0) { + if(i < argc) { + prefilter1 = atoi(argv[++i]); + if (prefilter1 <= 0 ) { + printf("INVALID ARGUMENTS: --prefilter accepts positive integers\n\n"); + help(); + } + b_prefilter = true; + prefilter2 = prefilter1; + } else + help(); + } + else if(strcmp(argv[i], "--threads") == 0 || strcmp(argv[i], "-t") == 0) { + if(i < argc) + nThreads = atoi(argv[++i]); + else + help(); + } else if (strcmp(argv[i], "--verbose") == 0 || strcmp(argv[i], "-v") == 0) { + VERBOSE = true; + } + else if (strcmp(argv[i], "--useSHAPE") == 0){ + if( i < argc){ + shapeFile = argv[++i]; + SHAPE_ENABLED = true; + } + else + help(); + } + } else { + seqfile = argv[i]; + } + } + + // Must have an input file specified + if(seqfile.empty()) { + help(); + printf("Missing input file.\n"); + } + + // If no output file specified, create one + if(outputPrefix.empty()) { + // base it off the input file + outputPrefix += seqfile; + + size_t pos; + // extract file name from the path + if ((pos=outputPrefix.find_last_of('/')) > 0) { + outputPrefix = outputPrefix.substr(pos+1); + } + + // and if an extension exists, remove it ... + if(outputPrefix.find(".") != string::npos) + outputPrefix.erase(outputPrefix.rfind(".")); + } + + // If output dir specified + if (!outputDir.empty()) { + outputFile += outputDir; + outputFile += "/"; + } + // ... and append the .ct + outputFile += outputPrefix; + outputFile += ".ct"; + +} + + +void printRunConfiguration(string seq) { + bool standardRun = true; + + printf("Run Configuration:\n"); + if (RNAMODE == true) { + printf("+ running in rnafold mode\n"); + standardRun = false; + } + if (UNAMODE == true) { + printf("+ running in unafold mode\n"); + standardRun = false; + } + if (dangles == 0 || dangles == 2) { + printf("+ running in dangle %d mode\n", dangles); + standardRun = false; + } + if (T_MISMATCH == true) { + printf("+ enabled terminal mismatch calculations\n"); + standardRun = false; + } + if (b_prefilter == true) { + printf("+ running with prefilter value = %d\n",prefilter1); + standardRun = false; + } + + if(!constraintsFile.empty()) { + printf("- using constraint file: %s\n", constraintsFile.c_str()); + standardRun = false; + } + + if(!shapeFile.empty()){ + printf("- using SHAPE data file: %s\n", shapeFile.c_str()); + } + if (contactDistance != -1) { + printf("- maximum contact distance: %d\n", contactDistance); + standardRun = false; + } + + if(standardRun) + printf("- standard\n"); + + printf("- thermodynamic parameters: %s\n", EN_DATADIR.c_str()); + printf("- input file: %s\n", seqfile.c_str()); + printf("- sequence length: %d\n", (int)seq.length()); + printf("- output file: %s\n", outputFile.c_str()); +} + +static void help() { + printf("Usage: gtmfe [OPTION]... FILE\n\n"); + + printf(" FILE is an RNA sequence file containing only the sequence or in FASTA format.\n\n"); + + printf("OPTIONS\n"); + printf(" -c, --constraints FILE\n"); + printf(" Load constraints from FILE. See Constraint syntax below.\n"); + printf(" -d, --dangle INT Restricts treatment of dangling energies (INT=0,2),\n"); + printf(" see below for details.\n"); + printf(" -h, --help Output help (this message) and exit.\n"); + printf(" -l, --limitCD INT Set a maximum base pair contact distance to INT. If no\n"); + printf(" limit is given, base pairs can be over any distance.\n"); + printf(" -m --mismatch Enable terminal mismatch calculations\n"); +// printf(" -n, --noisolate Prevent isolated base pairs from forming.\n"); + printf(" -o, --output NAME Write output files with prefix given in NAME\n"); + printf(" -p --paramdir DIR Path to directory from which parameters are to be read\n"); + printf(" -t, --threads INT Limit number of threads used to INT.\n"); + printf(" -v, --verbose Run in verbose mode (includes loop-by-loop energy decomposition\n"); + printf(" and confirmation of constraints satisfied).\n"); + printf(" -w, --workdir DIR Path of directory where output files will be written.\n"); + printf(" --prefilter INT Prohibits any basepair which does not have appropriate\n"); + printf(" neighboring nucleotides such that it could be part of\n"); + printf(" a helix of length INT.\n"); + printf(" --rnafold Run as RNAfold default mode (ViennaPackage version 1.8.5).\n"); + printf(" --unafold Run as UNAfold default mode (version 3.8), subject to traceback\n"); + printf(" implementation.\n"); + + printf(" -s, --useSHAPE FILE Use SHAPE constraints from FILE.\n"); + + printf("\nConstraint syntax:\n"); + printf("\tF i j k # force (i,j)(i+1,j-1),.......,(i+k-1,j-k+1) pairs.\n"); + printf("\tP i j k # prohibit (i,j)(i+1,j-1),.......,(i+k-1,j-k+1) pairs.\n"); + printf("\tP i 0 k # make bases from i to i+k-1 single stranded bases.\n"); + + printf("\nDangle:\n"); + printf("\tINT=0 ignores dangling energies (mostly for debugging).\n"); + printf("\tINT=2 dangling energies are added for nucleotides on either\n"); + printf("\tside of each branch in multi-loops and external loops.\n"); + printf("\tAll other values for INT are ignored.\n"); + exit(-1); +} + diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc index 06c28c9..30889de 100644 --- a/gtfold-mfe/src/options.cc +++ b/gtfold-mfe/src/options.cc @@ -1,147 +1,292 @@ #include "loader.h" #include "options.h" +#include + using namespace std; bool ILSA; bool NOISOLATE; -bool USERDATA; -bool PARAMS; +bool PARAM_DIR = false; bool LIMIT_DISTANCE; bool BPP_ENABLED; bool SUBOPT_ENABLED; bool CONS_ENABLED = false; bool VERBOSE = false; +bool SHAPE_ENABLED = false; +bool T_MISMATCH = false; +bool UNAMODE = false; +bool RNAMODE = false; +bool b_prefilter = false; +bool CALC_PART_FUNC = false; +bool RND_SAMPLE = false; +bool PF_COUNT_MODE = false; string seqfile = ""; string constraintsFile = ""; +string outputPrefix = ""; string outputFile = ""; +string suboptFile = ""; +string bppOutFile = ""; +string outputDir = ""; +string shapeFile = ""; +string paramDir; // default value + +int num_rnd = 0; +int dangles=-1; +int prefilter1=2; +int prefilter2=2; -int suboptDelta = -1; +float suboptDelta = 0.0; int nThreads = -1; int contactDistance = -1; /** * Print the help message and quit. */ + +/* void help() { printf("Usage: gtfold [OPTION]... FILE\n\n"); - printf(" FILE is an RNA sequence file. Single line or FASTA formats are accepted.\n\n"); + printf(" FILE is an RNA sequence file containing only the sequence or in FASTA format.\n\n"); printf("OPTIONS\n"); printf(" -c, --constraints FILE\n"); - printf(" Load constraints from FILE. See Constraint syntax below\n"); - printf(" -d, --limitCD num Set a maximum base pair contact distance to num. If no\n"); - printf(" limit is given, base pairs can be over any distance\n"); - printf(" -n, --noisolate Prevent isolated base pairs from forming\n"); - printf(" -o, --output FILE Output to FILE (default output is to a .ct extension)\n"); - printf(" -t, --threads num Limit number of threads used\n"); - - printf("\n"); - printf(" -h, --help Output help (this message) and exit\n"); - printf(" -v, --verbose Run in verbose mode\n"); + printf(" Load constraints from FILE. See Constraint syntax below.\n"); + printf(" -d, --dangle INT Restricts treatment of dangling energies (INT=0,2),\n"); + printf(" see below for details.\n"); + printf(" -h, --help Output help (this message) and exit.\n"); + printf(" -l, --limitCD INT Set a maximum base pair contact distance to INT. If no\n"); + printf(" limit is given, base pairs can be over any distance.\n"); + printf(" -m --mismatch Enable terminal mismatch calculations\n"); +// printf(" -n, --noisolate Prevent isolated base pairs from forming.\n"); + printf(" -o, --output NAME Write output files with prefix given in NAME\n"); + printf(" -p --paramdir DIR Path to directory from which parameters are to be read\n"); + printf(" -t, --threads INT Limit number of threads used to INT.\n"); + printf(" -v, --verbose Run in verbose mode (includes loop-by-loop energy decomposition\n"); + printf(" and confirmation of constraints satisfied).\n"); + printf(" -w, --workdir DIR Path of directory where output files will be written.\n"); + printf(" --prefilter INT Prohibits any basepair which does not have appropriate\n"); + printf(" neighboring nucleotides such that it could be part of\n"); + printf(" a helix of length INT.\n"); + printf(" --rnafold Run as RNAfold default mode (ViennaPackage version 1.8.5).\n"); + printf(" --unafold Run as UNAfold default mode (version 3.8), subject to traceback\n"); + printf(" implementation.\n"); printf("\nBETA OPTIONS\n"); - printf(" --bpp Calculate base pair probabilities\n"); - printf(" --subopt range Calculate suboptimal structures within 'range' kcal/mol\n"); - printf(" of the mfe\n"); + printf(" --bpp Calculate base pair probabilities.\n"); + printf(" --partition Calculate the partition function.\n"); + printf(" --pf_count Calculate the structure count using partition function and zero energy value.\n"); + printf(" --subopt NUM Calculate suboptimal structures within NUM kcal/mol\n"); + printf(" of the MFE. (Uses -d 2 treatment of dangling energies.)\n"); + printf(" -s, --useSHAPE FILE Use SHAPE constraints from FILE.\n"); printf("\nConstraint syntax:\n"); - printf("\tF i j k # force (i,j)(i+1,j-1),.......,(i+k-1,j-k+1) pairs\n"); - printf("\tP i j k # prohibit (i,j)(i+1,j-1),.......,(i+k-1,j-k+1) pairs\n"); + printf("\tF i j k # force (i,j)(i+1,j-1),.......,(i+k-1,j-k+1) pairs.\n"); + printf("\tP i j k # prohibit (i,j)(i+1,j-1),.......,(i+k-1,j-k+1) pairs.\n"); printf("\tP i 0 k # make bases from i to i+k-1 single stranded bases.\n"); + + printf("\nDangle:\n"); + printf("\tINT=0 ignores dangling energies (mostly for debugging).\n"); + printf("\tINT=2 dangling energies are added for nucleotides on either\n"); + printf("\tside of each branch in multi-loops and external loops.\n"); + printf("\tAll other values for INT are ignored.\n"); exit(-1); } +*/ /** * Parse the options from argc and argv and save them into global state. */ +/* void parse_options(int argc, char** argv) { - int i; - - for(i=1; i= 0 && !strcmp(ss.str().c_str(),argv[i])) + LIMIT_DISTANCE = true; + else + help(); + } + else + help(); + } else if(strcmp(argv[i], "--noisolate") == 0 || strcmp(argv[i], "-n") == 0) { + NOISOLATE = true; + } else if(strcmp(argv[i], "--prefix") == 0 || strcmp(argv[i], "-o") == 0) { + if(i < argc) + outputPrefix = argv[++i]; + else + help(); + } else if (strcmp(argv[i], "--workdir") == 0 || strcmp(argv[i], "-w") == 0) { + if(i < argc) + outputDir = argv[++i]; + else + help(); + } else if (strcmp(argv[i], "--paramdir") == 0 || strcmp(argv[i], "-p") == 0) { + if(i < argc) { + paramDir = argv[++i]; + PARAM_DIR = true; + } + else + help(); + } else if (strcmp(argv[i], "--dangle") == 0 || strcmp(argv[i], "-d") == 0) { + std::string cmd = argv[i]; + if(i < argc) { + dangles = atoi(argv[++i]); + if (!(dangles == 0 || dangles == 2)) { + dangles = -1; + printf("Ignoring %s option as it accepts either 0 or 2\n", cmd.c_str()); + } + } else + help(); + } else if (strcmp(argv[i], "-m") == 0 || strcmp(argv[i], "--mismatch") == 0) { + T_MISMATCH = true; + } else if (strcmp(argv[i], "--unafold") == 0) { + UNAMODE = true; + } else if (strcmp(argv[i], "--rnafold") == 0) { + RNAMODE = true; + } else if (strcmp(argv[i], "--prefilter") == 0) { + if(i < argc) { + prefilter1 = atoi(argv[++i]); + if (prefilter1 <= 0 ) { + printf("INVALID ARGUMENTS: --prefilter accepts positive integers\n\n"); + help(); + } + b_prefilter = true; + prefilter2 = prefilter1; + } else + help(); + } + else if(strcmp(argv[i], "--threads") == 0 || strcmp(argv[i], "-t") == 0) { + if(i < argc) + nThreads = atoi(argv[++i]); + else + help(); + } else if (strcmp(argv[i], "--verbose") == 0 || strcmp(argv[i], "-v") == 0) { + VERBOSE = true; + } + else if(strcmp(argv[i], "--bpp") == 0) { + BPP_ENABLED = true; + } else if(strcmp(argv[i], "--subopt") == 0) { + SUBOPT_ENABLED = true; + dangles = 2; + if(i < argc) + suboptDelta = atof(argv[++i]); + else + help(); + } else if (strcmp(argv[i],"--partition") == 0) { + CALC_PART_FUNC = true; + } else if (strcmp(argv[i],"--pf_count") == 0) { + CALC_PART_FUNC = true; + PF_COUNT_MODE = true; + } else if (strcmp(argv[i],"--sample") == 0) { + RND_SAMPLE = true; + if(i < argc) + num_rnd = atoi(argv[++i]); + else + help(); + } + else if (strcmp(argv[i], "--useSHAPE") == 0){ + if( i < argc){ + shapeFile = argv[++i]; + SHAPE_ENABLED = true; + } + else + help(); + } + } else { + seqfile = argv[i]; + } + } - // If no output file specified, create one - if(outputFile.empty()) { + // Must have an input file specified + if(seqfile.empty()) { + help(); + printf("Missing input file.\n"); + } - // base it off the input file - outputFile += seqfile; - - size_t pos; - // extract file name from the path - if ((pos=outputFile.find_last_of('/')) > 0) { - outputFile = outputFile.substr(pos+1); - } + // If no output file specified, create one + if(outputPrefix.empty()) { + // base it off the input file + outputPrefix += seqfile; - // and if an extension exists, remove it ... - if(outputFile.find(".") != string::npos) - outputFile.erase(outputFile.rfind(".")); + size_t pos; + // extract file name from the path + if ((pos=outputPrefix.find_last_of('/')) > 0) { + outputPrefix = outputPrefix.substr(pos+1); + } - // ... and append the .ct - outputFile += ".ct"; - } -} + // and if an extension exists, remove it ... + if(outputPrefix.find(".") != string::npos) + outputPrefix.erase(outputPrefix.rfind(".")); + } + + // If output dir specified + if (!outputDir.empty()) { + outputFile += outputDir; + outputFile += "/"; + suboptFile += outputDir; + suboptFile += "/"; + bppOutFile += outputDir; + bppOutFile += "/"; + } + // ... and append the .ct + outputFile += outputPrefix; + outputFile += ".ct"; + + suboptFile += outputPrefix; + suboptFile += "_ss.txt"; + bppOutFile += outputPrefix; + bppOutFile += "_bpp.txt"; +} +*/ /** * Prints the run configuration for this run. * * The lines that start with a '-' are normal options, the '+' are beta options. */ +/* void printRunConfiguration(string seq) { bool standardRun = true; printf("Run Configuration:\n"); - + if (RNAMODE == true) { + printf("+ running in rnafold mode\n"); + standardRun = false; + } + if (UNAMODE == true) { + printf("+ running in unafold mode\n"); + standardRun = false; + } + if (dangles == 0 || dangles == 2) { + printf("+ running in dangle %d mode\n", dangles); + standardRun = false; + } + if (T_MISMATCH == true) { + printf("+ enabled terminal mismatch calculations\n"); + standardRun = false; + } + if (b_prefilter == true) { + printf("+ running with prefilter value = %d\n",prefilter1); + standardRun = false; + } if (NOISOLATE == true) { printf("- preventing isolated base pairs\n"); standardRun = false; @@ -152,6 +297,9 @@ void printRunConfiguration(string seq) { standardRun = false; } + if(!shapeFile.empty()){ + printf("- using SHAPE data file: %s\n", shapeFile.c_str()); + } if (contactDistance != -1) { printf("- maximum contact distance: %d\n", contactDistance); standardRun = false; @@ -159,11 +307,13 @@ void printRunConfiguration(string seq) { if (BPP_ENABLED == true) { printf("+ calculating base pair probabilities\n"); + printf("+ BPP output file: %s\n", bppOutFile.c_str()); standardRun = false; } if (SUBOPT_ENABLED) { - printf("+ calculating suboptimal structures within %d kcal/mol of MFE\n", suboptDelta); + printf("+ calculating suboptimal structures within %f kcal/mol of MFE\n", suboptDelta); + printf("+ suboptimal structures file: %s\n", suboptFile.c_str()); standardRun = false; } @@ -172,7 +322,7 @@ void printRunConfiguration(string seq) { printf("- thermodynamic parameters: %s\n", EN_DATADIR.c_str()); printf("- input file: %s\n", seqfile.c_str()); - printf(" - sequence length: %d\n", (int)seq.length()); - printf(" - sequence contents: %s\n", seq.c_str()); + printf("- sequence length: %d\n", (int)seq.length()); printf("- output file: %s\n", outputFile.c_str()); } +*/ diff --git a/gtfold-mfe/src/partition-dangle.c b/gtfold-mfe/src/partition-dangle.c new file mode 100644 index 0000000..df677fc --- /dev/null +++ b/gtfold-mfe/src/partition-dangle.c @@ -0,0 +1,197 @@ +//Attempting to follow Ding and Lawrence as closely as possible + +/**s1 -> partial_external +* s2 -> partial_multi +* s3 -> partial_multi2 +* u1 -> u_multi +* f -> cond_dangle (conditional) +* ebi -> eL +**/ + +#include +#include + +#include "energy.h" +#include "utils.h" +#include "global.h" +#include "data.h" +#include "algorithms-partition.h" +#include "partition-dangle.h" + +#define MIN_TURN 4 +#define MAX_LOOP 30 + +//double RT = (0.00198721 * 310.15)/100.00; + +double cond_dangle(int j, int h, int l){ + if(j - 1 == l) + return 1; + else + return exp(-Ed3(h,l,l+1)/RT); +} + +dangle_struct malloc_partition_arrays_d(int length){ + dangle_struct ret_struct; + ret_struct.length = length; + + //Add 1 since we're not zero indexed + ret_struct.u = mallocTwoD(length + 1, length + 1); + ret_struct.up = mallocTwoD(length + 1, length + 1); + ret_struct.upm = mallocTwoD(length + 1, length + 1); + ret_struct.u1 = mallocTwoD(length + 1, length + 1); + ret_struct.s1 = mallocTwoD(length + 1, length + 1); + ret_struct.s2 = mallocTwoD(length + 1, length + 1); + ret_struct.s3 = mallocTwoD(length + 1, length + 1); + + int i,j; + + for(i = 0; i < length + 1; i++){ + for(j = 0; j < length + 1; j++){ + ret_struct.u[i][j] = 1; + ret_struct.up[i][j] = 0; + ret_struct.upm[i][j] = 0; + ret_struct.u1[i][j] = 0; + ret_struct.s1[i][j] = 0; + ret_struct.s2[i][j] = 0; + ret_struct.s3[i][j] = 0; + } + } + return ret_struct; +} + +void free_partition_arrays_d(struct partition_d part) +{ + freeTwoD(part.u, part.length, part.length); + freeTwoD(part.up, part.length, part.length); + freeTwoD(part.upm, part.length, part.length); + freeTwoD(part.u1, part.length, part.length); + freeTwoD(part.s1, part.length, part.length); + freeTwoD(part.s2, part.length, part.length); + freeTwoD(part.s3, part.length, part.length); +} + +void fill_partition_arrays_d(dangle_struct part_struct){ + //So that we don't have the /100 in every exponent + //Seeing as we missed some last time + + double ** partial_external = part_struct.s1; + double ** partial_multi = part_struct.s2; + double ** partial_multi2 = part_struct.s3; + double ** u_multi = part_struct.u1; + double ** u = part_struct.u; + double ** up = part_struct.up; + double ** upm = part_struct.upm; + int len = part_struct.length; + + int seg_length; + int i,j; + + for(seg_length = MIN_TURN; seg_length <= len; len++){ + //Insert parallelism here. + for(i = 1; i < len - seg_length; i++){ + j = i + seg_length - 1; + + int l; + if(canPair(i,j)){ + for(l = i+2; l < j; l++){ + upm[i][j] += up[i+1][l] * exp(-(Ea + 2 * Ec + auPenalty(i + 1,l)/RT)) * + (exp(-Ed3(i + 1,l,l+1)/RT) * u_multi[l + 2][j - 1] + + u_multi[l + 1][j - 1] - + u_multi[l + 2][j - 1]); + if(l != i+2){ //goes from i + 2 < l < j + upm[i][j] += up[i + 2][l] * + exp(-(Ea + 2 * Ec + Eb + Ed3(j,i,i + 1) + auPenalty(i + 2, l))/RT) * + (exp(-Ed3(i + 2,l,l + 1)/RT)*u_multi[l + 2][j - 1] + + u_multi[l + 1][j - 1] - + u_multi[l + 2][j - 1]); + + if(l != j - 1){ + upm[i][j] += exp(-Ed3(j,i,i + 1)/RT)*exp(-(Ea + 2 * Ec + (l - i - 1) * Eb)/RT) * + partial_multi[l][j]; + //Changed h in the paper to l it makes no difference + //other than unifying loops + } + } + } + + + up[i][j] += exp(-eH(i,j)/RT) + exp(-eS(i,j)/RT) * up[i + 1][j - 1] + upm[i][j]; + for(l = j - 1; l > i + 1; l--){ + if((j - l) - 2> MAX_LOOP){ + break; + } + int h; + for(h = i + 1 ; h < l; h++){ + if(!(i == h - 1 && j == l - 1)){ //If this is true we have a stack + up[i][j] += exp(-eL(i,j,h,l)/RT); + } + if((j - l) + (h - i) - 2 > MAX_LOOP){ + break; + } + } + } + }//End checkpair conditional + + for(l = i + 1; l <= j ; l++){ + u_multi[i][j] += up[i][l] * exp(-(Ec + auPenalty(i,l))/RT) * + (cond_dangle(j + 1,i,l) * exp(-(j - l) * Eb/RT) + + exp(-Ed3(i,l,l + 1)/RT) * u_multi[l + 2][j] + + u_multi[l + 1][j] - + u_multi[l + 2][j]); + if(l != i+1){ + u_multi[i][j] += up[i + 1][j]*exp(-(Ec + Eb + auPenalty(i + 1,l))/RT)* + (cond_dangle(j + 1, i + 1, l) * exp(-(j - l)*Eb/RT) + + exp(-Ed3(i + 1,l,l + 1)/RT) * u_multi[l + 2][j] + + u_multi[l + 1][j] - + u_multi[l + 2][j]); + if(l != j){ + u_multi[i][j] += exp(-(Ec + (l - i) * Eb)/RT) * partial_multi2[l][j]; + + } + } + } + + + int h = i; //To stay consistant with the notation in the paper. + + for(l = h+1; l < j; l++){ + partial_external[h][j] += up[h][l] * exp( -(Ed5(h,l,h - 1) + auPenalty(h,l)) / RT) * + (exp(-Ed3(h,l,l + 1)/RT)*u[l + 2][j - 1] + + u[l + 1][j] - + u[l + 2][j]); + + partial_multi[h][j] += up[h][l] * exp( -(Ed5(h,l,h - 1) + auPenalty(h,l)) / RT) * + (exp(-Ed3(h,l,l + 1)/RT)*u_multi[l + 2][j - 1] + + u_multi[l + 1][j - 1] - + u_multi[l + 2][j - 1]); + + partial_multi2[h][j] += up[h][l] * exp( -(Ed5(h,l,h - 1) + auPenalty(h,l)) / RT) * + (cond_dangle(j + 1, h, l)*exp(-(j - l) * Eb / RT) + + exp(-Ed3(h,l,l + 1)/RT)*u_multi[l + 2][j] + + u_multi[l + 1][j] - + u_multi[l + 2][j]); + + } + /** partial_multi2 goes up to j **/ + partial_multi2[h][j] += up[h][l] * exp( -(Ed5(h,l,h - 1) + auPenalty(h,l)) / RT) * + (cond_dangle(j + 1, h, l)*exp(-(j-l) * Eb / RT) + + exp(-Ed3(h,l,l + 1)/RT) * u_multi[l + 2][j] + + u_multi[l + 1][j] - + u_multi[l + 2][j]); + + //Finally we do the u matrix + u[i][j] = 1 + up[i][j]*exp(-auPenalty(i,j) /RT); + + for(l = i + 1; l < j; l++){ + //Replaced l with h in the next line to unify loops + u[i][j] += up[l][j] * exp(-(Ed5(l, j , l - 1) + auPenalty(h,j))/RT); + + u[i][j] += exp(-(auPenalty(i,l))/RT)*(exp(-Ed3(i,l,l + 1)/RT) * u[l + 2][j] + + u[l + 1][j] - u[l + 2][j]); + if(l != j - 1) { + u[i][j] += partial_external[l][j]; + } + } + }//end of minor (paralellizeable) for loop + }//End of major for loop +} diff --git a/gtfold-mfe/src/partition-func.c b/gtfold-mfe/src/partition-func.c new file mode 100644 index 0000000..4547364 --- /dev/null +++ b/gtfold-mfe/src/partition-func.c @@ -0,0 +1,820 @@ +#include +#include +#include +#include "partition-func.h" +#include "energy.h" +#include "algorithms-partition.h" +#include "global.h" +#include "utils.h" +#include +//#include "options.h" + +double ** u; +double ** up; +double ** upm; +double ** ud; +double ** u1d; + +double ** s1; +double ** s2; +double ** s3; +double ** u1; + +int part_len; +int PF_COUNT_MODE_; + +static void create_partition_arrays(); +static void init_partition_arrays(); +static void fill_partition_arrays(); +static void free_partition_arrays(); + +static void calc_u(int i, int j); +static void calc_ud(int i, int j); +static void calc_up(int i, int j); +static void calc_upm(int i, int j); +static void calc_u1(int i, int j); +static void calc_u1d(int i, int j); +static void calc_s1(int i, int j); +static void calc_s2(int i, int j); +static void calc_s3(int i, int j); + +static double get_u(int i, int j); +static double get_ud(int i, int j); +static double get_up(int i, int j); +static double get_upm(int i, int j); +static double get_u1(int i, int j); +static double get_u1d(int i, int j); +static double get_s1(int i, int j); +static double get_s2(int i, int j); +static double get_s3(int i, int j); + + +static void set_u(int i, int j, double val); +static void set_ud(int i, int j, double val); +static void set_up(int i, int j, double val); +static void set_upm(int i, int j, double val); +static void set_u1(int i, int j, double val); +static void set_u1d(int i, int j, double val); +static void set_s1(int i, int j, double val); +static void set_s2(int i, int j, double val); +static void set_s3(int i, int j, double val); + + +void errorAndExit(char* msg, int i, int j, double oldVal, double newVal){ + printf("%s", msg); + printf("i=%d,j=%d,oldVal=%0.1f,newVal=%0.1f\n",i,j,oldVal,newVal); + printf("%s","\nprogram is exiting now due to above error\n"); + exit(-1); +} + +double get_u(int i, int j) {if(u[i][j]==-1) errorAndExit("get_u entry is -1.",i,j,-1,0); return u[i][j];} +double get_ud(int i, int j) {if(ud[i][j]==-1) errorAndExit("get_ud entry is -1.\n",i,j,-1,0); return ud[i][j];} +double get_up(int i, int j) {if(up[i][j]==-1) errorAndExit("get_up entry is -1.\n",i,j,-1,0); return up[i][j];} +double get_upm(int i, int j) {if(upm[i][j]==-1) errorAndExit("get_upm entry is -1.\n",i,j,-1,0); return upm[i][j];} +double get_u1(int i, int j) {if(u1[i][j]==-1) errorAndExit("get_u1 entry is -1.\n",i,j,-1,0); return u1[i][j];} +double get_u1d(int i, int j) {if(u1d[i][j]==-1) errorAndExit("get_u1d entry is -1.\n",i,j,-1,0); return u1d[i][j];} +double get_s1(int i, int j) {if(s1[i][j]==-1) errorAndExit("get_s1 entry is -1.\n",i,j,-1,0); return s1[i][j];} +double get_s2(int i, int j) {if(s2[i][j]==-1) errorAndExit("get_s2 entry is -1.\n",i,j,-1,0); return s2[i][j];} +double get_s3(int i, int j) {if(s3[i][j]==-1) errorAndExit("get_s3 entry is -1.\n",i,j,-1,0); return s3[i][j];} + + +void set_u(int i, int j, double val) {if(u[i][j]!=-1 && u[i][j]!=val) errorAndExit("set_u entry is not -1.\n",i,j,u[i][j],val); u[i][j]=val;} +void set_ud(int i, int j, double val) {if(ud[i][j]!=-1 && ud[i][j]!=val) errorAndExit("set_ud entry is not -1.\n",i,j,ud[i][j],val); ud[i][j]=val;} +void set_up(int i, int j, double val) {if(up[i][j]!=-1 && up[i][j]!=val) errorAndExit("set_up entry is not -1.\n",i,j,up[i][j],val); up[i][j]=val;} +void set_upm(int i, int j, double val) {if(upm[i][j]!=-1 && upm[i][j]!=val) errorAndExit("set_upm entry is not -1.\n",i,j,upm[i][j],val); upm[i][j]=val;} +void set_u1(int i, int j, double val) {if(u1[i][j]!=-1 && u1[i][j]!=val) errorAndExit("set_u1 entry is not -1.\n",i,j,u1[i][j],val); u1[i][j]=val;} +void set_u1d(int i, int j, double val) {if(u1d[i][j]!=-1 && u1d[i][j]!=val) errorAndExit("set_u1d entry is not -1.\n",i,j,u1d[i][j],val); u1d[i][j]=val;} +void set_s1(int i, int j, double val) {if(s1[i][j]!=-1 && s1[i][j]!=val) errorAndExit("set_s1 entry is not -1.\n",i,j,s1[i][j],val); s1[i][j]=val;} +void set_s2(int i, int j, double val) {if(s2[i][j]!=-1 && s2[i][j]!=val) errorAndExit("set_s2 entry is not -1.\n",i,j,s2[i][j],val); s2[i][j]=val;} +void set_s3(int i, int j, double val) {if(s3[i][j]!=-1 && s3[i][j]!=val) errorAndExit("set_s3 entry is not -1.\n",i,j,s3[i][j],val); s3[i][j]=val;} + +double myExp(double arg){ + double posArgMultRT = (-1)*arg*RT; + if(posArgMultRT>=INFINITY_){ + //printf("WARN: posArgMultRT is greater than or equal to INFINITY_, hence returning zero\n"); + return 0; + } + return exp(arg); +} + +double eS_new(int i, int j){ + if(PF_COUNT_MODE_) return 0; + return eS(i,j); +} + +double eH_new(int i, int j){ + if(PF_COUNT_MODE_) return 0; + return eH(i,j); +} + +double eL_new(int i, int j, int p, int q){ + if(PF_COUNT_MODE_) return 0; + return eL(i,j,p,q); +} + +double ED3_new(int i, int j, int k){ + if(PF_COUNT_MODE_) return 0; + //if (j-i > TURN && canPair(RNA[i],RNA[j])) { + // assert(Ed5(j,i,k)<0.1); + //} + return Ed5(j,i,k); +} + +double ED5_new(int i, int j, int k){ + if(PF_COUNT_MODE_) return 0; + if (k<1) return 0; + + //if (j-i > TURN && canPair(RNA[i],RNA[j])) { + // assert(Ed3(j,i,k)<0.1); + //} + return Ed3(j,i,k); +} + +double EA_new(){ + if(PF_COUNT_MODE_) return 0; + return Ea; +} + +double EB_new(){ + if(PF_COUNT_MODE_) return 0; + return Ec; +} + +double EC_new(){ + if(PF_COUNT_MODE_) return 0; + return Eb; +} + +double auPenalty_new(int i, int j){ + if(PF_COUNT_MODE_) return 0; + return auPenalty(i,j); +} + +double f(int j, int h, int l){ + if(j - 1 == l) + return 1; + else + return myExp(-ED3_new(h,l,l+1)/RT); +} + +void printMatrix(double** u, int part_len){ + int i,j; + for (i = 0; i <= part_len+1; ++i) + { + for (j = 0; j <= part_len+1; ++j) + printf("%0.1f ",u[i][j]); + printf("\n"); + } +} + +void printAllMatrixes(){ + printf("\n\nAfter calculation, u matrix:\n\n"); + printMatrix(u,part_len); + printf("\n\nAfter calculation, ud matrix:\n\n"); + printMatrix(ud,part_len); + printf("\n\nAfter calculation, up matrix:\n\n"); + printMatrix(up,part_len); + printf("\n\nAfter calculation, upm matrix:\n\n"); + printMatrix(upm,part_len); +printf("\n\nAfter calculation, u1 matrix:\n\n"); + printMatrix(u1,part_len); +printf("\n\nAfter calculation, u1d matrix:\n\n"); + printMatrix(u1d,part_len); +printf("\n\nAfter calculation, s1 matrix:\n\n"); + printMatrix(s1,part_len); +printf("\n\nAfter calculation, s2 matrix:\n\n"); + printMatrix(s2,part_len); +printf("\n\nAfter calculation, s3 matrix:\n\n"); + printMatrix(s3,part_len); + +} + +double calculate_partition(int len, int pf_count_mode) +{printf("RT=%f\n",RT);//RT=RT/100; + PF_COUNT_MODE_ = pf_count_mode; + //int i, j; + part_len = len; + create_partition_arrays(); + init_partition_arrays(); + + /*printf("\nAfter initialization but before calculation, u matrix:\n\n"); + for (i = 0; i <= part_len+1; ++i) + { + for (j = 0; j <= part_len+1; ++j) + printf("%0.1f ",u[i][j]); + printf("\n"); + } + + printf("%4.4f\n",u[1][part_len]);*/ + + fill_partition_arrays(); + + //printAllMatrixes(); + + printf("%4.4f\n",u[1][part_len]); + + return u[1][part_len]; +} + +void free_partition() +{ + free_partition_arrays(); +} + +void init_part_arrays_zeros(){ + int i,j,n; + n = part_len+1; + for(i=0; i<=n; ++i){ + for(j=0; j<=n; ++j){ + u[i][j]=0; + up[i][j]=0; + upm[i][j]=0; + ud[i][j]=0; + u1d[i][j]=0; + + s1[i][j]=0; + s2[i][j]=0; + s3[i][j]=0; + u1[i][j]=0; + } + } +} + +void init_part_arrays_ones(){ + int i,j,n; + n = part_len+1; + for(i=0; i<=n; ++i){ + for(j=0; j<=n; ++j){ + u[i][j]=1; + up[i][j]=1; + upm[i][j]=1; + ud[i][j]=1; + u1d[i][j]=1; + + s1[i][j]=1; + s2[i][j]=1; + s3[i][j]=1; + u1[i][j]=1; + } + } +} + + +void init_part_arrays_negatives(){ + int i,j,n; + n = part_len+1; + for(i=0; i<=n; ++i){ + for(j=0; j<=n; ++j){ + u[i][j]=-1; + up[i][j]=-1; + upm[i][j]=-1; + ud[i][j]=-1; + u1d[i][j]=-1; + + s1[i][j]=-1; + s2[i][j]=-1; + s3[i][j]=-1; + u1[i][j]=-1; + } + } + for(i=0; i<=n+1; ++i){ + for(j=0; j<=n+1; ++j){ + u1[i][j]=-1; + } + } +} + +void init_partition_arrays() +{//ERROR_FOUND first nested for loop was wrongly written and iterated + //init_part_arrays_zeros(); + //init_part_arrays_ones(); + init_part_arrays_negatives(); + + int i, j; + int n = part_len; + for(i=1; i<=n; ++i){ + for(j=i; j<=i+TURN && j<=n; ++j){ //if(j>n)continue; + u[i][j] = 1; + up[i][j] = 0; + ud[i][j] = 0; + u1[i][j] = 0; + u1d[i][j] =0 ; + s1[i][j] = 0; + s2[i][j] = 0; + s3[i][j] = 0; + } + } + for(i=1; (i+TURN)<=n; ++i){ + //s1[i][i+TURN] = 0; + //s2[i][i+TURN] = 0; + } + + for(i=1; (i+TURN+1)<=n; ++i){//ERROR no need to do this as it will already be calculated as zero only + //s1[i][i+TURN+1] = 0; + //s2[i][i+TURN+1] = 0; + } + + /*for(i=1; i<=n-4; ++i){ + s1[i][i+4] = 0; + s2[i][i+4] = 0; + }*/ + for(i=1; i<=n; ++i){ + u[i+1][i] = 1; + u1[i+1][i] = 0; + u1d[i+1][i] = 0; + } + for(i=1; i<=n; i++){//for(i=1; i<=n-1; i++){ + u1[i+2][i] = 0; + } + +} + +/* +void init_partition_arrays() +{ + //init_part_arrays_zeros(); + init_part_arrays_negatives(); + + int i, j; + int n = part_len; + for(i=1; i<=n-3; ++i){ + for(j=i; j<=i+3; ++j){ + u[i][j] = 1; + up[i][j] = 0; + ud[i][j] = 0; + u1[i][j] = 0; + u1d[i][j] =0 ; + s1[i][j] = 0; + s2[i][j] = 0; + s3[i][j] = 0; + } + } + for(i=1; i<=n-4; ++i){ + s1[i][i+4] = 0; + s2[i][i+4] = 0; + } + for(i=1; i<=n; ++i){ + u[i+1][i] = 1; + u1[i+1][i] = 0; + u1d[i+1][i] = 0; + } + for(i=1; i<=n-1; i++){ + u1[i+2][i] = 0; + } +}*/ +/* +void fill_partition_arrays() +{ + int b,i,j; + int n=part_len; + for(b=TURN+1; b TURN) + { + for(l=i+2; l TURN) + { + for (p = i+1; p <= MIN(j-2-TURN,i+MAXLOOP+1) ; p++) { + int minq = j-i+p-MAXLOOP-2; + if (minq < p+1+TURN) minq = p+1+TURN; + int maxq = (p==(i+1))?(j-2):(j-1); + + for (q = minq; q <= maxq; q++) { + if (canPair(p,q)==0) continue; + up_val += (up[p][q] * myExp(-eL_new(i,j,p,q)/RT)); + } + } + + up_val = up_val * myExp(-ED3_new(i,j,i+1)/RT); + up_val = up_val + myExp(-eH_new(i,j)/RT ); + up_val = up_val + myExp(-eS_new(i,j)/RT ) * up[i+1][j-1]; + up_val = up_val + upm[i][j]; + + up[i][j] = up_val; + } + else { + up[i][j] = 0; + } +}*/ + +void printUPprobabilities(int i, int j){ + int h,l; + double maxIntLoopProb = 0.0; + int h_max=-1, l_max=-1; + double sum=0.0; + for (h = i+1; h < j ; h++) { + for (l = h+1; l < j; l++) { + if (canPair(RNA[h],RNA[l])==0) continue; + if(h==(i+1) && l==(j-1)) continue; + //if((l-h)<=TURN) continue; + double intLoopProb = (get_up(h,l) * myExp(-((double)eL_new(i,j,h,l))/RT))/up[i][j]; + sum+=intLoopProb; + if(intLoopProb > maxIntLoopProb){ maxIntLoopProb = intLoopProb; h_max=h; l_max=l;} + } + } + + //ERROR below line should not be there + //up_val = up_val * myExp(-ED3_new(i,j,i+1)/RT); + double hpProb = myExp(-((double)eH_new(i,j))/RT )/up[i][j]; + double stackProb = (myExp(-((double)eS_new(i,j))/RT ) * get_up(i+1,j-1))/up[i][j]; + double upmProb = get_upm(i,j)/up[i][j]; + + if(maxIntLoopProb>=hpProb && maxIntLoopProb>=stackProb && maxIntLoopProb >=upmProb) printf("INT "); + else if(hpProb>=maxIntLoopProb && hpProb>=stackProb && hpProb>=upmProb) printf("HPL "); + else if(stackProb>=hpProb && stackProb>=maxIntLoopProb && stackProb>=upmProb) printf("STK "); + else if(upmProb>=hpProb && upmProb>=stackProb && upmProb>=maxIntLoopProb) printf("UPM "); + + printf("printing probabilities: i=%d, j =%d, upmProb=%.6f, stackProb=%.6f, hpProb=%.6f, maxIntLoopProb=%.6f, sumIntLoopProbs=%.6f, h_max=%d, l_max=%d\n",i,j, upmProb, stackProb, hpProb, maxIntLoopProb,sum,h_max,l_max); + +} + +void calc_up(int i, int j) +{//printf("Entering calc_up: i=%d, j =%d\n",i,j); + double up_val = 0.0; + //int p,q; + + if (canPair(RNA[i],RNA[j]))// if(j-i>TURN) + { + int h,l; + for (h = i+1; h < j ; h++) { + for (l = h+1; l < j; l++) { + if (canPair(RNA[h],RNA[l])==0) continue; + if(h==(i+1) && l==(j-1)) continue; + up_val += (get_up(h,l) * myExp(-((double)eL_new(i,j,h,l))/RT)); + } + } + + //ERROR below line should not be there + //up_val = up_val * myExp(-ED3_new(i,j,i+1)/RT); + up_val = up_val + myExp(-((double)eH_new(i,j))/RT ); + up_val = up_val + (myExp(-((double)eS_new(i,j))/RT ) * get_up(i+1,j-1)); + up_val = up_val + get_upm(i,j); + + set_up(i, j, up_val);//up[i][j] = up_val; + + } + else { + set_up(i, j, 0.0);//up[i][j] = 0; + } +} diff --git a/gtfold-mfe/src/random-sample.cc b/gtfold-mfe/src/random-sample.cc new file mode 100644 index 0000000..c336b68 --- /dev/null +++ b/gtfold-mfe/src/random-sample.cc @@ -0,0 +1,559 @@ +#include +#include +#include + +#include "partition-dangle.h" +#include "algorithms-partition.h" +#include "energy.h" +#include "random-sample.h" + +using namespace std; + +#define MIN_TURN 4 + +//double RT=(0.00198721 * 310.15)/100.00; + + +//I don't know why not having this function +//gives me a link error it should get this function +//from partition-dangle + +/*double cond_dangle(int j, int h, int l){ + if(j - 1 == l) + return 1; + else + return exp(-Ed3(h,l,l+1)/RT); +}*/ + +double randdouble(){ + return rand()/(double(RAND_MAX)+1); +} + +//P_0 +double single_stranded_prob(int i, int j, dangle_struct d_struct){ + return 1 / d_struct.u[i][j]; +} + +//P_{ij} +double ends_pair_prob(int i, int j, dangle_struct d_struct){ + return d_struct.up[i][j] * exp(-auPenalty(i,j)/RT)/d_struct.u[i][j]; +} + +//P_{hj} +double prob_h_pairs_with_5_end + (int i, int h, int j, dangle_struct d_struct){ + + return d_struct.up[h][j] * + exp(-(Ed5(h,j,h - 1) + + auPenalty(h,j))/RT) / + d_struct.u[i][j]; +} + +//P_{il} +double prob_l_pairs_with_3_end + (int i, int l, int j, dangle_struct d_struct){ + + return d_struct.up[i][l] * exp(-auPenalty(i,l)/RT) * + (exp(-Ed3(i,l,l+1)/RT) * d_struct.u[l + 2][j] + + d_struct.u[l + 1][j] - + d_struct.u[l + 2][j]) / + d_struct.u[i][j]; +} + +//P_{s1h} +double prob_h_pairs_in_ij(int i, int h, int j, dangle_struct d_struct){ + return d_struct.s1[h][j] / d_struct.u[i][j]; +} + +//P_{hl} +//This is the probability h pairs with l +//**Given that h pairs before j** +double prob_h_pairs_with_l(int h, int l, int j, dangle_struct d_struct){ + return d_struct.up[h][l] * exp(-(Ed5(h,l,h - 1) + auPenalty(h,l))/RT) * + (exp(-Ed3(h,l,l + 1)/RT) * d_struct.u[l + 2][j] + + d_struct.u[l + 1][j] - + d_struct.u[l + 2][j]) / + d_struct.s1[h][j]; +} + +//Q_{ijH} +double prob_ij_pair_is_hairpin(int i, int j, dangle_struct d_struct){ + return exp(-eH(i,j)/RT)/d_struct.up[i][j]; +} + +//Q_{ijS} +double prob_ij_pair_is_stack(int i, int j, dangle_struct d_struct){ + return exp(-eS(i,j)/RT) * d_struct.up[i + 1][j - 1]/d_struct.u[i][j]; +} +//To find Q_{ijBl} take the rest of the probabilities and subtract +//them from 1. + +//Q_{ijM} +double prob_ij_pair_is_multiloop(int i, int j, dangle_struct d_struct){ + return d_struct.upm[i][j]/d_struct.up[i][j]; +} + +//This the probability hl closes a multiloop +//**GIVEN IJ CLOSES A MULTILOOP** +double prob_ijhl_is_internal_loop + (int i, int j, int h, int l, double partition_sum, dangle_struct d_struct){ + return exp(-eL(i,j,h,l)/RT) * d_struct.up[h][l] / partition_sum; +} + +//P_{ij(1+1)l} +double first_multi_prob_pair_next_base + (int i, int l, int j, dangle_struct d_struct){ + return d_struct.up[i + 1][l] * + (exp( - (Ea + 2 * Ec + auPenalty(i + 1, l))/RT) * + (exp(-Ed3(i + 1,l,l +1))/RT) * d_struct.u1[l + 2][j - 1] + + d_struct.u1[l + 1][j - 1] - + d_struct.u1[l + 1][j - 1]) / + d_struct.upm[i][j]; +} + +//P_{ij(1+2)l} +double first_multi_prob_pair_after_base + (int i, int l, int j, dangle_struct d_struct){ + + return d_struct.up[i + 2][l] * + exp(-(Ea + 2 * Ec + Eb + Ed3(j, i, i + 1) + auPenalty(i + 2,l))/RT) * + (exp(-Ed3(i + 2,l,l+1)/RT) * d_struct.u1[l + 2][j - 1] + + d_struct.u1[l + 1][j - 1] - + d_struct.u1[l + 2][j - 1]) / + d_struct.upm[i][j]; +} + +//P_{ijs2h) +double first_multi_prob_pair_rest_base(int i, int h, int j, dangle_struct d_struct){ + return exp(-(Ea + 2 * Ec + (h - i - 1) * Eb + Ed3(j,i,i+1))/RT) * + d_struct.s2[h][j] / d_struct.upm[i][j]; +} +//P_{ijhl} +double first_multi_prob_base_rest + (int i, int h, int l, int j, dangle_struct d_struct){ + + return d_struct.up[h][l] * exp(-(Ed5(h,l,h-1) + auPenalty(h,l))/RT) * + (exp( -Ed3(h,l,l+1)/RT) * d_struct.u1[l + 2][j - 1] + + d_struct.u1[l + 1][j - 1] - + d_struct.u1[l + 2][j - 1])/d_struct.s2[h][j]; +} + +//Q_{(l1 + 1)(j -1)(l1 +1)} +double rest_multi_prob_next_base_pairs (int l1, int l, int j, dangle_struct d_struct){ + + return d_struct.up[l1 +1][l] * exp(-(Ec + auPenalty(l1 + 1, l))/RT) * + (cond_dangle(j, l1 + 1, l) * exp( -(j - 1 - l) * Eb /RT) + + exp(-(j - 1 - l) * Eb) / RT + + exp(-Ed3(l1 + 1, l, l + 1)/RT) * d_struct.u1[l + 2][j - 1] + + d_struct.u1[l + 1][j - 1] - + d_struct.u1[l + 1][j - 1]) / + d_struct.u1[l1 + 1][j - 1]; +} + +//Q_{(l1 + 1)(j - 1)(l1 + 2)l} +double rest_multi_prob_after_base_pairs + (int l1, int l, int j, dangle_struct d_struct){ + + return d_struct.up[l1 + 2][l] * exp(-(Ec + Eb + auPenalty(l1 + 2,l))/RT) * + (cond_dangle(j, l1 + 2, l) * exp( -(j - 1 - l) * Eb / RT) + + exp(-Ed3(l1 + 1,l ,l + 1)/RT) * d_struct.u1[l + 2][j - 1] + + d_struct.u1[l + 1][j - 1] - + d_struct.u1[l + 2][j - 1]) / + d_struct.u1[l1 + 1][j - 1]; + +} + +//Q_{(l1 + 1)(j - 1)s3h} +double rest_multi_prob_rest_base_pairs + (int l1, int h, int j, dangle_struct d_struct){ + + return exp( -(Ec + (h - l1 - 1) * Eb)/RT) * d_struct.s3[h][j - 1] / + d_struct.u1[l1 + 1][j - 1]; +} + +//Q_{(j-1)hl} +//GIVEN THAT H PAIRS BEFORE J +double rest_multi_prob_h_pairs_with_l + (int l1, int h, int l, int j, dangle_struct d_struct){ + + return d_struct.up[h][l] * exp(-(Ed5(h,l,h - 1) + auPenalty(h,l))/RT) * + (cond_dangle(j,h,l) * exp(-(j - 1 -l) * Eb/RT) + + exp(-Ed3(h,l,l + 1)/RT) * d_struct.u1[l + 2][j - 1] + + d_struct.u1[l + 1][j - 1] - + d_struct.u1[l + 2][j - 1]) / + d_struct.s3[h][j - 1]; +} + +//P_{Bh2l2} +int there_is_another_helix(int h2, int l2, int j, dangle_struct d_struct){ + double counter = randdouble(); + double coin_flip = cond_dangle(j,h2,l2) * exp(-(j - 1 - l2) * Eb / RT) / + (cond_dangle(j,h2,l2) * exp(-(j - 1 - l2) * Eb / RT) + + exp(Ed3(h2,l2,l2 + 1)/RT) * d_struct.u1[l2 + 2][j - 1] + + d_struct.u1[l2 + 1][j - 1] - + d_struct.u1[l2 + 2][j - 1]); + + //If I was slick and mean I would have put + + //return counter > coin-flip + + if(counter <= coin_flip){ + return 0; + } + else{ + return 1; + } +} + +void single_stranded(int i, int j, int * structure){ + for(;i <= j; i++) + { + structure[i] = 0; + } +} + +void unknown_strand(int i, int j, dangle_struct d_struct, int * structure, list * stack){ +//Unknown strand from i,j + double counter = randdouble(); + counter -= single_stranded_prob(i, j, d_struct); + if (counter <= 0){ + single_stranded(i,j, structure); + return; + } + counter -= ends_pair_prob(i, j, d_struct); + if(counter <= 0){ + sub_seq seq; + seq.start = i; + seq.end = j; + seq.paired = 1; + //put i j on paired and push i j on stack as paired + + structure[i] = j; + structure[j] = i; + stack->push_front(seq); + return; + } + for (int h = i + MIN_TURN; h < j; h++){ + counter -= prob_h_pairs_with_5_end(i,h,j,d_struct); + if(counter < 0){ + sub_seq seq1; + sub_seq seq2; + + seq1.start = i; + seq1.end = h; + seq1.paired = 1; + + seq2.start = h + 1; + seq2.end = j; + seq2.paired = 0; + + //Push i h as paired and h + 1 to j as unknown + structure[i] = h; + structure[h] = i; + stack->push_front(seq1); + stack->push_front(seq2); + return; + } + } + + for(int l = i + 1; l <= j - MIN_TURN; l++){ + counter -= prob_l_pairs_with_3_end(i,l,j,d_struct); + if (counter < 0){ + + sub_seq seq; + seq.start = l; + seq.end = j; + seq.paired = 1; + + //put from i to l - 1 as unpaired and push l and j as paired + single_stranded(i, l - 1, structure); + structure[l] = j; + structure[j] = l; + stack->push_front(seq); + return; + } + } + int h; //The loop is just to find h we need it later + for(h = i + 1; i <= j - MIN_TURN - 1; h++){ + counter -= prob_h_pairs_in_ij(i,h,j,d_struct); + if(counter < 0) + { + break; + } + } + + //Now to find l + counter = randdouble(); //reset counter, this is a seperate case + for(int l = h + MIN_TURN; l <= j - MIN_TURN; l++){ + counter -= prob_h_pairs_with_l(h,l,j,d_struct); + if (counter < 0){ + sub_seq seq1; + sub_seq seq2; + + seq1.start = h; + seq1.end = l; + seq1.paired = 1; + + seq2.start = l + 1; + seq2.end = j; + seq2.paired = 0; + + //set from i to h - 1 as single stranded + //Push h l as paired and l + 1 to j + //as unknown. + + single_stranded(i, h - 1, structure); + structure[h] = l; + structure[l] = h; + stack->push_front(seq1); + stack->push_front(seq2); + return; + } + } + //If we hit here, that's bad +} + +void paired_strand(int i, int j, dangle_struct d_struct, int * structure, list * stack){ + double counter = randdouble(); + double cumulative_prob = 0; + + + cumulative_prob = prob_ij_pair_is_hairpin(i,j,d_struct); + if(counter - cumulative_prob < 0){ + //i + 1, j - 1 is single stranded + single_stranded(i + 1, j - 1, structure); + return; + } + + cumulative_prob += prob_ij_pair_is_stack(i,j,d_struct); + if(counter - cumulative_prob < 0){ + sub_seq seq; + seq.start = i + 1; + seq.end = j - 1; + seq.paired = 1; + + //i + 1, j - 1 is pushed as stack + stack->push_front(seq); + structure[i + 1] = j - 1; + structure[j - 1] = i + 1; + return; + } + + cumulative_prob += prob_ij_pair_is_multiloop(i,j,d_struct); + if(counter - cumulative_prob < 0){ + multi_loop_strand(i,j,d_struct,structure,stack); + return; + } + + //else we know we have an internal loop. + //The probabilities should work out so that + //we never get more than 30 base internal loops. + //Might need to put guards in here. + counter = randdouble(); + for(int h = i + 1; h < j; h++){ + for(int l = h + MIN_TURN; l < j; l++){ + if(!(h == i + 1 && l == j - 1)) //Don't want a stack + counter -= exp(-eL(i,j,h,l)/RT) * d_struct.up[h][l] / (1 - cumulative_prob); + if(counter < 0){ + sub_seq seq; + seq.start = h; + seq.end = l; + seq.paired = 1; + + //hl goes on the stack as a pair and the rest of the internal loop + //gets put on a single stranded + + stack->push_front(seq); + structure[h] = l; + structure[l] = h; + single_stranded(i + 1, h - 1,structure); + single_stranded(l + 1, j - 1,structure); + } + } + } +} + +//It returns where it stops. +int multi_first_loop(int i, int j, dangle_struct d_struct, int * structure, list * stack){ + double counter = randdouble(); + for(int l= i + MIN_TURN + 1; l < j - 1; l++){ + counter -= first_multi_prob_pair_next_base(i,l,j,d_struct); + if(counter < 0){ + sub_seq seq; + seq.start = i + 1; + seq.end = l; + seq.paired = 1; + + //Under this condition i + 1 pairs with l; + + stack->push_front(seq); + structure[i + 1] = l; + structure[l] = i + 1; + return l + 1; + } + } + for(int l = i + MIN_TURN + 2; l < j - 1; l++){ + counter -= first_multi_prob_pair_after_base(i,l,j,d_struct); + if(counter < 0){ + sub_seq seq; + seq.start = i + 2; + seq.end = l; + seq.paired = 1; + + //Under this condition i + 2 pairs with l; + //and i + 1 is unpaired + + stack->push_front(seq); + structure[i + 1] = 0; + structure[i + 2] = l; + structure[l] = i + 2; + return l + 1; + } + } + + //We need h after this loop so we declare it here. + int h; + for(h = i + 3; h < j - 1; h ++){ + counter -= first_multi_prob_pair_rest_base(i,h,j,d_struct); + if(counter < 0){ + break; + } + } + + //Now h is the opening base in a base pair now we need to find the closing one + //So first we start a new counter + counter = randdouble(); + for (int l = h + MIN_TURN; l < j - 1; l++){ + counter -= first_multi_prob_base_rest(i,h,l,j,d_struct); + if(counter < 0){ + sub_seq seq; + seq.start = h; + seq.end = l; + seq.paired = 1; + + //H pairs with l and i + 1 to h - 1 is single stranded + single_stranded(i + 1, h - 1, structure); + stack->push_front(seq); + structure[h] = l; + structure[l] = h; + return l + 1; + } + } + + return -1; //We have an underflow or calculation error. +} + +void multi_loop_strand(int i, int j, dangle_struct d_struct, int * structure, list * stack){ + int l1 = multi_first_loop(i,j,d_struct, structure,stack);//l1 is the name of the closing base of the first loop + int h1 = i; + int notdone = 1; + int breakflag = 0; + + while(notdone){ + double counter = randdouble(); + for(int l = l1 + MIN_TURN + 1; l < j - 1; l++){ + counter -= rest_multi_prob_next_base_pairs(l1,l,j,d_struct); + if(counter < 0){ + sub_seq seq; + seq.start = l1 + 1; + seq.end = l; + seq.paired = 1; + + //Under this condition i + 1 pairs with l; + + stack->push_front(seq); + structure[l1 + 1] = l; + structure[l] = i + 1; + h1 = l1 + 1; + l1 = l; + breakflag = 1; + break; + } + } + if(breakflag){ + notdone = there_is_another_helix(h1, l1, j, d_struct); + breakflag = 0; + continue; //Starts while loop over + } + for(int l = l1 + MIN_TURN + 2; l < j - 1; l++){ + counter -= rest_multi_prob_after_base_pairs(l1,l,j,d_struct); + if(counter < 0){ + sub_seq seq; + seq.start = l1 + 2; + seq.end = l; + seq.paired = 1; + + //Under this condition i + 2 pairs with l; + //and i + 1 is unpaired + + stack->push_front(seq); + structure[l1 + 1] = 0; + structure[l1 + 2] = l; + structure[l] = l1 + 2; + h1 = l1 + 2; + l1 = l; + breakflag = 1; + break; + } + } + if(breakflag){ + notdone = there_is_another_helix(h1, l1, j, d_struct); + breakflag = 0; + continue; //Starts while loop over + } + //We need h after this loop so we declare it here. + int h; + for(h = l1 + 3; h < j - 1; h ++){ + counter -= rest_multi_prob_rest_base_pairs(i,h,j,d_struct); + if(counter < 0){ + break; + } + } + + //Now h is the opening base in a base pair now we need to find the closing one + //So first we start a new counter + counter = randdouble(); + for (int l = h + MIN_TURN; l < j - 1; l++){ + counter -= rest_multi_prob_h_pairs_with_l(l1,h,l,j,d_struct); + if(counter < 0){ + sub_seq seq; + seq.start = h; + seq.end = l; + seq.paired = 1; + + //H pairs with l and i + 1 to h - 1 is single stranded + single_stranded(l1 + 1, h - 1, structure); + stack->push_front(seq); + structure[h] = l; + structure[l] = h; + l1 = l + 1; + h1 = h; + } + } + notdone = there_is_another_helix(h1, l1, j, d_struct); + }//End while +}//End function + + +void sample_structure(int * structure, dangle_struct d_struct){ + sub_seq seq; + seq.start = 1; + seq.end = d_struct.length; + seq.paired = 0; + + list da_stack; + da_stack.push_front(seq); + while(!da_stack.empty()){ + sub_seq cur_seq = da_stack.front(); + if(cur_seq.paired) + { + paired_strand(cur_seq.start, cur_seq.end, d_struct, structure, &da_stack); + } + else + { + unknown_strand(cur_seq.start, cur_seq.end, d_struct, structure, &da_stack); + } + da_stack.pop_front(); + } + +} diff --git a/gtfold-mfe/src/shapereader.cc b/gtfold-mfe/src/shapereader.cc new file mode 100644 index 0000000..006f8a1 --- /dev/null +++ b/gtfold-mfe/src/shapereader.cc @@ -0,0 +1,95 @@ +#include +#include +#include +#include +#include +#include + +#include "shapereader.h" +#include "global.h" +#include "options.h" + +using namespace std; + +double* SHAPEarray; +int* SHAPEenergies; + +static bool SHAPE_ENABLED = false; + +void enable_shape(bool b) { + SHAPE_ENABLED = b; +} + +void free_shapeArray(int len){ + free(SHAPEarray); +} + +void print_shapeArray(int len){ + for(int i=0; i0){ + if(sscanf(line.c_str(), "%d %lf", &position, &SHAPEnumber)==2){ + if(position <= seqlength){ + SHAPEarray[position] = SHAPEnumber; + SHAPEenergies[position] = calcShapeEnergy(SHAPEnumber); + } + else{ + printf("Invalid SHAPE position indicator (ignoring line): %s\n", line.c_str()); + } + }else{ + printf("Invalid line (ignoring): %s\n", line.c_str()); + } + } + +} + +int getShapeEnergy(int position){ + if(SHAPE_ENABLED){ + return SHAPEenergies[position]; + } + else{ + return 0; + } +} + +int calcShapeEnergy(double shapeNumber){ +//ZS: This function returns the free energy contribution as an integer. + if(shapeNumber<(double)0){ + return 0; + } + else{ + double energy = shapeModel(shapeNumber); + return (int)floor(100.0*energy+ .5); + } +} + + +double shapeModel(double SHAPE_value){ +//ZS: This function calculates the free energy contribution due to SHAPE. + double m = 2.6; + double b = -0.8; + return m*log(SHAPE_value+1)+b; +} + + + + diff --git a/gtfold-mfe/src/stochastic-sampling.cc b/gtfold-mfe/src/stochastic-sampling.cc new file mode 100644 index 0000000..b831ff8 --- /dev/null +++ b/gtfold-mfe/src/stochastic-sampling.cc @@ -0,0 +1,759 @@ +#include "stochastic-sampling.h" + +#include "global.h" +#include +#include +#include +#include +#include +#include + +int ss_verbose = 0; + +std::stack g_stack; + +double energy = 0; + +double randdouble() +{ + return rand()/(double(RAND_MAX)+1); +} + +bool feasible(int i, int j) +{ + return j-i > TURN && canPair(RNA[i],RNA[j]); +} + +double U_0(int i, int j) +{ + return 1.0/u[i][j]; +} + +double U_ij(int i, int j) +{ + return (feasible(i,j) == true)?up[i][j]*exp(-auPenalty_new(i,j)/RT)/u[i][j]:0; +} + +double U_hj(int i, int h, int j) +{ + return (feasible(h,j) == true)?up[h][j]*exp(-(ED5_new(h,j,h-1)+auPenalty_new(h,j))/RT)/u[i][j]:0; +} + +double U_il(int i, int j) +{ + return ud[i][j]/u[i][j]; +} + +double U_s1h(int i, int h, int j) +{ + return s1[h][j]/u[i][j]; +} + +double U_ihlj_case1(int i, int h, int l, int j) +{ + return feasible(h,l)?up[h][l]*exp(-(ED5_new(h,l,h-1)+auPenalty_new(h,l))/RT)* (exp(-ED3_new(h,l,l+1)/RT)*u[l+2][j]) /s1[h][j]:0; +} + +double U_ihlj_case2(int i, int h, int l, int j) +{ + return feasible(h,l)?up[h][l]*exp(-(ED5_new(h,l,h-1)+auPenalty_new(h,l))/RT)* (ud[l+1][j]) /s1[h][j]:0; +} + +double U_ihlj_case3(int i, int h, int l, int j) +{ + return (feasible(h,l)&&feasible(l+1,j))?up[h][l]*exp(-(ED5_new(h,l,h-1)+auPenalty_new(h,l))/RT)* (up[l+1][j]*exp(-(auPenalty_new(l+1,j)/RT))) /s1[h][j]:0; +} + +double UD_il_case1(int i, int l, int j) +{ + return feasible(i,l)?(up[i][l]*exp(-1*auPenalty_new(i,l)/RT)*exp(-1*ED3_new(i,l,l+1)/RT)*u[l+2][j])/ud[i][j]:0; +} + +double UD_il_case2(int i, int l, int j) +{ + return feasible(i,l)?(up[i][l]*exp(-1*auPenalty_new(i,l)/RT)*ud[l+1][j])/ud[i][j]:0; +} + +double UD_il_case3(int i, int l, int j) +{ + return (feasible(i,l)&&feasible(l+1,j))?up[i][l]*exp(-1*auPenalty_new(i,l)/RT)*up[l+1][j]*exp(-1*auPenalty_new(l+1,j))/ud[i][j]:0; +} + +double Q_ijH(int i, int j) +{ + return exp(-eH_new(i,j)/RT)/up[i][j]; +} + +double Q_ijS(int i, int j) +{ + return exp(-eS_new(i,j)/RT)*up[i+1][j-1]/up[i][j]; +} + +double Q_ijM(int i, int j) +{ + return upm[i][j]/up[i][j]; +} + +/* +double Q_ijBI(int i, int j) +{ + double sum = 0; + for (int h = i+1; h < j-1; ++h) + for (int l = h+1; l < j; ++l) + { + if (h == i+1 && l == j-1) continue; + sum += feasible(h,l)?(exp(-1*eL_new(i,j,h,l)/RT)*up[h][l]):0; + } + return sum/up[i][j]; +}*/ + +double Q_ijhlBI(int i, int j, int h, int l) +{ + return feasible(h,l)?exp(-1*eL_new(i,j,h,l)/RT)*up[h][l]/up[i][j]:0; +} + +double UPM_ip1l_case1(int i, int l, int j) +{ + return feasible(i+1,l)?(up[i+1][l] * exp((-1)*(EA_new()+2*EC_new()+auPenalty_new(i+1,l))/RT) * exp(-1*(ED3_new(i+1,l,l+1)+EB_new())/RT) * u1[l+2][j-1])/upm[i][j]:0; +} + +double UPM_ip1l_case2(int i, int l, int j) +{ + return feasible(i+1,l)?(up[i+1][l] * exp((-1)*(EA_new()+2*EC_new()+auPenalty_new(i+1,l))/RT) * u1d[l+1][j-1])/upm[i][j]:0; +} + +double UPM_ip2l_case1(int i, int l , int j) +{ + return feasible(i+2,l)?up[i+2][l]*exp((-1)*(EA_new()+2*EC_new()+EB_new()+ED3_new(j,i,i+1)+auPenalty_new(i+2,l))/RT) * (exp((-1)*(ED3_new(i+2,l,l+1)+EB_new())/RT)*u1[l+2][j-1])/upm[i][j]:0; +} + +double UPM_ip2l_case2(int i, int l , int j) +{ + return feasible(i+2,l)?(up[i+2][l]*exp((-1)*(EA_new()+2*EC_new()+EB_new()+ED3_new(j,i,i+1)+auPenalty_new(i+2,l))/RT) * u1d[l+1][j-1])/upm[i][j]:0; +} + + +double UPM_ijs2h(int i, int h , int j) +{ + return exp((-1)*ED3_new(j,i,i+1)/RT)* (s2[h][j] * exp((-1)*(EA_new()+2*EC_new()+(h-i-1)*EB_new())/RT))/upm[i][j]; +} + + +double UPM_ijhl_case1(int i, int h, int l, int j) +{ + return feasible(h,l)?up[h][l]*(exp(-(ED5_new(h,l,h-1)+auPenalty_new(h,l))/RT))* (exp(-ED3_new(h,l,l+1)/RT)*u1[l+2][j-1])/s2[h][j]:0; +} + +double UPM_ijhl_case2(int i, int h, int l, int j) +{ + return feasible(h,l)?up[h][l]*(exp(-(ED5_new(h,l,h-1)+auPenalty_new(h,l))/RT))* (u1d[l+1][j-1])/s2[h][j]:0; +} + +// u1d : case 1 +double U1D_ij_il_case1(int i, int l, int j) +{ + return feasible(i,l)?(up[i][l]*exp((-1)*(EC_new()+auPenalty_new(i,l))/RT) * (f(j+1,i,l)*exp((-1)*(j-l)*EB_new()/RT)))/u1d[i][j]:0; +} + +// u1d : case 2 +double U1D_ij_il_case2(int i, int l, int j) +{ + return feasible(i,l)?(up[i][l]*exp((-1)*(EC_new()+auPenalty_new(i,l))/RT)*(exp((-1)*(ED3_new(i,l,l+1)+EB_new())/RT)*u1[l+2][j]))/u1d[i][j]:0; +} + +// u1d : case 3 +double U1D_ij_il_case3(int i, int l, int j) +{ + return feasible(i,l)?(up[i][l]*exp((-1)*(EC_new()+auPenalty_new(i,l))/RT) * u1d[l+1][j])/u1d[i][j]:0; +} + +// u1 +double U1_ij(int i, int j) +{ + return u1d[i][j]/u1[i][j]; +} + +// u1 : sample h +double U1_ij_s3h(int i, int h, int j) +{ + return (s3[h][j] * exp((-1)*(EC_new()+(h-i)*EB_new())/RT))/u1[i][j]; +} + +// u1 : sample l +double U1_j_hl_case1(int h, int l, int j) +{ + return feasible(h,l)?(up[h][l]*(exp(-(ED5_new(h,l,h-1)+auPenalty_new(h,l))/RT))* (f(j+1,h,l)*exp(-((j-l)*EB_new())/RT))) /s3[h][j]:0; +} + +double U1_j_hl_case2(int h, int l, int j) +{ + return feasible(h,l)?(up[h][l]*(exp(-(ED5_new(h,l,h-1)+auPenalty_new(h,l))/RT))* (exp(-(ED3_new(h,l,l+1)+EB_new())/RT)*u1[l+2][j])) /s3[h][j]:0; +} + +double U1_j_hl_case3(int h, int l, int j) +{ + return feasible(h,l)?(up[h][l]*(exp(-(ED5_new(h,l,h-1)+auPenalty_new(h,l))/RT))* (u1d[l+1][j])) /s3[h][j]:0; +} + +void rnd_u(int i, int j, int* structure) +{ + double rnd = randdouble(); + double cum_prob = 0.0; + + + cum_prob += U_0(i,j); + if (rnd < cum_prob) + { + return; + } + + cum_prob += U_ij(i, j); + if (rnd < cum_prob) + { + energy += auPenalty_new(i,j); + if (ss_verbose == 1) + printf("(%d %d) %lf\n",i,j,auPenalty_new(i,j)/100.0); + base_pair bp(i,j,UP); + g_stack.push(bp); + return; + } + + for (int h = i+1; h < j; ++h) + { + cum_prob += U_hj(i,h,j); + if (rnd < cum_prob) + { + energy += ED5_new(h,j,h-1)+auPenalty_new(h,j); + if (ss_verbose == 1) + printf("(%d %d) %lf\n",i,j,(ED5_new(h,j,h-1)+auPenalty_new(h,j)) /100.0); + base_pair bp(h,j,UP); + //set_single_stranded(i,h-1,structure); + g_stack.push(bp); + return; + } + } + + cum_prob += U_il(i,j); + if (rnd < cum_prob) + { + base_pair bp1(i,j,UD); + g_stack.push(bp1); + return; + } + + int h1 = -1; + for (int h = i+1; h < j-1; ++h) + { + cum_prob += U_s1h(i,h,j); + if (rnd < cum_prob) + { + h1 = h; + break; + } + } + + assert (h1 != -1) ; + + rnd = randdouble(); + cum_prob = 0; + for (int l = h1+1; l < j; ++l) + { + cum_prob += U_ihlj_case1(i,h1,l,j); + if (rnd < cum_prob) + { + energy += (ED5_new(h1,l,h1-1)+ auPenalty_new(h1,l) + ED3_new(h1,l,l+1)); + if (ss_verbose == 1) + printf("(%d %d) %lf\n",i,j,(ED5_new(h1,l,h1-1)+ auPenalty_new(h1,l) + ED3_new(h1,l,l+1)) /100.0); + base_pair bp1(h1,l,UP); + base_pair bp2(l+2,j,U); + g_stack.push(bp1); + g_stack.push(bp2); + return ; + } + + cum_prob += U_ihlj_case2(i,h1,l,j); + if (rnd < cum_prob) + { + energy += (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l)); + if (ss_verbose == 1) + printf("(%d %d) %lf\n",i,j,(ED5_new(h1,l,h1-1)+auPenalty_new(h1,l))/100.0); + + base_pair bp1(h1,l,UP); + base_pair bp2(l+1,j,UD); + g_stack.push(bp1); + g_stack.push(bp2); + return ; + } + + cum_prob += U_ihlj_case3(i,h1,l,j); + if (rnd < cum_prob) + { + energy += (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l) + auPenalty_new(l+1,j)); + if (ss_verbose == 1) + printf("(%d %d) %lf\n",i,j, (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l) + auPenalty_new(l+1,j))/100.0); + //set_single_stranded(i,h1-1,structure); + base_pair bp1(h1,l,UP); + base_pair bp2(l+1,j,UP); + g_stack.push(bp1); + g_stack.push(bp2); + return ; + } + + } + assert(0); +} + +void rnd_ud(int i, int j, int* structure) +{ + double rnd = randdouble(); + double cum_prob = 0.0; + for (int l = i+1; l < j ; ++l) + { + cum_prob += UD_il_case1(i,l,j); + if (rnd < cum_prob) + { + energy += (auPenalty_new(i,l) + ED3_new(i,l,l+1)); + if (ss_verbose == 1) + printf("(%d %d) %lf\n",i,j, (auPenalty_new(i,l) + ED3_new(i,l,l+1))/100.0); + base_pair bp1(i,l,UP); + base_pair bp2(l+2,j,U); + g_stack.push(bp1); + g_stack.push(bp2); + return; + } + + cum_prob += UD_il_case2(i,l,j); + if (rnd < cum_prob) + { + energy += auPenalty_new(i,l); + if (ss_verbose == 1) + printf("(%d %d) %lf\n",i,j, (auPenalty_new(i,l))/100.0); + base_pair bp1(i,l,UP); + base_pair bp2(l+1,j,UD); + g_stack.push(bp1); + g_stack.push(bp2); + return; + } + + cum_prob += UD_il_case3(i,l,j); + if (rnd < cum_prob) + { + energy += (auPenalty_new(i,l) + auPenalty_new(l+1,j)); + if (ss_verbose == 1) + printf("(%d %d) %lf\n",i,j, (auPenalty_new(i,l) + auPenalty_new(l+1,j))/100.0); + base_pair bp1(i,l,UP); + base_pair bp2(l+1,j,UP); + g_stack.push(bp1); + g_stack.push(bp2); + return; + } + } + assert(0); +} + +void rnd_up(int i, int j, int* structure) +{ + double rnd = randdouble(); + double cum_prob = 0; + assert(structure[i] == 0); + assert(structure[j] == 0); + + set_base_pair(i,j,structure); + + cum_prob += Q_ijH(i,j); + if (rnd < cum_prob) + { + energy += eH_new(i,j); + if (ss_verbose == 1) + printf("Hairpin(%d %d) %lf\n",i,j, (eH_new(i,j))/100.0); + //set_single_stranded(i+1,j-1,structure); + return ; + } + + cum_prob += Q_ijS(i,j); + if (rnd < cum_prob) + { + energy += eS_new(i,j); + if (ss_verbose == 1) + printf("Stack(%d %d) %lf\n",i,j, (eS_new(i,j))/100.0); + base_pair bp(i+1,j-1,UP); + g_stack.push(bp); + return ; + } + + cum_prob += Q_ijM(i,j); + if (rnd < cum_prob) + { + rnd_upm(i,j,structure); + return; + } + + for (int h = i+1; h < j-1; ++h) + for (int l = h+1; l < j; ++l) + { + if (h == i+1 && l == j-1) continue; + cum_prob += Q_ijhlBI(i,j,h,l); + if (rnd < cum_prob) + { + energy += eL_new(i,j,h,l); + if (ss_verbose == 1) + printf("IntLoop(%d %d) %lf\n",i,j, (eL_new(i,j,h,l))/100.0); + base_pair bp(h,l,UP); + g_stack.push(bp); + return; + } + } + + assert(0); +} + +void rnd_u1(int i, int j, int* structure) +{ + double rnd = randdouble(); + double cum_prob = 0; + + cum_prob += U1_ij(i,j); + if (rnd < cum_prob) + { + base_pair bp(i,j,U1D); + g_stack.push(bp); + return; + } + + int h1 = -1; + for (int h = i+1; h < j-1; ++h) + { + cum_prob += U1_ij_s3h(i,h,j); + if (rnd < cum_prob) + { + energy += (EC_new()+(h-i)*EB_new()); + if (ss_verbose == 1) + printf("U1_ij_s3h(%d) %lf\n",h, (EC_new()+(h-i)*EB_new())/100.0); + h1 = h; + break; + } + } + + assert(h1 != -1); + // sample l given h1 + rnd = randdouble(); + cum_prob = 0; + for (int l = h1+1; l <= j ; ++l) + { + cum_prob += U1_j_hl_case1(h1,l,j); + if (rnd < cum_prob) + { + int tt = (j == l)?0:ED3_new(h1,l,l+1); + energy += (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l) + tt + (j-l)*EB_new()); + if (ss_verbose == 1) + printf("U1_j_hl_case1(%d %d) %lf\n",h1,l, (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l) + tt + (j-l)*EB_new())/100.0); + base_pair bp(h1,l,UP); + g_stack.push(bp); + return; + } + + cum_prob += U1_j_hl_case2(h1,l,j); + if (rnd < cum_prob) + { + energy += (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l)+ ED3_new(h1,l,l+1)+EB_new()); + if (ss_verbose == 1) + printf("U1_j_hl_case2(%d %d) %lf\n",h1,l, (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l)+ ED3_new(h1,l,l+1)+EB_new())/100.0); + base_pair bp1(h1,l,UP); + base_pair bp2(l+2,j,U1); + g_stack.push(bp1); + g_stack.push(bp2); + return; + } + + cum_prob += U1_j_hl_case3(h1,l,j); + if (rnd < cum_prob) + { + energy += ED5_new(h1,l,h1-1)+auPenalty_new(h1,l); + if (ss_verbose == 1) + printf("U1_j_hl_case3(%d %d) %lf\n",h1,l, (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l))/100.0); + base_pair bp1(h1,l,UP); + base_pair bp2(l+1,j,U1D); + g_stack.push(bp1); + g_stack.push(bp2); + return; + } + } + + assert(0); +} + +void rnd_u1d(int i, int j, int* structure) +{ + double rnd = randdouble(); + double cum_prob = 0; + + for (int l = i+1; l <= j; ++l) + { + cum_prob += U1D_ij_il_case1(i,l,j); + if (rnd < cum_prob) + { + int tt = (j==l)?(0):(ED3_new(i,l,l+1)); + energy += ( EC_new()+auPenalty_new(i,l) + tt + (j-l)*EB_new()); + if (ss_verbose == 1) { + printf("U1D_ij_il_case1(%d %d %d) %lf\n",i,l,j, ( EC_new()+auPenalty_new(i,l) + tt + (j-l)*EB_new())/100.0); + } + base_pair bp1(i,l,UP); + g_stack.push(bp1); + return; + } + + cum_prob += U1D_ij_il_case2(i,l,j); + if (rnd < cum_prob) + { + energy += (EC_new()+auPenalty_new(i,l)+ ED3_new(i,l,l+1)+EB_new()); + if (ss_verbose == 1) + printf("U1D_ij_il_case2(%d %d) %lf\n",i,l, (EC_new()+auPenalty_new(i,l)+ ED3_new(i,l,l+1)+EB_new())/100.0); + base_pair bp1(i,l,UP); + base_pair bp2(l+2,j,U1); + g_stack.push(bp1); + g_stack.push(bp2); + return; + } + + cum_prob += U1D_ij_il_case3(i,l,j); + if (rnd < cum_prob) + { + energy += (EC_new()+auPenalty_new(i,l)); + if (ss_verbose == 1) + printf("U1D_ij_il_case3(%d %d) %lf\n",i,l, (EC_new()+auPenalty_new(i,l))/100.0); + base_pair bp1(i,l,UP); + base_pair bp2(l+1,j,U1D); + g_stack.push(bp1); + g_stack.push(bp2); + return; + } + } + assert(0); +} + +void rnd_upm(int i, int j, int* structure) +{ + double rnd = randdouble(); + double cum_prob = 0; + if (ss_verbose == 1) + printf("Multiloop (%d %d)\n",i,j); + + for (int l = i+2; l < j; ++l) + { + cum_prob += UPM_ip1l_case1(i,l,j); + if (rnd < cum_prob) + { + energy += (EA_new()+2*EC_new()+auPenalty_new(i+1,l) + ED3_new(i+1,l,l+1)+EB_new()) ; + if (ss_verbose == 1) { + printf("(%d %d) %s %lf\n",i,j, "UPM_ip1l_case1",(EA_new()+2*EC_new()+auPenalty_new(i+1,l) + ED3_new(i+1,l,l+1)+EB_new())/100.0); + } + base_pair bp1(i+1,l,UP); + base_pair bp2(l+2,j-1,U1); + g_stack.push(bp2); + g_stack.push(bp1); + return ; + } + + cum_prob += UPM_ip1l_case2(i,l,j); + if (rnd < cum_prob) + { + energy += (EA_new()+2*EC_new()+auPenalty_new(i+1,l)); + if (ss_verbose == 1) + printf("(%d %d) %s %lf\n",i,j,"UPM_ip1l_case2", (EA_new()+2*EC_new()+auPenalty_new(i+1,l))/100.0); + base_pair bp1(i+1,l,UP); + base_pair bp2(l+1,j-1,U1D); + g_stack.push(bp2); + g_stack.push(bp1); + return ; + } + } + + for (int l = i+3; l < j; ++l) + { + cum_prob += UPM_ip2l_case1(i,l,j); + if (rnd < cum_prob) + { + energy += (EA_new()+2*EC_new()+EB_new()+ED3_new(j,i,i+1)+auPenalty_new(i+2,l)+ED3_new(i+2,l,l+1)+EB_new()); + if (ss_verbose == 1) + printf("%s(%d %d) %lf\n", "UPM_ip2l_case1", i,j,(EA_new()+2*EC_new()+EB_new()+ED3_new(j,i,i+1)+auPenalty_new(i+2,l)+ED3_new(i+2,l,l+1)+EB_new())/100.0); + base_pair bp1(i+2,l,UP); + base_pair bp2(l+2,j-1,U1); + g_stack.push(bp2); + g_stack.push(bp1); + return ; + } + + cum_prob += UPM_ip2l_case2(i,l,j); + if (rnd < cum_prob) + { + energy += (EA_new()+2*EC_new()+EB_new()+ED3_new(j,i,i+1)+auPenalty_new(i+2,l)); + if (ss_verbose == 1) + printf("%s(%d %d) %lf\n", "UPM_ip2l_case2",i,j,(EA_new()+2*EC_new()+EB_new()+ED3_new(j,i,i+1)+auPenalty_new(i+2,l))/100.0); + base_pair bp1(i+2,l,UP); + base_pair bp2(l+1,j-1,U1D); + g_stack.push(bp1); + g_stack.push(bp2); + return ; + } + } + int h1 = -1; + for (int h = i+3; h < j-1; ++h) + { + cum_prob += UPM_ijs2h(i,h,j); + if (rnd < cum_prob ) + { + energy += (ED3_new(j,i,i+1)+ EA_new()+2*EC_new()+(h-i-1)*EB_new()); + h1 = h; + if (ss_verbose == 1) { + printf("%s(%d) %lf\n", "UPM_ijs2h",h1,(ED3_new(j,i,i+1)+ EA_new()+2*EC_new()+(h-i-1)*EB_new())/100.0); + } + break; + } + } + assert(h1!=-1); + + rnd = randdouble(); + cum_prob = 0; + for (int l = h1+1; l < j; ++l) + { + cum_prob += UPM_ijhl_case1(i,h1,l,j); + if (rnd < cum_prob) + { + energy += (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l) + ED3_new(h1,l,l+1)); + if (ss_verbose == 1) + printf("%s(%d %d) %lf\n","UPM_ijhl_case1",h1,l, (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l) + ED3_new(h1,l,l+1))/100.0); + base_pair bp1(h1,l,UP); + base_pair bp2(l+2,j-1,U1); + g_stack.push(bp1); + g_stack.push(bp2); + return; + } + + cum_prob += UPM_ijhl_case2(i,h1,l,j); + if (rnd < cum_prob) + { + energy += (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l)); + if (ss_verbose == 1) + printf("%s(%d %d) %lf\n", "UPM_ijhl_case2",h1,l,(ED5_new(h1,l,h1-1)+auPenalty_new(h1,l))/100.0); + base_pair bp1(h1,l,UP); + base_pair bp2(l+1,j-1,U1D); + g_stack.push(bp1); + g_stack.push(bp2); + return; + } + } + assert(0); +} + +double rnd_structure(int* structure, int len) +{ + //printf("%lf %lf %lf\n", EA_new(), EB_new(), EC_new()); + srand(rand()); + base_pair first(1,len,U); + g_stack.push(first); + energy = 0.0; + + while (!g_stack.empty()) + { + base_pair bp = g_stack.top(); + // std::cout << bp; + g_stack.pop(); + + if (bp.type() == U) + rnd_u(bp.i,bp.j,structure); + else if (bp.type() == UD) + rnd_ud(bp.i,bp.j,structure); + else if (bp.type() == UP) + rnd_up(bp.i,bp.j,structure); + else if (bp.type() == U1) + rnd_u1(bp.i,bp.j,structure); + else if (bp.type() == U1D) + rnd_u1d(bp.i,bp.j,structure); + + } + return (double)energy/100.0; +} + +void batch_sample(int num_rnd, int length, double U) +{ + int* structure = new int[length+1]; + srand(time(NULL)); + std::map > uniq_structs; + + if (num_rnd > 0 ) { + printf("\nSampling structures...\n"); + int count; //nsamples =0; + for (count = 1; count <= num_rnd; ++count) + { + memset(structure, 0, (length+1)*sizeof(int)); + double energy = rnd_structure(structure, length); + + std::string ensemble(length+1,'.'); + for (int i = 1; i <= (int)length; ++ i) { + if (structure[i] > 0 && ensemble[i] == '.') + { + ensemble[i] = '('; + ensemble[structure[i]] = ')'; + } + } + //double myEnegry = -88.4; + //++nsamples; + //if (fabs(energy-myEnegry)>0.0001) continue; //TODO: debug + //++count; + + std::map >::iterator iter ; + if ((iter =uniq_structs.find(ensemble.substr(1))) != uniq_structs.end()) + { + std::pair& pp = iter->second; + pp.first++; + } + else { + uniq_structs.insert(make_pair(ensemble.substr(1),std::pair(1,energy))); + } + + // std::cout << ensemble.substr(1) << ' ' << energy << std::endl; + } + //std::cout << nsamples << std::endl; + int pcount = 0; + int maxCount = 0; std::string bestStruct; + double bestE = INFINITY; + + std::map >::iterator iter ; + for (iter = uniq_structs.begin(); iter != uniq_structs.end(); ++iter) + { + const std::string& ss = iter->first; + const std::pair& pp = iter->second; + const double& estimated_p = (double)pp.first/(double)num_rnd; + const double& energy = pp.second; + double actual_p = pow(2.718281,-1.0*energy/RT_)/U; + + printf("%s %lf %lf %lf %d\n",ss.c_str(),energy,actual_p,estimated_p,pp.first); + pcount += pp.first; + if (pp.first > maxCount) + { + maxCount = pp.first; + bestStruct = ss; + bestE = pp.second; + } + } + assert(num_rnd == pcount); + printf("\nMax frequency structure : \n%s e=%lf freq=%d p=%lf\n",bestStruct.c_str(),bestE,maxCount,(double)maxCount/(double)num_rnd); + + } + + delete [] structure; +} + +void set_single_stranded(int i, int j, int* structure) +{ + for(;i<=j;++i) + structure[i] = 0; +} + +void set_base_pair(int i, int j, int* structure) +{ + bool cond = j-i > TURN && canPair(RNA[i],RNA[j]); + assert(cond); + structure[i] = j; + structure[j] = i; +} diff --git a/gtfold-mfe/src/subopt_main.cc b/gtfold-mfe/src/subopt_main.cc new file mode 100644 index 0000000..96b2ac5 --- /dev/null +++ b/gtfold-mfe/src/subopt_main.cc @@ -0,0 +1,163 @@ +#include +#include +#include +#include +#include +#include +#include + +#include "loader.h" +#include "algorithms.h" +#include "subopt_traceback.h" +#include "global.h" +#include "utils.h" +#include "mfe_main.h" + + +using namespace std; + +static string seqfile = ""; +static string suboptFile = ""; +static double suboptDelta = 0; +static string outputPrefix = ""; +static string outputFile = ""; +static string outputDir = ""; +static string paramDir = ""; +static bool PARAM_DIR = false; +static void help(); + +void save_subopt_file(string outputFile, ss_map_t& ss_data, + const string& seq, int energy) +{ + ofstream outfile; + outfile.open(outputFile.c_str()); + char buff[4096]; + + sprintf(buff,"%s %6.2f", seq.c_str(), energy/100.0); + outfile << buff << std::endl; + for (ss_map_t::iterator it = ss_data.begin(); it!= ss_data.end(); ++it) + { + sprintf(buff,"%s %6.2f", (it->first).c_str(), it->second/100.0); + //outfile << it->first << '\t' << it->second/100.0 << std::endl; + outfile << buff << std::endl; + } + + outfile.close(); +} + +void parse_options(int argc, char** argv) { + int i; + + for(i=1; i 0) { + outputPrefix = outputPrefix.substr(pos+1); + } + + // and if an extension exists, remove it ... + if(outputPrefix.find(".") != string::npos) + outputPrefix.erase(outputPrefix.rfind(".")); + } + + // If output dir specified + if (!outputDir.empty()) { + outputFile += outputDir; + outputFile += "/"; + suboptFile += outputDir; + suboptFile += "/"; + } + // ... and append the .ct + outputFile += outputPrefix; + outputFile += ".ct"; + suboptFile += outputPrefix; + suboptFile += "_ss.txt"; + + +} + +static void help() { + printf("Usage: gtsubopt [OPTION]... FILE\n\n"); + + printf(" FILE is an RNA sequence file containing only the sequence or in FASTA format.\n\n"); + + printf("OPTIONS\n"); + printf(" --subopt NUM Calculate suboptimal structures within NUM kcal/mol\n"); + printf(" of the MFE. (Uses -d 2 treatment of dangling energies.)\n"); + printf("\n"); + printf(" -o, --output NAME Write output files with prefix given in NAME\n"); + printf(" -p --paramdir DIR Path to directory from which parameters are to be read\n"); + printf(" -h, --help Output help (this message) and exit.\n"); + printf(" -w, --workdir DIR Path of directory where output files will be written.\n"); + exit(-1); +} + +void subopt_main(int argc, char** argv) { + + string seq = ""; + parse_options(argc, argv); + + if (read_sequence_file(seqfile.c_str(), seq) == FAILURE) { + printf("Failed to open sequence file: %s.\n\n", seqfile.c_str()); + exit(-1); + } + init_fold(seq.c_str()); + + readThermodynamicParameters(paramDir.c_str(), PARAM_DIR, 0, 1, 0); + + int energy = calculate(seq.length()) ; + + double t1 = get_seconds(); + ss_map_t subopt_data = subopt_traceback(seq.length(), 100.0*suboptDelta); + t1 = get_seconds() - t1; + + printf("- thermodynamic parameters: %s\n", EN_DATADIR.c_str()); + printf("- input file: %s\n", seqfile.c_str()); + printf("- sequence length: %d\n", (int)seq.length()); + printf("\n"); + printf("Subopt traceback running time: %9.6f seconds\n", t1); + + printf("Subopt structures saved in %s\n", suboptFile.c_str()); + save_subopt_file(suboptFile, subopt_data, seq, energy); + + printf("+ calculating suboptimal structures within %f kcal/mol of MFE\n", suboptDelta); + printf("+ suboptimal structures file: %s\n", suboptFile.c_str()); + + free_fold(seq.length()); +} diff --git a/gtfold-mfe/src/subopt_traceback.cc b/gtfold-mfe/src/subopt_traceback.cc index 45c72d9..d67a852 100644 --- a/gtfold-mfe/src/subopt_traceback.cc +++ b/gtfold-mfe/src/subopt_traceback.cc @@ -1,22 +1,22 @@ /** - GTfold: compute minimum free energy of RNA secondary structure - Copyright (C) 2008 David A. Bader - http://www.cc.gatech.edu/~bader +GTfold: compute minimum free energy of RNA secondary structure +Copyright (C) 2008 David A. Bader +http://www.cc.gatech.edu/~bader - This program is free software: you can redistribute it and/or modify - it under the terms of the GNU General Public License as published by - the Free Software Foundation, either version 3 of the License, or - (at your option) any later version. +This program is free software: you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation, either version 3 of the License, or +(at your option) any later version. - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - GNU General Public License for more details. +This program is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +GNU General Public License for more details. - You should have received a copy of the GNU General Public License - along with this program. If not, see . - - @author prashant {pgaurav@gatech.edu} +You should have received a copy of the GNU General Public License +along with this program. If not, see . + +@author prashant {pgaurav@gatech.edu} */ @@ -28,380 +28,459 @@ #include "global.h" #include "subopt_traceback.h" -const char* lstr[] = {"W", "V", "VBI", "VM", "WM"}; - -void (*trace_func[5]) (int i, int j, ps_t& ps, ps_stack_t& gs, int energy); - -void print_stack(ps_stack_t temp) -{ - std::cout << "{\n"; - while (!temp.empty()) - { - ps_t ps = temp.top(); - temp.pop(); - ps.print(); - std::cout << '\n' ; - } - std::cout << "}\n"; +#include +#include +#include + +//#define DEBUG 1 + +using std::pair; +using std::cout; +using std::endl; + +const char* lstr[] = {"W", "V", "VBI", "VM", "WM", "WMPrime", "fm", "fm1"}; + +void (*trace_func[8]) (int i, int j, ps_t& ps, ps_stack_t& gs); +static int delta = 0; +static int mfe = INFINITY_; +static int length = -1; +static int gflag = 0; + +#ifdef UNIQUE_MULTILOOP_DECOMPOSITION + +static int FM1[1500][1500] = {{0}}; +static int FM[1500][1500] = {{0}}; + +static inline int Ed5_new(int i, int j, int k) { + return (k!=0) ? Ed3(j, i, k) : Ed3(j,i,length); } -void process(ss_map_t& subopt_data, int energy, int len) -{ - int count = 0 ; - ps_stack_t gstack; - - // initialize the partial structure - // segment stack = {[1,n]}, label = W, list_bp = {} - ps_t first(0, len); - first.push(segment(5, len, lW, W[len])); - gstack.push(first); // initialize the partial structure stacka - - while (1) - { - if (gstack.empty()) break; // exit - - ps_t ps = gstack.top(); - gstack.pop(); - - if (ps.empty()) - { - //std::cout << ps.str << " dG =" << ps.ae_ << std::endl; - if (subopt_data.find(ps.str) == subopt_data.end()) - { - subopt_data.insert(std::make_pair(ps.str,ps.ae_)); - count++; - } - continue; - } - else - { - segment smt = ps.top(); - ps.pop(); - size_t s1 = gstack.size(); - - if (smt.j_ - smt.i_ >=4) - { - (*trace_func[smt.label_])(smt.i_, smt.j_, ps, gstack, energy); - } - - if (gstack.size() == s1 && ps.total() <= energy) - { - ps_t ps1(ps); - gstack.push(ps1); - } - } - } +static inline int Ed3_new(int i, int j, int k) { + return (k!=length+1)?Ed5(j, i, k) : Ed5(j, i, 1); } -ss_map_t subopt_traceback(int len, int delta) -{ - trace_func[0] = traceW; - trace_func[1] = traceV; - trace_func[2] = traceVBI; - trace_func[3] = traceVM; - //trace_func[4] = traceWM; +void calculate_fm1() { + + //printf("length %d\n", length); + //printf("Ea: %d , Eb: %d , Ec: %d\n", Ea, Eb, Ec); + + for (int i = 1; i <= length; ++i) { + for (int j = i+1; j <= length; ++j) { + //printf("\nFinding FM1[%d][%d]\n", i, j); + int min = INFINITY_; + for (int l = i+TURN+1; l <= j; ++l) { + int d5 = Ed5_new(i,l,i-1); + int d3 = Ed3_new(i,l,l+1); + + int fm1 = V(i,l) + auPenalty(i,l) + d5 + d3 + Ec*(j-l) + Eb; + + //printf("l: %d\n", l); + //printf("V(%d, %d): %d, auPenalty: %d, Ed3(%d, %d, %d): %d, Ed5(%d, %d, %d): %d\n", + // i, l, V(i,l), + // auPenalty(i,l), + // i, l, i-1, d5, + // i, l, l+1, d3 + // ); + //printf("min: %d, fm1: %d, final_min: %d\n", min, fm1, MIN(min,fm1)); + min = MIN(min, fm1); + } + FM1[i][j] = min; + //printf("Value: %d ", FM1[i][j]); + } + //printf("\n"); + } - int mfe = W[len]; - int level = 0; +} - ss_map_t subopt_data; +void calculate_fm() { + + for (int i = 1; i <= length; ++i) { + for (int j = i+1; j <= length;++j) { + int min1 = INFINITY_; + for (int k = i+TURN+1; k <= j-TURN-1; ++k) { + int x = FM[i][k-1] + FM1[k][j]; + min1 = MIN(min1, x); + } + int min2 = INFINITY_; + for (int k = i; k <= j-TURN-1; ++k) { + int x = FM1[k][j] + Ec*(k-i); + min2 = MIN(min2, x); + } + FM[i][j] = MIN(min1, min2); + //printf("%d %d %d ", i, j, FM[i][j]); + } + //printf("\n"); + } +} - for (level = mfe; level <= mfe + delta; level += 10) - process(subopt_data, level, len); +#endif + +void process(ss_map_t& subopt_data, int len) { + int count = 0; + length = len; + +#ifdef UNIQUE_MULTILOOP_DECOMPOSITION + calculate_fm1(); + calculate_fm(); +#endif + + ps_stack_t gstack; + + + // initialize the partial structure, segment stack = {[1,n]}, label = W, list_bp = {} + ps_t first(0, len); + first.push(segment(1, len, lW, W[len])); + gstack.push(first); // initialize the partial structure stacka + + while (1) { + if (gstack.empty()) break; // exit + ps_t ps = gstack.top(); + gstack.pop(); + + if (ps.empty()) { + count++; + pair ins_result; + ins_result = subopt_data.insert(std::make_pair(ps.str,ps.ae_)); + if (ins_result.second == false) { + printf("Duplicate Structure!!!"); + exit(1); + } + //cout << ps.str << endl; + continue; + } + else { + segment smt = ps.top(); + ps.pop(); + + gflag = 0; + if (smt.j_ - smt.i_ > TURN) { + (*trace_func[smt.label_])(smt.i_, smt.j_, ps, gstack); + } + + // discarded current segment, using remaining ones + if (!gflag) { + ps_t ps1(ps); + gstack.push(ps1); + } + } + } + +#ifdef DEBUG + //printf("# SS = %d\n", count); +#endif +} - return subopt_data; +ss_map_t subopt_traceback(int len, int _delta) { + trace_func[0] = traceW; + trace_func[1] = traceV; + trace_func[2] = traceVBI; + trace_func[3] = traceVM; + trace_func[4] = traceWM; + trace_func[5] = traceWMPrime; +#ifdef UNIQUE_MULTILOOP_DECOMPOSITION + trace_func[6] = traceM; + trace_func[7] = traceM1; +#endif + + mfe = W[len]; + delta = _delta; + length = len; + + ss_map_t subopt_data; + process(subopt_data, len); + + return subopt_data; } -void traceV(int i, int j, ps_t& ps, ps_stack_t& gstack, int energy) -{ - // Hairpin Loop - if (eH(i,j) + ps.total() <= energy ) - { - // std::cout << "Hairpin " << i << ' ' << j << std::endl; - ps_t ps1(ps); - ps1.accumulate(eH(i,j)); - ps1.update(i, j, '(', ')'); - push_to_gstack(gstack, ps1); - } - - // Stack - if (eS(i, j) + V(i+1, j-1) + ps.total() <= energy) - { - // std::cout << "Stack " << i << ' ' << j << std::endl; - ps_t ps1(ps); - ps1.push(segment(i+1, j-1, lV, V(i+1, j-1))); - ps1.accumulate(eS(i,j)); - ps1.update(i, j , '(', ')'); - push_to_gstack(gstack, ps1); - } - - // Internal Loop - if (VBI(i,j) + ps.total() <= energy ) - { - //std::cout << "Internal " << i << ' ' << j << std::endl; - ps_t ps1(ps); - ps1.push(segment(i, j, lVBI, VBI(i,j))); - ps1.update(i, j, '(', ')'); - push_to_gstack(gstack, ps1); - } - - // Multiloop - if ( VM(i,j) + ps.total() <= energy ) - { - // std::cout << "Multi " << i << ' ' << j << std::endl; - ps_t ps1(ps); - ps1.push(segment(i, j, lVM, VM(i,j))); - ps1.update(i, j, '(', ')'); - push_to_gstack(gstack, ps1); - } +void traceV(int i, int j, ps_t& ps, ps_stack_t& gstack) { + + //printf("V %d %d\n", i, j); + // Hairpin Loop + if (eH(i,j) + ps.total() <= mfe + delta) { + //printf("hairpin\n"); + ps_t ps1(ps); + ps1.accumulate(eH(i,j)); + ps1.update(i, j, '(', ')'); + push_to_gstack(gstack, ps1); + } + + // Stack + if (eS(i, j) + V(i+1, j-1) + ps.total() <= mfe + delta) { + //printf("stack %d %d %d %d\n", i, j, eS(i,j), V(i+1,j-1)); + ps_t ps1(ps); + ps1.push(segment(i+1, j-1, lV, V(i+1, j-1))); + ps1.accumulate(eS(i,j)); + ps1.update(i, j , '(', ')'); + push_to_gstack(gstack, ps1); + } + + // Internal Loop + if (VBI(i,j) + ps.total() <= mfe + delta) { + //printf("internal loop\n"); + traceVBI(i,j,ps,gstack); + } + +#ifdef UNIQUE_MULTILOOP_DECOMPOSITION + int k; + + for (k = i+2; k <= j-TURN-1; ++k) { + + int kenergy1 = FM[i+1][k] + FM1[k+1][j-1]; + int d5 = Ed5(i, j, i+1); + int d3 = Ed3(i, j, j-1); + int aup = auPenalty(i,j); + int kenergy2 = d5 + d3 + aup + Ea + Eb; + int kenergy_total = kenergy1 + kenergy2; + if (i == 4 && j == 41) { + //printf("ps: "); + ps.print(); + //printf("\n"); + } + //printf("FM[%d][%d]: %d FM1[%d][%d]: %d\n", i+1, k, FM[i+1][k], k+1, j-1, FM1[k+1][j-1]); + //printf("Ed3(%d, %d, %d): %d Ed5(%d, %d, %d): %d Ea: %d\n", + // i,j,i+1, Ed5_new(i,j,i+1), i, j, j-1, Ed3_new(i,j,j-1), Ea); + //printf("Ed5(%d, %d, %d): %d Ed3(%d, %d, %d): %d Ea: %d %d %d\n", + // i,j,i+1, Ed5(i,j,i+1), i, j, i+1, Ed3(i,j,j-1), Ea, auPenalty(i,j), Eb); + //printf("kenergy_total: %d ps.total(): %d mfe+delta: %d i: %d j: %d k: %d\n", kenergy_total, + // ps.total(), mfe+delta, i, j, k); + if (kenergy_total + ps.total() <= mfe + delta) { + //printf("multiloop\n"); + ps_t ps1(ps); + ps1.push(segment(i+1,k, lM, FM[i+1][k])); + ps1.push(segment(k+1,j-1, lM1, FM1[k+1][j-1])); + ps1.accumulate(kenergy2); + ps1.update(i,j,'(',')'); + //printf("auPenalty: %d\n", auPenalty(i,j)); + push_to_gstack(gstack, ps1); + } + } +#else + + // Multiloop + if (VM(i,j) + ps.total() <= mfe + delta) { + ps_t ps1(ps); + ps1.push(segment(i, j, lVM, VM(i,j))); + ps1.update(i, j, '(', ')'); + push_to_gstack(gstack, ps1); + } + +#endif + +} + +void traceVBI(int i, int j, ps_t& ps, ps_stack_t& gstack) { + int p,q; + + for (p = i+1; p <= MIN(j-2-TURN,i+MAXLOOP+1) ; p++) { + int minq = j-i+p-MAXLOOP-2; + if (minq < p+1+TURN) minq = p+1+TURN; + int maxq = (p==(i+1))?(j-2):(j-1); + for (q = minq; q <= maxq; q++) { + if (V(p, q) + eL(i, j, p, q) + ps.total() <= mfe + delta) { + ps_t ps1(ps); + ps1.push(segment(p, q, lV, V(p, q))); + ps1.update(i, j , '(', ')'); + ps1.accumulate(eL(i, j, p, q)); + push_to_gstack(gstack, ps1); + } + } + } +} +void traceW(int i, int j, ps_t& ps, ps_stack_t& gstack) { + + //printf("W %d %d\n", i, j); + for (int l = i; l < j-TURN; ++l) { + int wim1 = MIN(0, W[l-1]); + int d3 = (l>i)?Ed3(j,l,l-1):0; + int d5 = (j=j) || j == 0 || j == 1) return; - - for (int i = h; i < j; ++i) - { - int wim1 = MIN(0, W[i-1]); - - int wij = V(i,j) + auPenalty(i, j) + wim1; - if (wij + ps.total() <= energy ) - { - ps_t ps1(ps); - ps1.push(segment(i, j, lV, V(i,j))); - if (wim1 <= 0 && i > 1) ps1.push(segment(1, i-1, lW, W[i-1])); - ps1.accumulate(auPenalty(i, j)); - push_to_gstack(gstack, ps1); - } - - int wijd = V(i,j-1) + auPenalty(i,j-1) + Ed5(j-1,i,j) + wim1; - if (wijd + ps.total() <= energy ) - { - ps_t ps3(ps); - ps3.push(segment(i, j-1, lV, V(i, j-1))); - if (wim1 <= 0 && i > 1) ps3.push(segment(1, i-1, lW, W[i-1])); - ps3.accumulate(auPenalty(i,j-1) + Ed5(j-1,i,j)); - push_to_gstack(gstack, ps3); - } - - int widj = V(i+1,j) + auPenalty(i+1,j) + Ed3(j,i+1,i) + wim1; - if (widj + ps.total() <= energy ) - { - ps_t ps4(ps); - ps4.push(segment(i+1, j, lV, V(i+1,j))); - if (wim1 <= 0 && i > 1) ps4.push(segment(1, i-1, lW, W[i-1])); - ps4.accumulate(auPenalty(i+1, j) + Ed3(j,i+1,i)); - push_to_gstack(gstack, ps4); - } - - int widjd = V(i+1, j-1) + auPenalty(i+1,j-1) + Ed3(j-1, i+1, i) + Ed5(j-1, i+1, j) + wim1; - if (widjd + ps.total() <= energy ) - { - ps_t ps2(ps); - ps2.push(segment(i+1, j-1, lV, V(i+1,j-1))); - if (wim1 <= 0 && i > 1) ps2.push(segment(1, i-1, lW, W[i-1])); - ps2.accumulate(auPenalty(i+1,j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j)); - push_to_gstack(gstack, ps2); - } - } - - if (W[j-1] + ps.total() <= energy ) - { - ps_t ps1(ps); - ps1.push(segment(1, j-1, lW, W[j-1])); - push_to_gstack(gstack, ps1); - } +void traceM(int i, int j, ps_t& ps, ps_stack_t& gstack) { + + //printf("M %d %d\n", i, j); + int d5, d3; + int aup; + + if (FM[i][j-1] + Ec + ps.total() <= mfe + delta) { + //printf("here11\n"); + ps_t ps1(ps); + ps1.push(segment(i, j-1, lM, FM[i][j-1])); + ps1.accumulate(Ec); + push_to_gstack(gstack, ps1); + } + + //printf("V(i,j):%d Ed5_new: %d Ed3_new: %d\n", V(i,j), Ed5_new(i,j,i-1), Ed3_new(i,j,j+1)); + //d5 = (i != 1) ? Ed3(i,j,i-1) : Ed3(i,j,length); + //d3 = (j != length) ? Ed5(i,j,j+1) : Ed5(i,j,1); + d5 = Ed5_new(i, j, i-1); + d3 = Ed3_new(i, j, j+1); + aup = auPenalty(i,j); + if (V(i,j) + d5 + d3 + Eb + aup + ps.total() <= mfe + delta) { + //printf("here12\n"); + ps_t ps1(ps); + ps1.push(segment(i, j, lV, V(i,j))); + ps1.accumulate(d5 + d3 + Eb + aup); + ps1.update(i,j,'(',')'); + push_to_gstack(gstack, ps1); + } + + + for (int k = i+TURN+1; k <= j-TURN-1; ++k) { + + d5 = Ed5_new(k+1, j, k); + d3 = Ed3_new(k+1, j, j+1); + aup = auPenalty(k+1, j); + + if (FM[i][k] + V(k+1,j) + d5 + d3 + + Eb + aup + ps.total() <= mfe + delta) { + //printf("here3\n"); + ps_t ps1(ps); + ps1.push(segment(i, k, lM, FM[i][k])); + ps1.push(segment(k+1, j, lV, V(k+1,j))); + ps1.accumulate(d5 + d3 + Eb + aup); + //printf("auPenalty: %d\n", auPenalty(i,k)); + ps1.update(k+1,j,'(',')'); + push_to_gstack(gstack, ps1); + } + } + + for (int k = i; k <= j-TURN-1; ++k) { + + d5 = Ed5_new(k+1, j, k); + d3 = Ed3_new(k+1, j, j+1); + aup = auPenalty(k+1, j); + + if (V(k+1,j) + d5 + d3 + + Eb + Ec*(k-i+1) + aup + ps.total() <= mfe+delta) { + //printf("here4\n"); + ps_t ps1(ps); + ps1.push(segment(k+1, j, lV, V(k+1,j))); + ps1.accumulate(d5 + d3 + Eb + Ec*(k-i+1) + aup); + ps1.update(k+1, j, '(', ')'); + //printf("auPenalty: %d\n", auPenalty(k+1,j)); + push_to_gstack(gstack, ps1); + } + } } -void traceWM(ps_t& ps, ps_map_t& filter, int energy) -{ - ps_stack_t wm_stack; - wm_stack.push(ps); - - while (!wm_stack.empty()) - { - ps_t pss = wm_stack.top(); - wm_stack.pop(); - - // check if all segments in pss are Vs - if (pss.empty()) - { - std::string key = pss.str; - while (!pss.empty_v()) - { - segment ss = pss.top_v(); - pss.pop_v(); - - pss.push(ss); - key[ss.i_-1] = '*'; key[ss.j_-1] = '*'; - } - filter.insert(std::pair(key, pss)); - continue; - } - - segment wm_seg = pss.top(); - pss.pop(); - - int i1 = wm_seg.i_; int j1 = wm_seg.j_; - - if (wm_seg.label_ == lV) - { - ps_t ps1(pss); - ps1.push_v(wm_seg); - wm_stack.push(ps1); - continue; - } - int h = i1; int k = j1; - - int wmij = V(h,k) + auPenalty(h,k) + Eb; - if (pss.total() + wmij <= energy ) - { - ps_t ps1(pss); - ps1.push_v(segment(h,k,lV, V(h,k))); - ps1.accumulate(auPenalty(h,k) + Eb); - wm_stack.push(ps1); - } - - int wmijd = V(h,k-1) + Ed5(k-1,h,k)+ auPenalty(h,k-1) +Eb+ Ec ; - if (pss.total() + wmijd <= energy ) - { - ps_t ps1(pss); - ps1.push_v(segment(h,k-1,lV, V(h,k-1))); - ps1.accumulate(Ed5(k-1,h,k)+ auPenalty(h,k-1) +Eb+Ec); - wm_stack.push(ps1); - } - - int wmidj = V(h+1,k) + Ed3(k,h+1,h) + auPenalty(h+1, k) + Eb+Ec ; - if (pss.total() + wmidj <= energy ) - { - ps_t ps1(pss); - ps1.push_v(segment(h+1, k, lV, V(h+1,k))); - ps1.accumulate(Ed3(k,h+1,h) + auPenalty(h+1,k) +Eb+Ec); - wm_stack.push(ps1); - } - - int wmidjd = V(h+1, k-1) + Ed3(k-1,h+1,h) + Ed5(k-1,h+1,k) + auPenalty(h+1,k-1) +Eb+ 2*Ec ; - if (pss.total() + wmidjd <= energy ) - { - ps_t ps1(pss); - ps1.push_v(segment(h+1, k-1, lV, V(h+1,k-1))); - ps1.accumulate(Ed3(k-1,h+1,h) + Ed5(k-1,h+1,k) + auPenalty(h+1,k-1) +Eb+ 2*Ec); - wm_stack.push(ps1); - } - - - if (pss.total() + WM(i1,j1-1) + Ec <= energy ) - { - ps_t ps1(pss); - ps1.push(segment(i1,j1-1, lWM, WM(i1,j1-1))); - ps1.accumulate(Ec); - wm_stack.push(ps1); - } - - if (pss.total() + WM[i1+1][j1] + Ec <= energy ) - { - ps_t ps1(pss); - ps1.push(segment(i1+1,j1, lWM, WM(i1+1,j1))); - ps1.accumulate(Ec); - wm_stack.push(ps1); - } - - for (int h = i1+1; h <= j1-1; ++h) - { - if (WM(i1,h) + WM(h+1,j1) + pss.total() <= energy ) - { - ps_t ps1(pss); - ps1.push(segment(i1, h, lWM, WM(i1,h))); - ps1.push(segment(h+1, j1, lWM, WM(h+1,j1))); - wm_stack.push(ps1); - } - } - } +#endif + +void traceWM(int i, int j, ps_t& ps, ps_stack_t& gstack) { + int d3 = (i==1)?Ed3(j,i,length):Ed3(j,i,i-1); + int d5 = Ed5(j,i,j+1); + + //printf("WM %d %d\n", i, j); + //printf("normal auPenalty: %d\n", auPenalty(i,j)); + if (V(i,j) + auPenalty(i, j) + Eb + d3 + d5 + ps.total() <= mfe + delta) { + ps_t ps_new(ps); + ps_new.accumulate(auPenalty(i, j) + Eb + d3 + d5); + ps_new.push(segment(i,j, lV, V(i,j))); + push_to_gstack(gstack, ps_new); + } + + if (WMPrime[i][j] + ps.total() <= mfe + delta) { + ps_t ps_new(ps); + ps_new.push(segment(i,j, lWMPrime, WMPrime[i][j])); + push_to_gstack(gstack, ps_new); + } + + if (WM(i+1,j) + Ec + ps.total() <= mfe + delta) { + ps_t ps_new(ps); + ps_new.accumulate(Ec); + ps_new.push(segment(i+1,j, lWM, WM(i+1,j))); + push_to_gstack(gstack, ps_new); + } + + if (WM(i,j-1) + Ec + ps.total() <= mfe + delta) { + ps_t ps_new(ps); + ps_new.accumulate(Ec); + ps_new.push(segment(i,j-1, lWM, WM(i,j-1))); + push_to_gstack(gstack, ps_new); + } } -void traceVM(int i, int j, ps_t& ps, ps_stack_t& gstack, int energy) -{ - std::map filter; - int h; - - for (h = i+1; h <= j-1; ++h) - { - int dG; - int d5 = Ed5(i,j,i+1); - int d3 = Ed3(i,j,j-1); - int common = auPenalty(i,j) + Ea + Eb; - - dG = common + WM[i+1][h-1] + WM[h][j-1]; - if (dG + ps.total() <= energy ) - { - ps_t ps1(ps); - ps1.push(segment(i+1,h-1, lWM, WM[i+1][h-1])); - ps1.push(segment(h, j-1, lWM, WM[h][j-1])); - ps1.accumulate(common) ; - traceWM(ps1, filter, energy); - } - - dG = common + WM[i+2][h-1] + WM[h][j-1] + d5 + Ec; - if (dG + ps.total() <= energy ) - { - ps_t ps1(ps); - ps1.push(segment(i+2,h-1, lWM, WM[i+2][h-1])); - ps1.push(segment(h, j-1, lWM, WM[h][j-1])); - ps1.accumulate(common + d5 + Ec); - traceWM(ps1, filter, energy); - } - - dG = common + WM[i+1][h-1] + WM[h][j-2] + d3 + Ec; - if (dG + ps.total() <= energy ) - { - ps_t ps1(ps); - ps1.push(segment(i+1,h-1, lWM, WM[i+1][h-1])); - ps1.push(segment(h, j-2, lWM, WM[h][j-2])); - ps1.accumulate(common + d3 + Ec); - traceWM(ps1, filter, energy); - } - - dG = common + WM[i+2][h-1] + WM[h][j-2] + d5 + d3 + 2*Ec; - if (dG + ps.total() <= energy ) - { - ps_t ps1(ps); - ps1.push(segment(i+2,h-1, lWM, WM[i+2][h-1])); - ps1.push(segment(h, j-2, lWM, WM[h][j-2])); - ps1.accumulate(common + d3 + d5 + 2*Ec) ; - traceWM(ps1, filter, energy); - } - } - - ps_map_t::iterator it ; - for (it = filter.begin(); it != filter.end(); ++it) - { - push_to_gstack(gstack, it->second); - } +void traceWMPrime(int i, int j, ps_t& ps, ps_stack_t& gstack) { + for (int h = i+TURN+1 ; h <= j-TURN-2; h++) { + if (WM(i,h-1) + WM(h,j) + ps.total() <= mfe + delta) { + ps_t ps_new(ps); + ps_new.push(segment(i,h-1, lWM, WM(i,h-1))); + ps_new.push(segment(h,j, lWM, WM(h,j))); + push_to_gstack(gstack, ps_new); + } + } +} + +void traceVM(int i, int j, ps_t& ps, ps_stack_t& gstack) { + + //printf("VM %d %d\n", i, j); + int d3 = Ed3(i,j,j-1); + int d5 = Ed5(i,j,i+1); + + if (WMPrime[i+1][j-1] + Ea + Eb + auPenalty(i, j) + d3 + d5 + ps.total() <= mfe + delta) { + ps_t ps_new(ps); + ps_new.accumulate(Ea + Eb + auPenalty(i, j) + d3 + d5); + ps_new.push(segment(i+1,j-1, lWMPrime,WMPrime[i+1][j-1] )); + push_to_gstack(gstack, ps_new); + } } -void push_to_gstack(ps_stack_t& gstack , const ps_t& v) -{ - gstack.push(v); +void push_to_gstack(ps_stack_t& gstack, const ps_t& v) { + gflag = 1; + gstack.push(v); + //printf("Pushing to gstack: \n"); +// v.print(); + //printf("\n"); } diff --git a/gtfold-mfe/src/test_ss_constraint.c b/gtfold-mfe/src/test_ss_constraint.c new file mode 100644 index 0000000..e3bd2d3 --- /dev/null +++ b/gtfold-mfe/src/test_ss_constraint.c @@ -0,0 +1,155 @@ +/*This program is used for testing single stranded constraints. Functions written in this file can be used for other scripts as well +Author: Manoj Soni +Email: manoj6891@gmail.com +*/ +#include +#include +#include +//#include +#define LENGTH 10 +#define MAX_CONSTRS 10 + +void executeCommand(char* cmd){ + printf("Executing command: %s\n", cmd); + int returnVal = system(cmd); + printf("return value: %d\n", returnVal); + if(returnVal != 0){ + printf("Error: returnVal:%d, Exiting...\n", returnVal); + exit(-1); + } +} + +char* getToken(char* str, char* sep, int index){ + char * pch; + pch = strtok (str,sep); + char* fName = pch; + if(index==0) return fName; + if(index != -1){ + printf("Error: index can be only 0 or -1. 0 means first and -1 means last token\n"); + exit(-1); + } + while (pch != NULL) + { + //printf ("%s\n",pch); + fName=pch; + pch = strtok (NULL, sep); + } + printf("%s\n",fName); + return fName; +} + +char* getSeqName(char* seqFileName1){ + char* seqFileName = malloc(200); + strcpy(seqFileName,seqFileName1); + char* seq = getToken(seqFileName, "/", -1); + char* seqName = getToken(seq, ".", 0); + printf("seqName: %s\n",seqName); + return seqName; + +} + +void parseCtFileToFindForcedConstraintRegion(char* ctFileName, char* constrs[MAX_CONSTRS]){//printf("Entering parse method\n"); +//ct file contents are +//dG = -5.8 +//1 C 0 2 12 1 +//2 C 1 3 11 2 +//... ... ... +//then 1 is pairing with 12, 2 is pairing with 11 .. ? +//in other words, first column is i and 5th column is j for a pair (i,j) + //char* constrs[MAX_CONSTRS]; + int index=0; + FILE* ctFile = fopen(ctFileName, "r"); + char str[100]; + int arr[5]; + char c; + fscanf(ctFile, "%[^\n]", str);printf("first line: %s\n",str); + int start=-1, end=-1; + while(feof(ctFile)==0){ + fscanf(ctFile, "%d %c %d %d %d %d\n", &arr[0],&c,&arr[1],&arr[2],&arr[3],&arr[4]); + if(arr[3]!=0){ + if(start==-1){ start=arr[0]; end=arr[0];} + else end=arr[0]; + if (start!=-1 && end-start+1 >= LENGTH){ + //char* ss_constr; + char* ss_constr = (char*)malloc(30);//new char[30]; + sprintf(ss_constr, "%s%d%s%d", "P ", start, " 0 ", (end-start+1)); + constrs[index++] = ss_constr; + printf("constraint is: %s\n",ss_constr); + if(index>=MAX_CONSTRS) break; + start=-1; + } + } + else{ + if(start==-1) continue; + // char* ss_constr; + char* ss_constr = malloc(30);//new char[30]; + sprintf(ss_constr, "%s%d%s%d", "P ", start, " 0 ", (end-start+1)); + constrs[index++] = ss_constr; + printf("constraint is: %s\n",ss_constr); + if(index>=MAX_CONSTRS) break; + start=-1; + + } + // printf("line is: %d %c %d %d %d %d\n", arr[0],c,arr[1],arr[2],arr[3],arr[4]); + } + if(index>=MAX_CONSTRS) return ;//constrs; + //char* ss_constr; + char* ss_constr = malloc(30);//new char[30]; + if(start!=-1){ + sprintf(ss_constr, "%s%d%s%d", "P ", start, " 0 ", (end-start+1)); + printf("constraint is: %s\n",ss_constr); + constrs[index++] = ss_constr; + } + fclose(ctFile); + return ;//ss_constr; +} + +char* createConstraintFile(char* constrs[MAX_CONSTRS]){ + char* constrFileName = "constraints.txt"; + FILE* constrFile = fopen(constrFileName, "w+"); + int i; + for(i=0; i" if @ARGV < 1; + +my $seqName = $ARGV[0]; + +system("gcc -o test_ss_constraint test_ss_constraint.c"); +system("./test_ss_constraint $seqName"); diff --git a/gtfold-mfe/src/traceback.c b/gtfold-mfe/src/traceback.c index b052cda..6d461a8 100644 --- a/gtfold-mfe/src/traceback.c +++ b/gtfold-mfe/src/traceback.c @@ -28,99 +28,135 @@ #include "global.h" #include "traceback.h" #include "utils.h" +#include "shapereader.h" -int verbose = -1; int total_en = 0; int total_ex = 0; +int length = 0; -void trace(int len, int vbose) { +void trace(int len) { int i; - verbose = vbose; - for (i = 0; i < len+1; i++) - structure[i] = 0; + for (i = 0; i <= len; i++) structure[i] = 0; + length = len; if (W[len] >= MAXENG) { - printf("\n No Structure "); + printf("- No Structure \n"); return; } printf("\n"); + traceW(len); - printf("- sum of energy of Loops: %12.2f kcal/mol\n", total_en/100.0); - printf("- sum of energy of External Loop: %12.2f kcal/mol\n", total_ex/100.0); - return; + if (g_verbose == 1) { + printf("- sum of energy of Loops: %12.2f kcal/mol\n", total_en/100.0); + printf("- sum of energy of External Loop: %12.2f kcal/mol\n", total_ex/100.0); + } + return; } void traceW(int j) { - int done, i, Wj,Wj_temp; - int wim1, flag, Widjd, Wijd, Widj, Wij; - Wj = INFINITY_; - flag = 1; - done = 0; + int done = 0, i; + int wim1, flag = 1 ; + + if (j == 0 || j == 1) + return; - if (j == 0 || j == 1) return; - for (i = 1; i < j && !done; i++) { if (j-i < TURN) continue; wim1 = MIN(0, W[i-1]); flag = 1; - if (wim1 != W[i-1]) flag = 0; - - Widjd = Wijd = Widj = INFINITY_; - Wij = V(i,j) + auPenalty(i, j) + wim1; - Widjd =(check_base(i)&&check_base(j))?(V(i+1,j-1) + auPenalty(i+1, j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j) + wim1): INFINITY_; - Wijd = (check_base(j))?(V(i,j-1) + auPenalty(i,j-1) + Ed5(j-1,i,j) + wim1):INFINITY_; - Widj = (check_base(i))?(V(i+1,j) + auPenalty(i+1,j) + Ed3(j,i+1,i) + wim1):INFINITY_; - Wj_temp=Wj; - Wj = MIN(MIN(MIN(Wij, Widjd), MIN(Wijd, Widj)), Wj); - - if (W[j] == Wj) { - if (W[j] == Wij) { - done = 1; - if (verbose == 1) - printf("i %5d j %5d ExtLoop %12.2f\n", i, j, auPenalty(i, j)/100.00); - total_ex += auPenalty(i, j); - structure[i] = j; - structure[j] = i; - traceV(i, j); - if (flag || is_ss(1,i)) traceW(i - 1); - break; - } else if (W[j] == Widjd && check_base(i) && check_base(j)) { - done = 1; - if (verbose == 1) - printf("i %5d j %5d ExtLoop %12.2f\n", i+1, j-1, (auPenalty(i+1, j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j))/100.00); - total_ex += (auPenalty(i+1, j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j)); - structure[i + 1] = j - 1; - structure[j - 1] = i + 1; - traceV(i + 1, j - 1); - if (flag || is_ss(1,i)) traceW(i - 1); - break; - } else if (W[j] == Wijd && check_base(j)) { - done = 1; - if (verbose == 1) - printf("i %5d j %5d ExtLoop %12.2f\n", i, j-1, (auPenalty(i,j-1) + Ed5(j-1,i,j))/100.00); - total_ex += (auPenalty(i,j-1) + Ed5(j-1,i,j)); - structure[i] = j - 1; - structure[j - 1] = i; - traceV(i, j - 1); - if (flag || is_ss(1,i)) traceW(i - 1); - break; - } else if (W[j] == Widj && check_base(i)) { - done = 1; - if (verbose == 1) - printf("i %5d j %5d ExtLoop %12.2f\n", i+1, j, (auPenalty(i+1,j) + Ed3(j,i+1,i))/100.00); - total_ex += (auPenalty(i+1,j) + Ed3(j,i+1,i)); - structure[i + 1] = j; - structure[j] = i + 1; - traceV(i + 1, j); - if (flag || is_ss(1,i)) traceW(i - 1); - break; + if ( wim1 != W[i-1] && canSSregion(0,i)) flag = 0; + + if (g_unamode||g_mismatch) { + if ((W[j] == V(i,j) + auPenalty(i, j) + wim1 && canStack(i,j)) || forcePair(i,j)) { + done = 1; + if (g_verbose == 1) printf("i %5d j %5d ExtLoop %12.2f\n", i, j, auPenalty(i, j)/100.00); + total_ex += auPenalty(i, j); + traceV(i, j); + if (flag ) traceW(i - 1); + break; + } else if ((W[j] == V(i,j-1) + auPenalty(i,j-1) + Ed5(j-1,i,j) + wim1 && canSS(j) && canStack(i,j-1)) || forcePair(i, j-1)) { + done = 1; + if (g_verbose == 1) printf("i %5d j %5d ExtLoop %12.2f\n", i, j-1, (auPenalty(i,j-1) + Ed5(j-1,i,j))/100.00); + total_ex += (auPenalty(i,j-1) + Ed5(j-1,i,j)); + traceV(i, j - 1); + if (flag ) traceW(i - 1); + break; + } else if ((W[j] == V(i+1,j) + auPenalty(i+1,j) + Ed3(j,i+1,i) + wim1 && canSS(i) && canStack(i+1,j)) || forcePair(i+1,j)){ + done = 1; + if (g_verbose == 1) printf("i %5d j %5d ExtLoop %12.2f\n", i+1, j, (auPenalty(i+1,j) + Ed3(j,i+1,i))/100.00); + total_ex += (auPenalty(i+1,j) + Ed3(j,i+1,i)); + traceV(i + 1, j); + if (flag ) traceW(i - 1); + break; + } else if ((W[j] == V(i+1,j-1) + auPenalty(i+1, j-1) + Estacke(j-1,i+1) + wim1 && canSS(i) && canSS(j) && canStack(i+1,j-1)) || forcePair(i+1,j-1)) { + done = 1; + if (g_verbose == 1) printf("i %5d j %5d ExtLoop %12.2f\n", i+1, j-1, (auPenalty(i+1, j-1) + Estacke(j-1,i+1))/100.00); + total_ex += (auPenalty(i+1, j-1) + Estacke(j-1,i+1)); + traceV(i + 1, j - 1); + if (flag ) traceW(i - 1); + break; } + } else if (g_dangles == 2) { + int e_dangles = 0; + if (i>1) e_dangles += Ed3(j,i,i-1); + if (j= j) - return 0; - else { - for (h = i; h < j && !done; h++) { - int aa = WM(i,h) + WM(h + 1,j); - if (aa == WM(i,j)) { - done = 1; - h1 = h; - break; - } + if (!done){ + if (g_unamode||g_mismatch) { + if (WM(i,j) == V(i,j) + auPenalty(i, j) + Eb && canStack(i,j)) { + eWM += traceV(i, j); + done = 1; + } else if (WM(i,j) == V(i+1, j) + Ed3(j,i + 1,i) + auPenalty(i+1, j) + Eb + Ec && canSS(i) && canStack(i+1,j)) { + eWM += traceV(i + 1, j); + done = 1; + } else if (WM(i,j) == V(i,j-1) + Ed5(j-1,i,j) + auPenalty(i,j-1) + Eb + Ec && canSS(j) && canStack(i,j-1)) { + done = 1; + eWM += traceV(i, j - 1); + } else if (WM(i,j) == V(i+1,j-1) + Estackm(j-1,i+1) + auPenalty(i+1, j-1) + Eb + 2*Ec && canSS(i) && canSS(j) && canStack(i+1,j-1)) { + done = 1; + eWM += traceV(i + 1, j - 1); + } + } else if (g_dangles == 2) { + int energy = V(i,j) + auPenalty(i, j) + Eb; + energy += (i==1)?Ed3(j,i,length):Ed3(j,i,i-1); + /*if (j +#include #include +#include +#include + +double get_seconds() { + struct timeval tv; + gettimeofday(&tv, NULL); + return (double) tv.tv_sec + (double) tv.tv_usec / 1000000.0; +} + +int is_valid_base(char c) { + return ( (c-'A' == 0) || (c-'a' == 0) || + (c-'C' == 0) || (c-'c' == 0) || + (c-'G' == 0) || (c-'g' == 0) || + (c-'U' == 0) || (c-'u' == 0)); +} char baseToDigit(const char* base) { if (!strcmp(base, "A")) { diff --git a/gtfold-mfe/tests/README b/gtfold-mfe/tests/README new file mode 100644 index 0000000..7e55fcb --- /dev/null +++ b/gtfold-mfe/tests/README @@ -0,0 +1,4 @@ +This directory contains the Test Framework for GTFold. +The complete documentation can be accessed here: +http://goo.gl/OliVA + diff --git a/gtfold-mfe/tests/config/root-logger.conf b/gtfold-mfe/tests/config/root-logger.conf new file mode 100644 index 0000000..7fa2cc7 --- /dev/null +++ b/gtfold-mfe/tests/config/root-logger.conf @@ -0,0 +1,7 @@ +#root-logger.conf +log4perl.rootLogger = INFO, myFILE +log4perl.appender.myFILE = Log::Log4perl::Appender::File +log4perl.appender.myFILE.filename = ../logs/error_log +log4perl.appender.myFILE.mode = append +log4perl.appender.myFILE.layout = Log::Log4perl::Layout::PatternLayout +log4perl.appender.myFILE.layout.ConversionPattern = [%p] (%F line %L) %m%n diff --git a/gtfold-mfe/tests/config/test-list.conf b/gtfold-mfe/tests/config/test-list.conf new file mode 100644 index 0000000..bff0017 --- /dev/null +++ b/gtfold-mfe/tests/config/test-list.conf @@ -0,0 +1,5 @@ +#Scoregtwithunafold +#ExitCodes +#CompareGTCTwithUNACT +#SuboptMatchStructures +ConstraintsVerification diff --git a/gtfold-mfe/tests/config/test-params.conf b/gtfold-mfe/tests/config/test-params.conf new file mode 100644 index 0000000..81ad292 --- /dev/null +++ b/gtfold-mfe/tests/config/test-params.conf @@ -0,0 +1,36 @@ +# Important directory variables +G_GTFOLD_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/src/ +G_UNAFOLD_DIR=/home/users/rbanga/rna/unafold/install/bin/ +G_RNAFOLD_DIR=/usr/local/bin/ +G_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/5S_sequences/ +#G_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/16S_sequences/ +#G_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/ +#G_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/23S_sequences/ +#G_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/Other_sequences/ +G_WORK_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/work/ +G_TEST_LIST_FILE=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/config/test-list.conf + +# Sequence Inclusion Filters +#G_INCLUDE_SEQUENCES=rad +#G_INCLUDE_SEQUENCES=d.16.e.B.g* +#G_INCLUDE_SEQUENCES=d.16.e.B.m* +#G_INCLUDE_SEQUENCES=d.16.e.B.h* +#G_INCLUDE_SEQUENCES=d.16.e.E.bieneusi +#G_EXCLUDE_SEQUENCES=d.16.e.A.* +#G_EXCLUDE_SEQUENCES=d.16.e.B.ma* +#G_INCLUDE_SEQUENCES=acc1 +#G_INCLUDE_SEQUENCES=a.*j +#G_INCLUDE_SEQUENCES=a..tb* + +# Local Sequence Directories + +# Directory containing sequences for testing pseudoknot detection logic +L_EXITCODES_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/exitcodes_sequences/ +L_SUBOPTMATCHSTRUCTURES_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/5S_sequences/ +L_SUBOPTMATCHSTRUCTURES_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/subopt_sequences/ +L_SUBOPTMATCHSTRUCTURES_MIN_ENERGY=0 +L_SUBOPTMATCHSTRUCTURES_MAX_ENERGY=1 +L_SUBOPTMATCHSTRUCTURES_ENERGY_STRIDE=1 +L_SUBOPTMATCHSTRUCTURES_INCLUDE_SEQUENCES=d.5.a.H.* +L_CONSTRAINTSVERIFICATION_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/constraints_sequences/ +L_CONSTRAINTSVERIFICATION_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/constraints_sequences/ diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.a.H.volcanii.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.a.H.volcanii.seq new file mode 100644 index 0000000..b8c95c6 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.a.H.volcanii.seq @@ -0,0 +1,2 @@ +>d.16.a.H.volcanii +AUUCCGGUUGAUCCUGCCGGAGGUCAUUGCUAUUGGGGUCCGAUUUAGCCAUGCUAGUUGCACGAGUUCAUACUCGUGGCGAAAAGCUCAGUAACACGUGGCCAAACUACCCUACAGAGAACGAUAACCUCGGGAAACUGAGGCUAAUAGUUCAUACGGGAGUCAUGCUGGAAUGCCGACUCCCCGAAACGCUCAGGCGCUGUAGGAUGUGGCUGCGGCCGAUUAGGUAGACGGUGGGGUAACGGCCCACCGUGCCGAUAAUCGGUACGGGUUGUGAGAGCAAGAGCCCGGAGACGGAAUCUGAGACAAGAUUCCGGGCCCUACGGGGCGCAGCAGGCGCGAAACCUUUACACUGCACGCAAGUGCGAUAAGGGGACCCCAAGUGCGAGGGCAUAUAGUCCUCGCUUUUCUCGACCGUAAGGCGGUCGAGGAAUAAGAGCUGGGCAAGACCGGUGCCAGCCGCCGCGGUAAUACCGGCAGCUCAAGUGAUGACCGAUAUUAUUGGGCCUAAAGCGUCCGUAGCCGGCCACGAAGGUUCAUCGGGAAAUCCGCCAGCUCAACUGGCGGGCGUCCGGUGAAAACCACGUGGCUUGGGACCGGAAGGCUCGAGGGGUACGUCCGGGGUAGGAGUGAAAUCCCGUAAUCCUGGACGGACCACCGAUGGCGAAAGCACCUCGAGAAGACGGAUCCGACGGUGAGGGACGAAAGCUAGGGUCUCGAACCGGAUUAGAUACCCGGGUAGUCCUAGCUGUAAACGAUGCUCGCUAGGUGUGACACAGGCUACGAGCCUGUGUUGUGCCGUAGGGAAGCCGAGAAGCGAGCCGCCUGGGAAGUACGUCCGCAAGGAUGAAACUUAAAGGAAUUGGCGGGGGAGCACUACAACCGGAGGAGCCUGCGGUUUAAUUGGACUCAACGCCGGACAUCUCACCAGCUCCGACUACAGUGAUGACGAUCAGGUUGAUGACCUUAUCACGACGCUGUAGAGAGGAGGUGCAUGGCCGCCGUCAGCUCGUACCGUGAGGCGUCCUGUUAAGUCAGGCAACGAGCGAGACCCGCACUUCUAAUUGCCAGCAGCAGUUUCGACUGGCUGGGUACAUUAGAAGGACUGCCGCUGCUAAAGCGGAGGAAGGAACGGGCAACGGUAGGUCAGUAUGCCCCGAAUGAGCUGGGCUACACGCGGGCUACAAUGGUCGAGACAAUGGGUUGCUAUCUCGAAAGAGAACGCUAAUCUCCUAAACUCGAUCGUAGUUCGGAUUGAGGGCUGAAACUCGCCCUCAUGAAGCUGGAUUCGGUAGUAAUCGCAUUUCAAUAGAGUGCGGUGAAUACGUCCCUGCUCCUUGCACACACCGCCCGUCAAAGCACCCGAGUGAGGUCCGGAUGAGGCCACCACACGGUGGUCGAAUCUGGGCUUCGCAAGGGGGCUUAAGUCGUAACAAGGUAGCCGUAGGGGAAUCUGCGGCUGGAUCACCUCCUG diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.a.Halobacterium.sp.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.a.Halobacterium.sp.seq new file mode 100644 index 0000000..e3a500d --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.a.Halobacterium.sp.seq @@ -0,0 +1,2 @@ +>d.16.a.Halobacterium.sp +AUUCCGGUUGAUCCUGCCGGAGGCCAUUGCUAUCGGAGUCCGAUUUAGCCAUGCUAGUUGUGCGGGUUUAGACCCGCAGCGGAAAGCUCAGUAACACGUGGCCAAGCUACCCUGUGGACGGGAAUACUCUCGGGAAACUGAGGCUAAUCCCCGAUAACGCUUUGCUCCUGGAAGGGGCAAAGCCGGAAACGCUCCGGCGCCACAGGAUGCGGCUGCGGUCGAUUAGGUAGACGGUGGGGUAACGGCCCACCGUGCCCAUAAUCGGUACGGGUUGUGAGAGCAAGAGCCCGGAGACGGAAUCUGAGACAAGAUUCCGGGCCCUACGGGGCGCAGCAGGCGCGAAACCUUUACACUGUACGAAAGUGCGAUAAGGGGACUCCGAGUGUGAAGGCAUAGAGCCUUCACUUUUGUACACCGUAAGGUGGUGCACGAAUAAGGACUGGGCAAGACCGGUGCCAGCCGCCGCGGUAAUACCGGCAGUCCGAGUGAUGGCCGAUCUUAUUGGGCCUAAAGCGUCCGUAGCUGGCUGAACAAGUCCGUUGGGAAAUCUGUCCGCUUAACGGGCAGGCGUCCAGCGGAAACUGUUCAGCUUGGGACCGGAAGACCUGAGGGGUACGUCUGGGGUAGGAGUGAAAUCCUGUAAUCCUGGACGGACCGCCGGUGGCGAAAGCGCCUCAGGAGAACGGAUCCGACAGUGAGGGACGAAAGCUAGGGUCUCGAACCGGAUUAGAUACCCGGGUAGUCCUAGCUGUAAACGAUGUCCGCUAGGUGUGGCGCAGGCUACGAGCCUGCGCUGUGCCGUAGGGAAGCCGAGAAGCGGACCGCCUGGGAAGUACGUCUGCAAGGAUGAAACUUAAAGGAAUUGGCGGGGGAGCACUACAACCGGAGGAGCCUGCGGUUUAAUUGGACUCAACGCCGGACAUCUCACCAGCCCCGACAGUAGUAAUGACGGUCAGGUUGAUGACCUUACCCGAGGCUACUGAGAGGAGGUGCAUGGCCGCCGUCAGCUCGUACCGUGAGGCGUCCUGUUAAGUCAGGCAACGAGCGAGACCCGCACUCCUAAUUGCCAGCAGUACCCUUUGGGUAGCUGGGUACAUUAGGUGGACUGCCGCUGCCAAAGCGGAGGAAGGAACGGGCAACGGUAGGUCAGUAUGCCCCGAAUGGGCUGGGCAACACGCGGGCUACAAUGGUCGAGACAAUGGGAAGCCACUCCGAGAGGAGGCGCUAAUCUCCUAAACUCGAUCGUAGUUCGGAUUGAGGGCUGAAACUCGCCCUCAUGAAGCUGGAUUCGGUAGUAAUCGCGUGUCAGCAGCGCGCGGUGAAUACGUCCCUGCUCCUUGCACACACCGCCCGUCAAAUCACCCGAGUGGGGUUCGGAUGAGGCCGGCAUGCGCUGGUCAAAUCUGGGCUCCGCAAGGGGGAUUAAGUCGUAACAAGGUAGCCGUAGGGGAAUCUGCGGCUGGAUCACCUCCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.a.P.abyssi.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.a.P.abyssi.seq new file mode 100644 index 0000000..c32cdc8 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.a.P.abyssi.seq @@ -0,0 +1,2 @@ +>d.16.a.P.abyssi +CGUACUCCCUUAAUUCCGGUUGAUCCUGCCGGAGGCCACUGCUAUGGGGGUCCGACUAAGCCAUGCGAGUCAAGGGGGCGUCCCUUCUGGGACGCCACCGGCGGACGGCUCAGUAACACGUCGGUAACCUACCCUCGGGAGGGGGAUAACCCCGGGAAACUGGGGCUAAUCCCCCAUAGGCCUGGGGUACUGGAAGGUCCCCAGGCCGAAAGGGAGCCGUAAGGCUCCGCCCGAGGAUGGGCCGGCGGCCGAUUAGGUAGUUGGUGGGGUAACGGCCCACCAAGCCGAAGAUCGGUACGGGCCGUGAGAGCGGGAGCCCGGAGAUGGACACUGAGACACGGGUCCAGGCCCUACGGGGCGCAGCAGGCGCGAAACCUCCGCAAUGCGGGAAACCGCGACGGGGGGACCCCCAGUGCCGUGCCUCUGGCACGGCUUUUCCGGAGUGUAAAAAGCUCCGGGAAUAAGGGCUGGGCAAGGCCGGUGGCAGCCGCCGCGGUAAUACCGGCGGCCCGAGUGGUGGCCACUAUUAUUGGGCCUAAAGCGGCCGUAGCCGGGCCCGUAAGUCCCUGGCGAAAUCCCACGGCUCAACCGUGGGGCUCGCUGGGGAUACUGCGGGCCUUGGGACCGGGAGAGGCCGGGGGUACCCCCGGGGUAGGGGUGAAAUCCUAUAAUCCCGGGGGGACCGCCAGUGGCGAAGGCGCCCGGCUGGAACGGGUCCGACGGUGAGGGCCGAAGGCCAGGGGAGCGAACCGGAUUAGAUACCCGGGUAGUCCUGGCUGUAAAGGAUGCGGGCUAGGUGUCGGGCGAGCUUCGAGCUCGCCCGGUGCCGUAGGGAAGCCGUUAAGCCCGCCGCCUGGGGAGUACGGCCGCAAGGCUGAAACUUAAAGGAAUUGGCGGGGGAGCACUACAAGGGGUGGAGCGUGCGGUUUAAUUGGAUUCAACGCCGGGAACCUCACCGGGGGCGACGGCAGGAUGAAGGCCAGGCUGAAGGUCUUGCCGGACGCGCCGAGAGGAGGUGCAUGGCCGCCGUCAGCUCGUACCGUGAGGCGUCCACUUAAGUGUGGUAACGAGCGAGACCCGCGCCCCCAGUUGCCAGUCCCUCCCGCUCGGGAGGGAGGCACUCUGGGGGGACUGCCGGCGAUAAGCCGGAGGAAGGGGCGGGCGACGGUAGGUCAGUAUGCCCCGAAACCCCCGGGCUACACGCGCGCUACAAUGGGCGGGACAAUGGGUGCCGACCCCGAAAGGGGGAGGUAAUCCCCUAAACCCGCCCUCAGUUCGGAUCGCGGGCUGCAACUCGCCCGCGUGAAGCUGGAAUCCCUAGUACCCGCGCGUCAUCAUCGCGCGGCGAAUACGUCCCUGCUCCUUGCACACACCGCCCGUCACUCCACCCGAGCGGGGCCUAGGUGAGGCCCGAUCUCCUUCGGGAGGUCGGGUCGAGCCUAGGCUCCGUGAGGGGGGAGAAGUCGUAACAAGGUAGCCGUAGGGGAACCUACGGCUCGAUCACCUCCUAUC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.a.P.horikoshii.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.a.P.horikoshii.seq new file mode 100644 index 0000000..14395d3 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.a.P.horikoshii.seq @@ -0,0 +1,2 @@ +>d.16.a.P.horikoshii +AUUCCGGUUGAUCCUGCCGGAGGCCACUGCUAUGGGGGUCCGACUAAGCCAUGCGAGUCAAGGGGGCGUCCCUUCUGGGACGCCACCGGCGGACGGCUCAGUAACACGUCGGUAACCUACCCUCGGGAGGGGGAUAACCCCGGGAAACUGGGGCUAAUCCCCCAUAGGCCUGGGGUACUGGAAGGUCCCCAGGCCGAAAGGGAGCCGUAAGGCUCCGCCCGAGGAUGGGCCGGCGGCCGAUUAGGUAGUUGGUGGGGUAACGGCCCACCAAGCCGAAGAUCGGUACGGGCCGUGAGAGCGGGAGCCCGGAGAUGGACACUGAGACACGGGUCCAGGCCCUACGGGGCGCAGCAGGCGCGAAACCUCCGCAAUGCGGGAAACCGCGACGGGGGGACCCCCAGUGCCGUGCCUCUGGCACGGCUUUUCCGGAGUGUAAAAAGCUCCGGGAAUAAGGGCUGGGCAAGGCCGGUGGCAGCCGCCGCGGUAAUACCGGCGGCCCGAGUGGUGGCCACUAUUAUUGGGCCUAAAGCGGCCGUAGCCGGGCCCGUAAGUCCCUGGCGAAAUCCCACGGCUCAACCGUGGGGCUCGCUGGGGAUACUGCGGGCCUUGGGACCGGGAGAGGCCGGGGGUACCCCCGGGGUAGGGGUGAAAUCCUAUAAUCCCGGGGGGACCGCCAGUGGCGAAGGCGCCCGGCUGGAACGGGUCCGACGGUGAGGGCCGAAGGCCAGGGGAGCGAACCGGAUUAGAUACCCGGGUAGUCCUGGCUGUAAAGGAUGCGGGCUAGGUGUCGGGCGAGCUUCGAGCUCGCCCGGUGCCGUAGGGAAGCCGUUAAGCCCGCCGCCUGGGGAGUACGGCCGCAAGGCUGAAACUUAAAGGAAUUGGCGGGGGAGCACUACAAGGGGUGGAGCGUGCGGUUUAAUUGGAUUCAACGCCGGGAACCUCACCGGGGGCGACGGCAGGAUGAAGGCCAGGCUGAAGGUCUUGCCGGACGCGCCGAGAGGAGGUGCAUGGCCGCCGUCAGCUCGUACCGUGAGGCGUCCACUUAAGUGUGGUAACGAGCGAGACCCGCGCCCCCAGUUGCCAGUCCCUCCCGCUCGGGAGGGAGGCACUCUGGGGGGACUGCCGGCGAUAAGCCGGAGGAAGGGGCGGGCGACGGUAGGUCAGUAUGCCCCGAAACCCCCGGGCUACACGCGCGCUACAAUGGGCGGGACAAUGGGUGCCGACCCCGAAAGGGGGAGGUAAUCCCCUAAACCCGCCCUCAGUUCGGAUCGCGGGCUGCAACUCGCCCGCGUGAAGCUGGAAUCCCUAGUACCCGCGCGUCAUCAUCGCGCGGCGAAUACGUCCCUGCUCCUUGCACACACCGCCCGUCACUCCACCCGAGCGGGGCCUAGGUGAGGCCCGAUCUCCUUCGGGAGGUCGGGUCGAGCCUAGGCUCCGUGAGGGGGGAGAAGUCGUAACAAGGUAGCCGUAGGGGAACCUACGGCUCGAUCACCUCCUAUC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.a.S.solfataricus.2.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.a.S.solfataricus.2.seq new file mode 100644 index 0000000..0afb8fa --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.a.S.solfataricus.2.seq @@ -0,0 +1,2 @@ +>d.16.a.S.solfataricus.2 +AAAUCCGGUUGAUCCUGCCGGACCCGACCGCUAUCGGGGUGGGGCUAAGCCAUGGGAGUCGUACGCUCCCGGGCAAGGGAGCGUGGCGGACGGCUGAGUAACACGUGGCUAACCUACCCUGAGGAGGGAGAUAACCCCGGGAAACUGGGGAUAAUCUCCCAUAGGCGAGGAGUCCUGGAACGGUUCCUCGCUGAAAGGCUCAUGGGCUAUUCCCCGCUCAUGAGCGCCUCAGGAUGGGGCUGCGGCCCAUCAGGUAGUUGGGGGGGUAAGGGCCCCCCAAGCCUAUAACGGGUAGGGGCCGUGAGAGCGGGAGCCCCCAGUUGGGCACUGAGACAAGGGCCCAGGCCCUACGGGGCGCACCAGGCGCGAAACGUCCCCAAUGCGCGGAAGCGUGAGGGCGCCACCCCGAGUGCUCCCGUAAGGGAGCUUUUCCCCGCUCUACAAAGGCGGGGGAAUAAGCGGGGGGCAAGUCUGGUGUCAGCCGCCGCGGUAAUACCAGCCCCGCGAGUGGUCGGGACUCUUACUGGGCCUAAAGCGCCCGUAGCCGGCCCGACAAGUCACUCCUUAAAGACCCCGGCUCAACCGGGGGAAUGGGGGUGAUACUGUCGGGCUAGGGGGCGGGAGAGGCCAGCGGUACUCCCGGAGUAGGGGCGAAAUCCUCAGAUCUCGGGAGGACCACCAGUGGCGAAAGCGGCUGGCUAGAACGCGCCCGACGGUGAGGGGCGAAAGCCGGGGCAGCAAAAGGGAUUAGAUACCCCUGUAGUCCCGGCUGUAAACAAUGCAGGCUAGGUGUCACAUGGGCUUAGAGCCCAUGUGGUGCCGCAGGGAAGCCGUUAAGCCUGCCGCCUGGGGAGUACGGUCGCAAGACUGAAACUUAAAGGAAUUGGCGGGGGAGCACCACAAGGGGUGGAACCUGCGGCUCAAUUGGAGUCAACGCCUGGAAUCUUACUAGGGGAGACCGCAGGAUGACGGCCAGGCUAACGACCUUGCCUGACUCGCGGAGAGGAGGUGCAUGGCCGUCGCCAGCUCGUGUUGUGAAAUGUCCUGUUAAGUCAGGCAACGAGCGAGACCCCCACCACUAGUUGGUAUCCUGGUCUCCGGGCCGGGACCACACUAGUGGGACUGCCGGCGUAAGCCGGAGGAGGGAGGGGGCCACGGCAGGUCAGCAUGCCCCGAAACCCCUGGGCCGCACGCGGGUUACAAUGGCAGGGACAGCGGGAUUCCGACCCCGAAAGGGGAAGGUAAUCCCUUAAACCCUGCCGCAGUUGGGAUCGAGGGCUGAAACUCGCCCUCGUGAACGAGGAAUCCCUAGUAACCGCAGAUCAACAAUCUGCGGUGAAUACGUCCCUGCUCCUUGCACACACCGCCCGUCGCUCCACCCGAGUAGGAGAGGGGUGAGGCCCCUUGCCUUUGGGUGGGGGGUCGAGCUUCUCUCCUGCAAGGGGGGAGAAGUCGUAACAAGGUAGCCGUAGGGGAACCUGCGGCUGGAUCACCUC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.A.globiformis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.A.globiformis.seq new file mode 100644 index 0000000..8d706e8 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.A.globiformis.seq @@ -0,0 +1,2 @@ +>d.16.b.A.globiformis +UUUCAACGGAGAGUUUGAUCCUGGCUCAGGAUGAACGCUGGCGGCGUGCUUAACACAUGCAAGUCGAACGAUGAUCCGGUGCUUGCACCGGGGAUUAGUGGCGAACGGGUGAGUAACACGUGAGUAACCUGCCCUUGACUCUGGGAUAAGCCUGGGAAACUGGGUCUAAUACCGGAUAUGACUCCUCAUCGCAUGGUGGGGGGUGGAAAGCUUUUUGUGGUUUUGGAUGGACUCGCGGCCUAUCAGCUUGUUGGUGAGGUAAUGGCUCACCAAGGCGACGACGGGUAGCCGGCCUGAGAGGGUGACCGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGAAAGCCUGAUGCAGCGACGCCGCGUGAGGGAUGACGGCCUUCGGGUUGUAAACCUCUUUCAGUAGGGAAGAAGCGAAAGUGACGGUACCUGCAGAAGAAGCGCCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGCGCAAGCGUUAUCCGGAAUUAUUGGGCGUAAAGAGCUCGUAGGCGGUUUGUCGCGUCUGCCGUGAAAGUCCGGGGCUCAACUCCGGAUCUGCGGUGGGUACGGGCAGACUAGAGUGAUGUAGGGGAGACUGGAAUUCCUGGUGUAGCGGUGAAAUGCGCAGAUAUCAGGAGGAACACCGAUGGCGAAGGCAGGUCUCUGGGCAUUAACUGACGCUGAGGAGCGAAAGCAUGGGGAGCGAACAGGAUUAGAUACCCUGGUAGUCCAUGCCGUAAACGUUGGGCACUAGGUGUGGGGGACAUUCCACGUUUUCCGCGCCGUAGCUAACGCAUUAAGUGCCCCGCCUGGGGAGUACGGCCGCAAGGCUAAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGCGGAGCAUGCGGAUUAAUUCGAUGCAACGCGAAGAACCUUACCAAGGCUUGACAUGGACCGGACCGCCGCAGAAAUGUGGUUUCUCCUUUUGGGGCCGGUUCACAGGUGGUGCAUGGUUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUCGUUCCAUGUUGCCAGCGCGUAAUGGCGGGGACUCAUGGGAGACUGCCGGGGUCAACUCGGAGGAAGGUGGGGACGACGUCAAAUCAUCAUGCCCCUUAUGUCUUGGGCUUCACGCAUGCUACAAUGGCCGGUACAAAGGGUUGCGAUACUGUGAGGUGGAGCUAAUCCCAAAAAGCCGGUCUCAGUUCGGAUUGGGGUCUGCAACUCGACCCCAUGAAGUCGGAGUCGCUAGUAAUCGCAGAUCAGCAACGCUGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCAAGUCACGAAAGUUGGUAACACCCGAAGCCGGUGGCCUAACCCCUUGUGGGAGGGAGCCGUCGAAGGUGGGACUGGCGAUUGGGACUAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGCGGCUGGAUCACCUCCUUUCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.A.tumefaciens.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.A.tumefaciens.seq new file mode 100644 index 0000000..dca4e6e --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.A.tumefaciens.seq @@ -0,0 +1,2 @@ +>d.16.b.A.tumefaciens +CUCAACUUGAGAGUUUGAUCCUGGCUCAGAACGAACGCUGGCGGCAGGCUUAACACAUGCAAGUCGAACGCCCCGCAAGGGGAGUGGCAGACGGGUGAGUAACGCGUGGGAAUCUACCGUGCCCUGCGGAAUAGCUCCGGGAAACUGGAAUUAAUACCGCAUACGCCCUACGGGGGAAAGAUUUAUCGGGGUAUGAUGAGCCCGCGUUGGAUUAGCUAGUUGGUGGGGUAAAGGCCUACCAAGGCGACGAUCCAUAGCUGGUCUGAGAGGAUGAUCAGCCACAUUGGGACUGAGACACGGCCCAAACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGGACAAUGGGCGCAAGCCUGAUCCAGCCAUGCCGCGUGAGUGAUGAAGGCCUUAGGGUUGUAAAGCUCUUUCACCGGAGAAGAUAAUGACGGUAUCCGGAGAAGAAGCCCCGGCUAACUUCGUGCCAGCAGCCGCGGUAAUACGAAGGGGGCUAGCGUUGUUCGGAAUUACUGGGCGUAAAGCGCACGUAGGCGGAUAUUUAAGUCAGGGGUGAAAUCCCAGAGCUCAACUCUGGAACUGCCUUUGAUACUGGGUAUCUUGAGUAUGGAAGAGGUAAGUGGAAUUCCGAGUGUAGAGGUGAAAUUCGUAGAUAUUCGGAGGAACGCCAGUGGCGAAGGCGGCUUACUGGUCCAUUACUGACGCUGAGGUGCGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGAAUGUUAGCCGUCGGGCAGUAUACUGUUCGGUGGCGCAGCUAACGCAUUAAACAUUCCGCCUGGGGAGUACGGUCGCAAGAUUAAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAAGCAACGCGCAGAACCUUACCAGCUCUUGACAUUCGGGGUUUGGGCAGUGGAGACAUUGUCCUUCAGUUAGGCUGGCCCCAGAACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUCGCCCUUAGUUGCCAGCAUUUAGUUGGGCACUCUAAGGGGACUGCCGGUGAUAAGCCGAGAGGAAGGUGGGGAUGACGUCAAGUCCUCAUGGCCCUUACGGGCUGGGCUACACACGUGCUACAAUGGUGGUGACAGUGGGCAGCGAGACAGCGAUGUCGAGCUAAUCUCCAAAAGCCAUCUCAGUUCGGAUUGCACUCUGCAACUCGAGUGCAUGAAGUUGGAAUCGCUAGUAAUCGCAGAUCAGCAUGCUGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUUGGUUUUACCCGAAGGUAGUGCGCUAACCGCAAGGAGGCAGCUAACCACGGUAGGGUCAGCGACUGGGGUGAAGUCGUAACAAGGUAGCCGUAGGGGAACCUGCGGCUGGAUCACCUCCUUUCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.Anabaena.sp.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.Anabaena.sp.seq new file mode 100644 index 0000000..040091c --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.Anabaena.sp.seq @@ -0,0 +1,2 @@ +>d.16.b.Anabaena.sp +GAAACGGAGAGUUUGAUCCUGGCUCAGGAUGAACGCUGGCGGUAUGCUUAACACAUGCAAGUCGAACGGUCUCUUCGGAGAUAGUGGCGGACGGGUGAGUAACGCGUGAGAAUCUAGCUUCAGGUCGGGGACAACCACUGGAAACGGUGGCUAAUACCGGAUGUGCCGAAAGGUGAAAGAUUUAUUGCCUGAAGAUGAGCUCGCGUCUGAUUAGCUAGUUGGUGUGGUAAGAGCGCACCAAGGCGACGAUCAGUAGCUGGUCUGAGAGGAUGAUCAGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUUUUCCGCAAUGGGCGAAAGCCUGACGGAGCAAUACCGCGUGAGGGAGGAAGGCUCUUGGGUUGUAAACCUCUUUUCUCAGGGAAUAAAAAAAUGAAGGUACCUGAGGAAUAAGCAUCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGAUGCAAGCGUUAUCCGGAAUGAUUGGGCGUAAAGCGUCCGCAGGUGGCACUGUAAGUCUGCUGUUAAAGAGCAAGGCUCAACCUUGUAAAGGCAGUGGAAACUACAGAGCUAGAGUACGUUCGGGGCAGAGGGAAUUCCUGGUGUAGCGGUGAAAUGCGUAGAGAUCAGGAAGAACACCGGUGGCGAAAGCGCUCUGCUAGGCCGUAACUGACACUGAGGGACGAAAGCUAGGGGAGCGAAUGGGAUUAGAUACCCCAGUAGUCCUAGCCGUAAACGAUGGAUACUAGGCGUGGCUUGUAUCGACCCGAGCCGUGCCGGAGCCAACGCGUUAAGUAUCCCGCCUGGGGAGUACGCACGCAAGUGUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGUAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCAAGACUUGACAUGUCGCGAAUCUUCUUGAAAGGGAAGAGUGCCUUAGGGAGCGCGAACACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUCGUUUUUAGUUGCCAGCAUUAAGUUGGGCACUCUAGAGAGACUGCCGGUGACAAACCGGAGGAAGGUGGGGAUGACGUCAAGUCAGCAUGCCCCUUACGUCUUGGGCUACACACGUACUACAAUGCUACGGACAGAGGGCAGCAAGCUAGCGAUAGCAAGCAAAUCCCGUAAACCGUAGCUCAGUUCAGAUCGCAGGCUGCAACUCGCCUGCGUGAAGGAGGAAUCGCUAGUAAUUGCAGGUCAGCAUACUGCAGUGAAUUCGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGAAGCUGGCAACGCCCGAAGUCAUUACUCCAACUUUUAGGAGAGGAGGAUGCCUAAGGCAGUGCUGGUGACUGGGGUGAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGUGGCUGGAUCACCUCCUUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.B.bronchiseptica2.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.B.bronchiseptica2.seq new file mode 100644 index 0000000..b4e37d1 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.B.bronchiseptica2.seq @@ -0,0 +1,2 @@ +>d.16.b.B.bronchiseptica2 +UGAACUGAAGAGUUUGAUCCUGGCUCAGAUUGAACGCUGGCGGGAUGCUUUACACAUGCAAGUCGGACGGCAGCACGGGCUUCGGCCUGGUGGCGAGUGGCGAACGGGUGAGUAAUGUAUCGGAACGUGCCCAGUAGCGGGGGAUAACUACGCGAAAGCGUGGCUAAUACCGCAUACGCCCUACGGGGGAAAGCGGGGGACCUUCGGGCCUCGCACUAUUGGAGCGGCCGAUAUCGGAUUAGCUAGUUGGUGGGGUAACGGCCUACCAAGGCGACGAUCCGUAGCUGGUUUGAGAGGACGACCAGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUUUUGGACAAUGGGGGCAACCCUGAUCCAGCCAUCCCGCGUGUGCGAUGAAGGCCUUCGGGUUGUAAAGCACUUUUGGCAGGAAAGAAACGGCACGGGCUAAUAUCCUGUGCAACUGACGGUACCUGCAGAAUAAGCACCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGUGCAAGCGUUAAUCGGAAUUACUGGGCGUAAAGCGUGCGCAGGCGGUUCGGAAAGAAAGAUGUGAAAUCCCAGGGCUUAACCUUGGAACUGCAUUUUUAACUACCGGGCUAGAGUGUGUCAGAGGGAGGUGGAAUUCCGCGUGUAGCAGUGAAAUGCGUAGAUAUGCGGAGGAACACCGAUGGCGAAGGCAGCCUCCUGGGAUAACACUGACGCUCAUGCACGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCCCUAAACGAUGUCAACUAGCUGUUGGGGCCUUCGGGCCUUGGUAGCGCAGCUAACGCGUGAAGUUGACCGCCUGGGGAGUACGGUCGCAAGAUUAAAACUCAAAGGAAUUGACGGGGACCCGCACAAGCGGUGGAUGAUGUGGAUUAAUUCGAUGCAACGCGAAAAACCUUACCUACCCUUGACAUGUCUGGAAUCCCGAAGAGAUUUGGGAGUGCUCGCAAGAGAACCGGAACACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUCAUUAGUUGCUACGAAAGGGCACUCUAAUGAGACUGCCGGUGACAAACCGGAGGAAGGUGGGGAUGACGUCAAGUCCUCAUGGCCCUUAUGGGUAGGGCUUCACACGUCAUACAAUGGUCGGGACAGAGGGUCGCCAACCCGCGAGGGGGAGCCAAUCCCAGAAACCCGAUCGUAGUCCGGAUCGCAGUCUGCAACUCGACUGCGUGAAGUCGGAAUCGCUAGUAAUCGCGGAUCAGCAUGUCGCGGUGAAUACGUUCCCGGGUCUUGUACACACCGCCCGUCACACCAUGGGAGUGGGUUUUACCAGAAGUAGUUAGCCUAACCGCAAGGGGGGCGAUUACCACGGUAGGAUUCAUGACUGGGGUGAAGUCGUAACAAGGUAGCCGUAUCGGAAGGUGCGGCUGGAUCACCUCCUUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.B.burgdorferi.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.B.burgdorferi.seq new file mode 100644 index 0000000..818a7c0 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.B.burgdorferi.seq @@ -0,0 +1,2 @@ +>d.16.b.B.burgdorferi +AUAACGAAGAGUUUGAUCCUGGCUUAGAACUAACGCUGGCAGUGCGUCUUAAGCAUGCAAGUCAAACGGGAUGUAGCAAUACAUUCAGUGGCGAACGGGUGAGUAACGCGUGGAUGAUCUACCUAUGAGAUGGGGAUAACUAUUAGAAAUAGUAGCUAAUACCGAAUAAGGUCAGUUAAUUUGUUAAUUGAUGAAAGGAAGCCUUUAAAGCUCUCGCUUGUAGAUGAGUCUGCGUCUUAUUAGCUAGUUGGUAGGGUAAAUGCCUACCAAGGCAAUGAUAAGUAACCGGCCUGAGAGGGUGAACGGUCACACUGGAACUGAGAUACGGUCCAGACUCCUACGGGAGGCAGCAGCUAAGAAUCUUCCGCAAUGGGCGGAAGCCUGACGGAGCGACACUGCGUGAAUGAAGAAGGUCGAAAGAUUGUAAAAUUCUUUUAUAAAUGAGGAAUAAGCUUUGUAGGAAAUGACAAAGUGAUGACGUUAAUUUAUGAAUAAGCCCCGGCUAAUUACGUGCCAGCAGCCGCGGUAAUACGUAAGGGGCGAGCGUUGUUCGGGAUUAUUGGGCGUAAAGGGUGAGUAGGCGGAUAUAUAAGUCUAUGCAUAAAAUACCACAGCUCAACUGUGGACCUAUGUUGGAAACUAUAUGUCUAGAGUCUGAUAGAGGAAGUUAGAAUUUCUGGUGUAAGGGUGGAAUCUGUUGAUAUCAGAAAGAAUACCGGAGGCGAAGGCGAACUUCUGGGUCAAGACUGACGCUGAGUCACGAAAGCGUAGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCUACGCUGUAAACGAUGCACACUUGGUGUUAACUAAAAGUUAGUACCGAAGCUAACGUGUUAAGUGUGCCGCCUGGGGAGUAUGCUCGCAAGAGUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGAUACGCGAGGAACCUUACCAGGGCUUGACAUAUAUAGGAUAUAGUUAGAGAUAAUUAUUCCCCGUUUGGGGUCUAUAUACAGGUGCUGCAUGGUUGUCGUCAGCUCGUGCUGUGAGGUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUUAUCUGUUACCAGCAUGUAAUGGUGGGGACUCAGAUAAGACUGCCGGUGAUAAGUCGGAGGAAGGUGAGGAUGACGUCAAAUCAUCAUGGCCCUUAUGUCCUGGGCUACACACGUGCUACAAUGGCCUGUACAAAGCGAAGCGAAACAGUGAUGUGAAGCAAAACGCAUAAAGCAGGUCUCAGUCCGGAUUGAAGUCUGAAACUCGACUUCAUGAAGUUGGAAUCGCUAGUAAUCGUAUAUCAGAAUGAUACGGUGAAUACGUUCUCGGGCCUUGUACACACCGCCCGUCACACCACCCGAGUUGAGGAUACCCGAAGCUAUUAUUCUAACCCGUAAGGGAGGAAGGUAUUUAAGGUAUGUUUAGUGAGGGGGGUGAAGUCGUAACAAGGUAGCCGUACUGGAAAGUGCGGCUGGAUCACCUCCUUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.B.japonicum.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.B.japonicum.seq new file mode 100644 index 0000000..4c06124 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.B.japonicum.seq @@ -0,0 +1,2 @@ +>d.16.b.B.japonicum +CCAACUUGAGAGUUUGAUCCUGGCUCAGAGCGAACGCUGGCGGCAGGCUUAACACAUGCAAGUCGAGCGGGCGUAGCAAUACGUCAGCGGCAGACGGGUGAGUAACGCGUGGGAACGUACCUUUUGGUUCGGAACAACACAGGGAAACUUGUGCUAAUACCGGAUAAGCCCUUACGGGGAAAGAUUUAUCGCCGAAAGAUCGGCCCGCGUCUGAUUAGCUAGUUGGUAGGGUAACGGCCUACCAAGGCGACGAUCAGUAGCUGGUCUGAGAGGAUGAUCAGCCACAUUGGGACUGAGACACGGCCCAAACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGGACAAUGGGGGCAACCCUGAUCCAGCCAUGCCGCGUGAGUGAUGAAGGCCCUAGGGUUGUAAAGCUCUUUUGUGCGGGAAGAUAAUGACGGUACCGCAAGAAUAAGCCCCGGCUAACUUCGUGCCAGCAGCCGCGGUAAUACGAAGGGGGCUAGCGUUGCUCGGAAUCACUGGGCGUAAAGGGUGCGUAGGCGGGUCUUUAAGUCAGGGGUGAAAUCCUGGAGCUCAACUCCAGAACUGCCUUUGAUACUGAAGAUCUUGAGUUCGGGAGAGGUGAGUGGAACUGCGAGUGUAGAGGUGAAAUUCGUAGAUAUUCGCAAGAACACCAGUGGCGAAGGCGGCUCACUGGCCCGAUACUGACGCUGAGGCACGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGAAUGCCAGCCGUUAGUGGGUUUACUCACUAGUGGCGCAGCUAACGCUUUAAGCAUUCCGCCUGGGGAGUACGGUCGCAAGAUUAAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGACGCAACGCGCAGAACCUUACCAGCCCUUGACAUGUCCAGGACCGGUCGCAGAGAUGUGACCUUCUCUUCGGAGCCUGGAACACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCCCGUCCUUAGUUGCUACCAUUUAGUUGAGCACUCUAAGGAGACUGCCGGUGAUAAGCCGCGAGGAAGGUGGGGAUGGCGUCAAGUCCUCAUGGCCCUUACGGGCUGGGCUACACACGUGCUACAAUGGCGGUGACAAUGGGAUGCUAAGGGGCGACCCUUCGCAAAUCUCAAAAAGCCGUCUCAGUUCGGAUUGGGCUCUGCAACUCGAGCCCAUGAAGUUGGAAUCGCUAGUAAUCGUGGAUCAGCACGCCACGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUUGGCUUUACCUGAAGACGGUGCGCUAACCAGCAAUGGAGGCAGCCGGCCACGGUAGGGUCAGCGACUGGGGUGAAGUCGUAACAAGGUAGCCGUAGGGGAACCUGCGGCUGGAUCACCUCCUUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.B.subtilis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.B.subtilis.seq new file mode 100644 index 0000000..9433d8f --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.B.subtilis.seq @@ -0,0 +1,2 @@ +>d.16.b.B.subtilis +UUUAUCGGAGAGUUUGAUCCUGGCUCAGGACGAACGCUGGCGGCGUGCCUAAUACAUGCAAGUCGAGCGGACAGGUGGGAGCUUGCUCCCGAUGUUAGCGGCGGACGGGUGAGUAACACGUGGGUAACCUGCCUGUAAGACUGGGAUAACUCCGGGAAACCGGGGCUAAUACCGGAUGGUUGUUUGAACCGCAUGGUUCAAACAUAAAAGGUGGCUUCGGCUACCACUUACAGAUGGACCCGCGGCGCAUUAGCUAGUUGGUGAGGUAACGGCUCACCAAGGCAACGAUGCGUAGCCGACCUGAGAGGGUGAUCGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUAGGGAAUCUUCCGCAAUGGACGAAAGUCUGACGGAGCAACGCCGCGUGAGUGAUGAAGGUUUUCGGAUCGUAAAGCUCUGUUGUUAGGGAAGAACAAGUACCGUUCGAAUAGGGCGGUACCUUGACGGUACCUAACCAGAAAGCCACGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGUGGCAAGCGUUGUCCGGAAUUAUUGGGCGUAAAGGGCUCGCAGGCGGUUUCUUAAGUCUGAUGUGAAAGCCCCCGGCUCAACCGGGGAGGGUCAUUGGAAACUGGGGAACUUGAGUGCAGAAGAGGAGAGUGGAAUUCCACGUGUAGCGGUGAAAUGCGUAGAGAUGUGGAGGAACACCAGUGGCGAAGGCGACUCUCUGGUCUGUAACUGACGCUGAGGAGCGAAAGCGUGGGGAGCGAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGAGUGCUAAGUGUUAGGGGGUUUCCGCCCCUUAGUGCUGCAGCUAACGCAUUAAGCACUCCGCCUGGGGAGUACGGUCGCAAGACUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAAGCAACGCGAAGAACCUUACCAGGUCUUGACAUCCUCUGACAAUCCUAGAGAUAGGACGUCCCCUUCGGGGGCAGAGUGACAGGUGGUGCAUGGUUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGAUCUUAGUUGCCAGCAUUCAGUUGGGCACUCUAAGGUGACUGCCGGUGACAAACCGGAGGAAGGUGGGGAUGACGUCAAAUCAUCAUGCCCCUUAUGACCUGGGCUACACACGUGCUACAAUGGACAGAACAAAGGGCAGCGAAACCGCGAGGUUAAGCCAAUCCCACAAAUCUGUUCUCAGUUCGGAUCGCAGUCUGCAACUCGACUGCGUGAAGCUGGAAUCGCUAGUAAUCGCGGAUCAGCAUGCCGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCACGAGAGUUUGUAACACCCGAAGUCGGUGAGGUAACCUUUUAGGAGCCAGCCGCCGAAGGUGGGACAGAUGAUUGGGGUGAAGUCGUAACAAGGUAGCCGUAUCGGAAGGUGCGGCUGGAUCACCUCCUUUCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.C.pneumoniae.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.C.pneumoniae.seq new file mode 100644 index 0000000..f65748e --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.C.pneumoniae.seq @@ -0,0 +1,2 @@ +>d.16.b.C.pneumoniae +UUUUCUGAGAAUUUGAUCUUAGUUCAGAUUGAACGCUGGCGGCGUGGAUGAGGCAUGCAAGUCGAACGGAAUAAUGACUUCGGUUGUUAUUUAGUGGCGGAAGGGUUAGUAGUACAUAGAUAAUCUGCCCUCAACUUGGGGAUAACGGUUGGAAACGAUCGCUAAUACCGAAUGUAGUGUAAUUAGGCAUCUAAUAUAUAUUAAAGAAGGGGAUCUUCGGACCUUUCGGUUGAGGAAGAGUUUAUGCGAUAUCAGCUUGUUGGUGGGGUAAAAGCCCACCAAGGCGAUGACGUCUAGGCGGAUUGAGAGAUUGACCGCCAACACUGGGACUGAGACACUGCCCAGACUCCUACGGGAGGCUGCAGUCGAGAAUCUUUCGCAAUGGACGAAAGUCUGACGAAGCGACGCCGCGUGUGUGAUGAAGGCCUUAGGGUUGUAAAGCACUUUCGCCUGGGAAUAAGAGAGAUUGGCUAAUAUCCAAUCGAUUUGAGCGUACCAGGUAAAGAAGCACCGGCUAACUCCGUGCCAGCAGCUGCGGUAAUACGGAGGGUGCUAGCGUUAAUCGGAUUUAUUGGGCGUAAAGGGCGUGUAGGCGGAAAGGAAAGUUAGAUGUUAAAUUUUGGGGCUCAACCCCAAGUCAGCAUUUAAAACUAUCUUUCUAGAGGAUAGAUGGGGAAAAGGGAAUUCCACGUGUAGCGGUGAAAUGCGUAGAUAUGUGGAAGAACACCAGUGGCGAAGGCGCUUUUCUAAUUUAUACCUGACGCUAAGGCGCGAAAGCAAGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCUUGCCGUAAACGAUGCAUACUUGAUGUGGAUGGUCUCAACCCCAUCCGUGUCGGAGCUAACGUGUUAAGUAUGCCGCCUGAGGAGUACACUCGCAAGGGUGAAACUCAAAAGAAUUGACGGGGGCCCGCACAAGCAGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGGACCUUACCUGGACUUGACAUGUAUUUGACAACUGUAGAAAUACAGCUUUCCGCAAGGACAGAUACACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGCCGUGAGGUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCGUUAGUUGCCAGCACUUAGGGUGGGAACUCUAACGAGACUGCCUGGGUUAACCAGGAGGAAGGCGAGGAUGACGUCAAGUCAGCAUGGCCCUUAUGUCCAGGGCGACACACGUGCUACAAUGGUUAGUACAGAAGGUAGCAAGAUCGUGAGAUGGAGCAAAUCCUAAAAGCUAGCCCCAGUUCGGAUUGUAGUCUGCAACUCGACUACAUGAAGUCGGAAUUGCUAGUAAUGGCGUGUCAGCCAUAACGCCGUGAAUACGUUCUCGGGCCUUGUACACACCGCCCGUCACAUCAUGGGAGUUGGUUUUACCUUAAGUCGUUGACUCAACCUAUUUAUAGGAGAGAGGCGCCCAAGGUGAGGCUGAUGACUGGGAUGAAGUCGUAACAAGGUAGCCCUACCGGAAGGUGGGGCUGGAUCACCUCCUUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.C.psittaci.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.C.psittaci.seq new file mode 100644 index 0000000..4218316 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.C.psittaci.seq @@ -0,0 +1,2 @@ +>d.16.b.C.psittaci +UUUUCUGAGAAUUUGAUCUUGGUUCAGAUUGAACGCUGGCGGCGUGGAUGAGGCAUGCAAGUCGAACGGAAUAAUGACUUCGGUUGUUAUUUAGUGGCGGAAGGGUUAGUAAUACAUAGAUAAUCUGUCCUCAACUUGGGAAUAACGGUUGGAAACGACCGCUAAUACCGAAUGUGGUAUGUUUAGGCAUCUAAAACAUAUUAAAGAAGGGGAUCUUCGGACCUUUCGGUUGAGGGAGAGUCUAUGGGAUAUCAGCUUGUUGGUGGGGUAAUGGCCUACCAAGGCUUUGACGUCUAGGCGGAUUGAGAGAUUGACCGCCAACACUGGGACUGAGACACUGCCCAGACUUCUACGGAAGGCUGCAGUCGAGAAUCUUUCGCAAUGGACGAAAGUCUGACGAAGCGACGCCGCGUGUGUGAUGAAGGCUCUAGGGUUGUAAAGCACUUUCGCUUGGGAAUAAGAGAGAUUGGCUAAUAUCCAAUCGAUUUGAGCGUACCAGGUAAAGAAGCACCGGCUAACUCCGUGCCAGCAGCUGCGGUAAUACGGAGGGUGCUAGCGUUAAUCGGAUUUAUUGGGCGUAAAGGGCGUGUAGGCGGAAAGGAAAGUUAGAUGUUAAAUCUUGGGGCUCAACCCCAAGCCAGCAUCUAAUACUAUCUUUCUAGAGGGUAGAUGGAGAAAAGGGAAUUCCACGUGUAGCGGUGAAAUGCGUAGAUAUGUGGAAGAACACCAGUGGCGAAGGCGCUUUUCUAAUUUACACCUGACGCUAAGGCGCGAAAGCAAGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCUUGCCGUAAACGAUGCAUACUUGAUGUGGAUAGUCUCAACCCUAUCCGUGUCGUAGCUAACGCGUUAAGUAUGCCGCCUGAGGAGUACACUCGCAAGGGUGAAACUCAAAAGAAUUGACGGGGGCCCGCACAAGCAGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCUGGGCUUGACAUGUAUUUGACCGCGGCAGAAAUGUCGUUUUCCGCAAGGACAGAUACACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGCCGUGAGGUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCGUUAGUUGCCAACACUUAGGGUGGGAACUCUAACGAGACUGCCUGGGUUAACCAGGAGGAAGGCGAGGAUGACGUCAAGUCAGCAUGGCCCUUAUGCCCAGGGCUACACACGUGCUACAAUGGCCAGUACAGAAGGUAGCAAUAUCGUGAGAUGGAGCAAAUCCUCAAAGCUGGCCCCAGUUCGGAUUGUAGUCUGCAACUCGACUACAUGAAGUCGGAAUUGCUAGUAAUGGCGUGUCAGCUAUAACGCCGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACAUCAUGGGAGUUGGUUUUGCCUUAAGUCGUUGACUCAACCUGCAAAGGAGAGAGGCGCCCAAGGUGAGGCUGAUGACUGGGAUGAAGUCGUAACAAGGUAGCCCUACCGGAAGGUGGGGCUGGAUCACCUCCUUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.C.testosteroni.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.C.testosteroni.seq new file mode 100644 index 0000000..5084a44 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.C.testosteroni.seq @@ -0,0 +1,2 @@ +>d.16.b.C.testosteroni +CGAACUAUAGAGUUUGAUCCUGGCUCAGAUUGAACGCUGGCGGCAUGCUUUACACAUGCAAGUCGAACGGUAACAGGUCUUCGGAUGCUGACGAGUGGCGAACGGGUGAGUAAUACAUCGGAACGUGCCUAGUAGUGGGGGAUAACUACUCGAAAGAGUAGCUAAUACCGCAUGAGAUCUACGGAUGAAAGCAGGGGACCUUCGGGCCUUGUGCUACUAGAGCGGCUGAUGGCAGAUUAGGUAGUUGGUGGGGUAAAGGCUUACCAAGCCUGCGAUCUGUAGCUGGUCUGAGAGGACGACCAGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUUUUGGACAAUGGGCGAAAGCCUGAUCCAGCAAUGCCGCGUGCAGGAUGAAGGCCCUCGGGUUGUAAACUGCUUUUGUACGGAACGAAAAGCCUGGGGCUAAUAUCCCCGGGUCAUGACGGUACCGUAAGAAUAAGCACCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGUGCAAGCGUUAAUCGGAAUUACUGGGCGUAAAGCGUGCGCAGGCGGUUUUGUAAGACAGUGGUGAAAUCCCCGGGCUCAACCUGGGAACUGCCAUUGUGACUGCAAGGCUAGAGUGCGGCAGAGGGGGAUGGAAUUCCGCGUGUAGCAGUGAAAUGCGUAGAUAUGCGGAGGAACACCGAUGGCGAAGGCAAUCCCCUGGGCCUGCACUGACGCUCAUGCACGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCCCUAAACGAUGUCAACUGGUUGUUGGGUCUUAACUGACUCAGUAACGAAGCUAACGCGUGAAGUUGACCGCCUGGGGAGUACGGCCGCAAGGUUGAAACUCAAAGGAAUUGACGGGGACCCGCACAAGCGGUGGAUGAUGUGGUUUAAUUCGAUGCAACGCGAAAAACCUUACCCACCUUUGACAUGGCAGGAACUUACCAGAGAUGGUUUGGUGCUCGAAAGAGAACCUGCACACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGCCAUUAGUUGCUACAUUCAGUUGAGCACUCUAAUGGGACUGCCGGUGACAAACCGGAGGAAGGUGGGGAUGACGUCAAGUCCUCAUGGCCCUUAUAGGUGGGGCUACACACGUCAUACAAUGGCUGGUACAAAGGGUUGCCAACCCGCGAGGGGGAGCUAAUCCCAUAAAGCCAGUCGUAGUCCGGAUCGCAGUCUGCAACUCGACUGCGUGAAGUCGGAAUCGCUAGUAAUCGUGGAUCAGAAUGUCACGGUGAAUACGUUCCCGGGUCUUGUACACACCGCCCGUCACACCAUGGGAGCGGGUCUCGCCAGAAGUAGGUAGCCUAACCGUAAGGAGGGCGCUUACCACGGCGGGGUUCGUGACUGGGGUGAAGUCGUAACAAGGUAGCCGUAUCGGAAGGUGCGGCUGGAUCACCUCCUUUCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.C.trachomatis.L2.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.C.trachomatis.L2.seq new file mode 100644 index 0000000..4ae3dc2 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.C.trachomatis.L2.seq @@ -0,0 +1,2 @@ +>d.16.b.C.trachomatis.L2 +UUUUCUGAGAAUUUGAUCUUGGUUCAGAUUGAACGCUGGCGGCGUGGAUGAGGCAUGCAAGUCGAACGGAGCAAUUGUUUCGGCAAUUGUUUAGUGGCGGAAGGGUUAGUAAUGCAUAGAUAAUUUGUCCUUAACUUGGGAAUAACGGUUGGAAACGGCCGCUAAUACCGAAUGUGGCGAUAUUUGGGCAUCCGAGUAACGUUAAAGAAGGGGAUCUUAGGACCUUUCGGUUAAGGGAGAGUCUAUGUGAUAUCAGCUAGUUGGUGGGGUAAAGGCCUACCAAGGCUAUGACGUCUAGGCGGAUUGAGAGAUUGGCCGCCAACACUGGGACUGAGACACUGCCCAGACUCCUACGGGAGGCUGCAGUCGAGAAUCUUUCGCAAUGGACGGAAGUCUGACGAAGCGACGCCGCGUGUGUGAUGAAGGCUCUAGGGUUGUAAAGCACUUUCGCUUGGGAAUAAGAGAAGGCGGUUAAUACCCGCUGGAUUUGAGCGUACCAGGUAAAGAAGCACCGGCUAACUCCGUGCCAGCAGCUGCGGUAAUACGGAGGGUGCUAGCGUUAAUCGGAUUUAUUGGGCGUAAAGGGCGUGUAGGCGGAAAGGUAAGUUAGUUGUCAAAGAUCGGGGCUCAACCCCGAGUCGGCAUCUAAUACUAUUUUUCUAGAGGGUAGAUGGAGAAAAGGGAAUUUCACGUGUAGCGGUGAAAUGCGUAGAUAUGUGGAAGAACACCAGUGGCGAAGGCGCUUUUCUAAUUUAUACCUGACGCUAAGGCGCGAAAGCAAGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCUUGCCGUAAACGAUGCAUACUUGAUGUGGAUGGUCUCAACCCCAUCCGUGUCGGAGCUAACGCGUUAAGUAUGCCGCCUGAGGAGUACACUCGCAAGGGUGAAACUCAAAAGAAUUGACGGGGGCCCGCACAAGCAGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGGACCUUACCUGGGUUUGACAUGUAUAUGACCGCGGCAGAAAUGUCGUUUUCCGCAAGGACAUAUACACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGCCGUGAGGUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCGUUAGUUGCCAGCACUUAGGGUGGGAACUCUAACGAGACUGCCUGGGUUAACCAGGAGGAAGGCGAGGAUGACGUCAAGUCAGCAUGGCCCUUAUGCCCAGGGCGACACACGUGCUACAAUGGCCAGUACAGAAGGUAGCAAGAUCGUGAGAUGGAGCAAAUCCUCAAAGCUGGCCCCAGUUCGGAUUGUAGUCUGCAACUCGACUACAUGAAGUCGGAAUUGCUAGUAAUGGCGUGUCAGCCAUAACGCCGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACAUCAUGGGAGUUGGUUUUACCUUAAGUCGUUGACUCAACCCGCAAGGGAGAGAGGCGCCCAAGGUGAGGCUGAUGACUAGGAUGAAGUCGUAACAAGGUAGCCCUACCGGAAGGUGGGGCUGGAUCACCUCCUUUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.E.coli.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.E.coli.seq new file mode 100644 index 0000000..6f67dd9 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.E.coli.seq @@ -0,0 +1,2 @@ +>d.16.b.E.coli +AAAUUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGGCCUAACACAUGCAAGUCGAACGGUAACAGGAAGAAGCUUGCUUCUUUGCUGACGAGUGGCGGACGGGUGAGUAAUGUCUGGGAAACUGCCUGAUGGAGGGGGAUAACUACUGGAAACGGUAGCUAAUACCGCAUAACGUCGCAAGACCAAAGAGGGGGACCUUCGGGCCUCUUGCCAUCGGAUGUGCCCAGAUGGGAUUAGCUAGUAGGUGGGGUAACGGCUCACCUAGGCGACGAUCCCUAGCUGGUCUGAGAGGAUGACCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGCAAGCCUGAUGCAGCCAUGCCGCGUGUAUGAAGAAGGCCUUCGGGUUGUAAAGUACUUUCAGCGGGGAGGAAGGGAGUAAAGUUAAUACCUUUGCUCAUUGACGUUACCCGCAGAAGAAGCACCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGUGCAAGCGUUAAUCGGAAUUACUGGGCGUAAAGCGCACGCAGGCGGUUUGUUAAGUCAGAUGUGAAAUCCCCGGGCUCAACCUGGGAACUGCAUCUGAUACUGGCAAGCUUGAGUCUCGUAGAGGGGGGUAGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGGAGGAAUACCGGUGGCGAAGGCGGCCCCCUGGACGAAGACUGACGCUCAGGUGCGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGUCGACUUGGAGGUUGUGCCCUUGAGGCGUGGCUUCCGGAGCUAACGCGUUAAGUCGACCGCCUGGGGAGUACGGCCGCAAGGUUAAAACUCAAAUGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCUGGUCUUGACAUCCACGGAAGUUUUCAGAGAUGAGAAUGUGCCUUCGGGAACCGUGAGACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUUGUGAAAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCCUUUGUUGCCAGCGGUCCGGCCGGGAACUCAAAGGAGACUGCCAGUGAUAAACUGGAGGAAGGUGGGGAUGACGUCAAGUCAUCAUGGCCCUUACGACCAGGGCUACACACGUGCUACAAUGGCGCAUACAAAGAGAAGCGACCUCGCGAGAGCAAGCGGACCUCAUAAAGUGCGUCGUAGUCCGGAUUGGAGUCUGCAACUCGACUCCAUGAAGUCGGAAUCGCUAGUAAUCGUGGAUCAGAAUGCCACGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUGGGUUGCAAAAGAAGUAGGUAGCUUAACCUUCGGGAGGGCGCUUACCACUUUGUGAUUCAUGACUGGGGUGAAGUCGUAACAAGGUAACCGUAGGGGAACCUGCGGUUGGAUCACCUCCUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.Frankia.sp.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.Frankia.sp.seq new file mode 100644 index 0000000..7592528 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.Frankia.sp.seq @@ -0,0 +1,2 @@ +>d.16.b.Frankia.sp +UUGAUGGAGAGUUUGAUCCUGGCUCAGGACGAACGCUGGCGGCGUGCUUAACACAUGCAAGUCGAGCGGGGAGCUUCGGCUCUCAGCGGCGAACGGGUGAGUAACACGUGGGCAACCUGCCCCGAGCUCUGGAAUAACCUCGGGAAACCGGGGCUAAUGCCGGAUAUGACAUUGCCGGGCAUCUGGUGGUGUGGAAAGAUUUAUCGGCUCGGGAUGGGCCCGCGGCCUAUCAGCUUGUUGGUGGGGUGAUGGCCUACCAAGGCGACGACGGGUAGCCGGCCUGAGAGGGCGACCGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCGCAAUGGGCGGAAGCCUGACGCAGCGACGCCGCGUGGGGGAUGACGGCCUUCGGGUUGUAAACCUCUUUCAGCAGGGACGAAGCGAGAGUGACGGUACCUGCAGAAGAAGCACCGGCCAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGUGCAAGCGUUGUCCGGAAUUAUUGGGCGUAAAGAGCUCGUAGGCGGCCUGUUGCGUCGGCUGUGAAAACCCGGGGCUCAACUCCGGGCCUGCAGUCGAUACGGGCAGGCUAGAGUCCGGCAGGGGAGACUGGAAUUCCUGGUGUAGCGGUGAAAUGCGCAGAUAUCAGGAGGAACACCGGUGGCGAAGGCGGGUCUCUGGGCCGGAACUGACGCUAAGGAGCGAAAGCGUGGGGAGCGAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGUUGGGCGCUAGGUGUGGGGGACCUUCCACGGCCUCCGUGCCGCAGCUAACGCAUUAAGCGCCCCGCCUGGGGAGUACGGCCGCAAGGCUAAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGCGGAGCAUGUGGCUUAAUUCGAUGCAACGCGAAGAACCUUACCAGGGCUUGACAUGCAGGGAAAUCUCGUAGAGAUACGGGGUCCGUAAGGGUCCUGCACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUCGUCCUAUGUUGCCAGCGAGUCGUGUCGGGGACUCAUAGGAGACUGCCGGGGUCAACUCGGAGGAAGGUGGGGAUGACGUCAAGUCAUCAUGCCCCUUACGUCCUGGGCUGCACACAUGCUACAAUGGCCGGUACAAAGGGCUGCGAUGCCGUGAGGUGGAGCGAAUCCCAAAAAGCCGGUCUCAGUUCGGAUCGGGGUCUGCAACUCGACCCCGUGAAGUCGGAGUCGCUAGUAAUCGCAGAUCAGCAAUGCUGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACGUCACGAAAGUCGGUAACACCCGAAGCCGGUGGCCUAACCCUUGUGGGGGGAGCCGUCGAAGGUGGGACCGGCGAUUGGGACGAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGCGGCUGGAUCACCUCCUUUCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.H.influenzae.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.H.influenzae.seq new file mode 100644 index 0000000..dada154 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.H.influenzae.seq @@ -0,0 +1,2 @@ +>d.16.b.H.influenzae +AAUUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGGCUUAACACAUGCAAGUCGAACGGUAGCAGGAGAAAGCUUGCUUUCUUGCUGACGAGUGGCGGACGGGUGAGUAAUGCUUGGGAAUCUGGCUUAUGGAGGGGGAUAACGACGGGAAACUGUCGCUAAUACCGCGUAUUAUCGGAAGAUGAAAGUGCGGGACUGAGAGGCCGCAUGCCAUAGGAUGAGCCCAAGUGGGAUUAGGUAGUUGGUGGGGUAAAUGCCUACCAAGCCUGCGAUCUCUAGCUGGUCUGAGAGGAUGACCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCGCAAUGGGGGGAACCCUGACGCAGCCAUGCCGCGUGAAUGAAGAAGGCCUUCGGGUUGUAAAGUUCUUUCGGUAUUGAGGAAGGUUGAUGUGUUAAUAGUACAUCAAAUUGACGUUAAAUACAGAAGAAGCACCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGUGCGAGCGUUAAUCGGAAUAACUGGGCGUAAAGGGCACGCAGGCGGUUAUUUAAGUGAGGUGUGAAAGCCCUGGGCUUAACCUAGGAAUUGCAUUUCAGACUGGGUAACUAGAGUACUUUAGGGAGGGGUAGAAUUCCACGUGUAGCGGUGAAAUGCGUAGAGAUGUGGAGGAAUACCGAAGGCGAAGGCAGCCCCUUGGGAAUGUACUGACGCUCAUGUGCGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCUGUAAACGCUGUCGAUUUGGGGAUUGGGCUUAGAGCUUGGUGCCCGUAGCUAACGUGAUAAAUCGACCGCCUGGGGAGUACGGCCGCAAGGUUAAAACUCAAAUGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCUACUCUUGACAUCCUAAGAAGAGCUCAGAGAUGAGCUUGUGCCUUCGGGAACUUAGAGACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUUGUGAAAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCCUUUGUUGCCAGCGACUUGGUCGGGAACUCAAAGGAGACUGCCAGUGAUAAACUGGAGGAAGGUGGGGAUGACGUCAAGUCAUCAUGGCCCUUACGAGUAGGGCUACACACGUGCUACAAUGGCGUAUACAGAGGGAAGCGAAGCUGCGAGGUGGAGCGAAUCUCAUAAAGUACGUCUAAGUCCGGAUUGGAGUCUGCAACUCGACUCCAUGAAGUCGGAAUCGCUAGUAAUCGCGAAUCAGAAUGUCGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUGGGUUGUACCAGAAGUAGAUAGCUUAACCUUUUGGAGGGCGUUUACCACGGUAUGAUUCAUGACUGGGGUGAAGUCGUAACAAGGUAACCGUAGGGGAACCUGCGGUUGGAUCACCUCCUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.L.interrogans.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.L.interrogans.seq new file mode 100644 index 0000000..042147f --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.L.interrogans.seq @@ -0,0 +1,2 @@ +>d.16.b.L.interrogans +AACACGGAGAGUUUGAUCCUGGCUCAGAACUAACGCUGGCGGCGCGUCUUAAACAUGCAAGUCAAGCGGAGUAGCAAUACUCAGCGGCGAACGGGUGAGUAACACGUGGGUAAUCUUCCUCUGAGUCUGGGAUAACUUUCCGAAAGGGAAGCUAAUACUGGAUGGUCCCGAGAGAUCACAAGAUUUUUCGGGUAAAGAUUUAUUGCUCGGAGAUGAGCCCGCGUCCGAUUAGCUAGUUGGUGAGGUAAAGGCUCACCAAGGCGACGAUCGGUAGCCGGCCUGAGAGGGUGUUCGGCCACAAUGGAACUGAGACACGGUCCAUACUCCUACGGGAGGCAGCAGUUAAGAAUCUUGCUCAAUGGGGGGAACCUGAAGCAGCGACGCCGCGUGAACGAUGAAGGUCUUCGGAUUGUAAAGUUCAGUAAGCAGGGAAAAAUAAGCAGCAAUGUGAUGAUGGUACCUGCCUAAAGCACCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAUGGUGCAAGCGUUGUUCGGAAUCAUUGGGCGUAAAGGGUGCGUAGGCGGACAUGUAAGUCAGGUGUGAAAACUGCGGGCUCAACUCGCAGCCUGCACUUGAAACUAUGUGUCUGGAGUUUGGGAGAGGCAAGUGGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAUAUCUGGAGGAACACCAGUGGCGAAGGCGACUUGCUGGCCUAAAACUGACGCUGAGGCACGAAAGCGUGGGUAGUGAACGGGAUUAGAUACCCCGGUAAUCCACGCCCUAAACGUUGUCUACCAGUUGUUGGGGGUUUUAACCCUCAGUAACGAACCUAACGGAUUAAGUAGACCGCCUGGGGACUAUGCUCGCAAGAGUGAAACUCAAAGGAAUUGACGGGGGUCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGAUACGCGAAAAACCUCACCUAGGCUUGACAUGGAGUGGAAUCAUGUAGAGAUACAUGAGCCUUCGGGCCGCUUCACAGGUGCUGCAUGGUUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUCACCUUAUGUUGCCAUCAUUCAGUUGGGCACUCGUAAGGAACUGCCGGUGACAAACCGGAGGAAGGCGGGGAUGACGUCAAAUCCUCAUGGCCUUUAUGUCUAGGGCAACACACGUGCUACAAUGGCCGGUACAAAGGGUAGCCAACUCGCGAGGGGGAGCUAAUCUCAAAAAUCCGGUCCCAGUUCGGAUUGGAGUCUGCAACUCGACUCCAUGAAGUCGGAAUCGCUAGUAAUCGCGGAUCAGCAUGCCGCGGUGAAUACGUUCCCGGACCUUGUACACACCGCCCGUCACACCACCUGAGUGGGGAGCACCCGAAGUGGUCUUUGCCAACCGCAAGGAAGCAGACUACUAAGGUGAAACUCGUGAAGGGGGUGAAGUCGUAACAAGGUAGCCGUAUCGGAAGGUGCGGCUGGAUCACCUCCUUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.M.gallisepticum.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.M.gallisepticum.seq new file mode 100644 index 0000000..1c5e7c6 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.M.gallisepticum.seq @@ -0,0 +1,2 @@ +>d.16.b.M.gallisepticum +UUUUCUGAGAGUUUGAUCCUGGCUCAGGAUUAACGCUGGCGGCAUGCCUAAUACAUGCAAGUCGAUCGGAUGUAGCAAUACAUUAGAGGCGAACGGGUGAGUAACACGUAUCCAAUCUGCCUUAUAGUGGGGGAUAACUAGUCGAAAGAUUAGCUAAUACCGCAUAACAAGUUAACUAUCGCAUGAGAAUAACUUUAAAGAAGCAACUGCUUCGCUAUAAGAUGAGGGUGCGGCAUAUCAGCUAGUUGGUGAGGGUAAUGGCCCACCAAGGCGAUGACGUGUAGUUAUGCUGAGAGGUAGAAUAACCACAAUGGGACUGAGACACGGCCCAUACUCCUACGGGAGGCAGCAGUAGGGAAUUUUUCACAAUGGACGAAAGUCUGAUGGAGCAAUGCCGCGUGAACGAUGAAGGUCUUUUUAGAUUGUAAAGUUCUUUUAUUUGGGAAGAACAGUUAGUAGAGUGGAAAGCUAUUAAUUUGACUGUACCAUUUGAAUAAGUAACGACUAACUAUGUGCCAGCAGUCGCGGUAAUACAUAGGUUGCAAGCGUUAUCCGGAUUUAUUGGGCGUAAAACAAGCGCAGGCGGAUUAGAAAGUCUGGUGUUAAAAGCAAUUGCUUAACGAUUGUAUGCAUUGGAAACUUCUAGUCUAGAGUUUGGUAGAGAGUCCUGGAACUCCAUGUGGAGCGGUGAAAUGCGUAGAUAUAUGGAAGAACACCAGAGGCGAAGGCGAGGACUUGGGCCAAUACUGACGCUUAGGCUUGAAAGUGUGGGGAGCAAAUAGGAUUAGAUACCCUAGUAGUCCACACUGUAAACGAUGGAUGUUAAGUGUCGGAGCGAAUACUUCGGUGCUGCAGUUAACACAUUAAACAUCCUGCCUGAGUAGUACAUUCGCAAGAAUGAAACUCAAACGGAAUUGACGGGGACCCGCACAAGUGGUGGAGCAUGUUGCUUAAUUCGACGGUACACGAAAAACCUUACCUAGACUUGACAUCUUGGGCGAAGCUAUAGAAAUAUAGUGGAGGUCAACCCAAUGACAGGUGGUGCAUGGUUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCGUUAGUUACUUUGUCUAACGAGACUGCCAACGUAAGUUGGAGGAAGGUGGGGAUGACGUCAAAUCAUCAUGCCCCUUAUGUCUAGGGCUGCAAACGUGCUACAAUGGCCAAUACAAACAGUUGCAAAUCCGUAAGGUGGAGCUAAUCUGUAAAGUUGGUCUCAGUUCGGAUUGAGGGCUGCAAUUCGCCCUCAUGAAGUCGGAAUCACUAGUAAUCGCGAAUCAGCCAUGUCGCGGUGAAUACGUUCUCGGGUCUUGUACACACCGCCCGUCAAACUAUGAGAGCUGGUAAUAUCUAAAACCGUGUUGCUAACCGCAAGGAAGCGCAUGUCUAGGGUAGGGCCGGUGAUUGGAGUUAAGUCGUAACAAGGUACCCCUACGAGAACGUGGGGGUGGAUUACCUCCUUUCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.M.genitalium.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.M.genitalium.seq new file mode 100644 index 0000000..b13dc11 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.M.genitalium.seq @@ -0,0 +1,2 @@ +>d.16.b.M.genitalium +CAAUUUUUUCUGAGAGUUUGAUCCUGGCUCAGGAUUAACGCUGGCGGCAUGCCUAAUACAUGCAAGUCGAUCGGAAGUAGCAAUACUUUAGAGGCGAACGGGUGAGUAACACGUAUCCAAUCUACCUUAUAAUGGGGGAUAACUAGUUGAAAAACUAGCUAAUACCGCAUAAGAACUUUAGUUCGCAUGAAUUAAAGUUGAAAGGACCUGCAAGGGUUCGUUAUUUGAUGAGGGUGCGCCAUAUCAGCUAGUUGGUAGGGUAAUGGCCUACCAAGGCAAUGACGUGUAGCUAUGCUGAGAAGUAGAAUAGCCACAAUGGGACUGAGACACGGCCCAUACUCCUACGGGAGGCAGCAGUAGGGAAUUUUUCACAAUGAGCGAAAGCUUGAUGGAGCAAUGCCGCGUGAACGAUGAAGGUCUUUUUGAUUGUAAAGUUCUUUUAUUUGGGAAGAAUGACUCUAGCAGGCAAUGGCUGGAGUUUGACUGUACCACUUUGAAUAAGUGACGACUAACUAUGUGCCAGCAGUCGCGGUAAUACAUAGGUCGCAAGCGUUAUCCGGAUUUAUUGGGCGUAAAGCAAGCGCAGGCGGAUUGAAAAGUCUGGUGUUAAAGGCAGCUGCUUAACAGUUGUAUGCAUUGGAAACUAUCAGUCUAGAGUGUGGUAGGGAGUUUUGGAAUUUCAUGUGGAGCGGUGAAAUGCGUAGAUAUAUGAAGGAACACCAGUGGCGAAGGCGAAAACUUAGGCCAUUACUGACGCUUAGGCUUGAAAGUGUGGGGAGCAAAUAGGAUUAGAUACCCUAGUAGUCCACACCGUAAACGAUAGAUACUAGCUGUCGGAGCGAUCCCUUCGGUAGUGAAGUUAACACAUUAAGUAUCUCGCCUGGGUAGUACAUUCGCAAGAAUGAAACUCAAACGGAAUUGACGGGGACCCGCACAAGUGGUGGAGCAUGUUGCUUAAUUCGACGGUACACGAAAAACCUUACCUAGACUUGACAUCCUUGGCAAAGUUAUGGAAACAUAAUGGAGGUUAACCGAGUGACAGGUGGUGCAUGGUUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCGUUAGUUACAUUGUUUAACGAGACUGCUAAUGUAAAUUGGAGGAAGGAAGGGAUGACGUCAAAUCAUCAUGCCCCUUAUGUCUAGGGCUGCAAACGUGCUACAAUGGCCAAUACAAACAGUAGCCAACUUGUAAAAGUGAGCAAAUCUGAAAAGUUGGUCUCAGUUCGGAUUGAGGGCUGCAAUUCGUCCUCAUGAAGCUGGAAUCACUAGUAAUCGCGAAUCAGCUAUGUCGCGGUGAAUACGUUCUCGGGUCUUGUACACACCGCCCGUCAAACUAUGAAAGCUGGUAAUAUUUAAAAACGUGUUGCUAACCUUUAUUGGAAGCGCAUGUCAAGGAUAGCACCGGUGAUUGGAGUUAAGUCGUAACAAGGUACCCCUACGAGAACGUGGGGGUGGAUCACCUC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.M.hyopneumoniae.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.M.hyopneumoniae.seq new file mode 100644 index 0000000..340893a --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.M.hyopneumoniae.seq @@ -0,0 +1,2 @@ +>d.16.b.M.hyopneumoniae +CGCAAUCAUGAGAGUUUGAUCCUGGCUCAGGAUAAACGCUAGCUGUGUGCUUAAUACAUGCAUGUUGAACGGAAUAUUUUAGUUCGCUAAAAUAUUUAGUAGCAAAUGGGUGAGUAACACGUACCUAACCUACCUUUUGGACUGGGAUAACCAUUGGAAACAGUGGCUAAUACCAGAUAUGAUAAAAAUUUGCAUGAAUUUUUAUUCAAAGGAGCCUUCAAGCUUCACCAAGAAAUGGGGGUGCGCAACAUUAGUUAGUUGGUAGGGUAAAAGCCUACCAAGACGAUGAUGUUUAGCGGGGCCAAGAGGUUGUACCGCCACACUGGGAUUGAGAUACGGCCCAGACUCCUACGGGAGGCAGCAGUAAGGAAUAUUCCACAAUAAGCGAAAGCUUGAUGGAGCGACACAGCGUGCAGGAUGAAGUCUUUCGGGAUGUAAACUGCUGUUGUAAGGGAAGAAAAAACUAGAUAGGAAAUGCUCUAGUCUUGACGGUACCUUAUUAGAAAGCGACGGCAAACUAUGUGCCAGCAGCCGCGGUAAUACAUAGGUCGCAAGCGUUAUCCGGAAUUAUUGGGCGUAAAGCGUCCGUAGGUUUUUUGUUAAGUUUAAAGUUAAAUGCUAAAGCUCAACUUUAGUCCGCUUUAGAUACUGGCAAAAUAGAAUUAUGAAGAGGUUAGCGGAAUUCCUAGUGGAGUGGUGGAAUACGUAGAUAUUAGGAAGAACACCAAUAGGCGAAGGCAGCUAACUGGUCAUAUAUUGACACUAAGGGACGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGAUCAUUAGUUGGUGGCAAAAGUCACUAACACAGCUAACGCGUUAAAUGAUCCGCCUGAGUAGUAUGCUCGCAAGAGUGAAACUUAAAGGAAUUGACGGGAACCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUUGAAGAUACGCGUAGAACCUUACCCACUCUUGACAUUCUCGCAAAACUAUAGAGAUAUAGCCGAGGCUAACGAGAUCACAGAUGGUGCAUGGUUGUCGUCAGCUCGUGUCGUGAGAUGUUAGGUUAAGUCCUGCAACGAGCGCAACCCUUUUCUUUAGUUGCUAACAUUUAGUUGAGAACCCUAAAGAUACUGCCGGCGCAAGCCGGAGGAAGGUGGGGACGACGUCAAAUCAUCAUGCCUCUUACGAGUGGGGCAACACACGUGCUACAAUGGCUACUACAAAGAGCAGCAAAACAGUGAUGUCAAGCUAAUCUCAAAAAAGUAGUCUCAGUUCGGAUUGAAGUCUGCAACUCGACUUCAUGAAGUCGGAAUCGCUAGUAAUCGCAGGUCAGCUAUACUGCGGUGAAUACGUUCUCGGGUUUUGUACACACCGCCCGUCACACCAUGGGAGUUGGUAAUGCCCAAAGUCGGUGAGUUAACUUCGGAGACCAUUGCCUAAGGCAGGACCGAUGACUGGGGUGAAGUCGUAACAAGGUAUCCCUACGAGAACGUGGGGAUGGAACACCUCCUUUCUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.M.leprae.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.M.leprae.seq new file mode 100644 index 0000000..86728a4 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.M.leprae.seq @@ -0,0 +1,2 @@ +>d.16.b.M.leprae +UUGUUUGGAGAGUUUGAUCCUGGCUCAGGACGAACGCUGGCGGCGUGCUUAACACAUGCAAGUCGAACGGAAAGGUCUCUAAAAAAUCUUUUUUAGAGAUACUCGAGUGGCGAACGGGUGAGUAACACGUGGGUAAUCUGCCCUGCACUUCAGGGAUAAGCUUGGGAAACUGGGUCUAAUACCGGAUAGGACUUCAAGGCGCAUGUCUUGUGGUGGAAAGCUUUUUGCGGUGCAGGAUGGGCCCGCGGCCUAUCAGCUUGUUGGUGGGGUGACGGCCUACCAAGGCGACGACGGGUAGCCGGCCUGAGAGGGUGUCCGGCCACACUGGGACUGAGAUACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGCAAGCCUGAUGCAGCGACGCCGCGUGGGGGAUGACGGCCUUCGGGUUGUAAACCUCUUUCACCAUCGACGAAGGUCUGGGUUUUCUCGGAUUGACGGUAGGUGGAGAAGAAGCACCGGCCAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGUGCGAGCGUUGUCCGGAAUUACUGGGCGUAAAGAGCUCGUAGGUGGUUUGUCGCGUUGUUCGUGAAAUCUCACGGCUUAACUGUGAGCGUGCGGGCGAUACGGGCAGACUAGAGUACUGCAGGGGAGACUGGAAUUCCUGGUGUAGCGGUGGAAUGCGCAGAUAUCAGGAGGAACACCAGUGGCGAAGGCGGGUCUCUGGGCAGUAACUGACGCUGAGGAGCGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGGUGGGUACUAGGUGUGGGUUUCCUUCCUUGGGAUCCGUGCCGUAGCUAACGCAUUAAGUACCCCGCCUGGGGAGUACGGCCGCAAGGCUAAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGCGGAGCAUGUGGAUUAAUUCGAUGCAACGCGAAGAACCUUACCUGGGUUUGACAUGCACAGGAUGCGUCUAGAGAUAGGCACUCCCUUGUGGCCUGUGUGCAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUCUCAUGUUGCCAGCACGUAAUGGUGGGGACUCGUGAGAGACUGCCGCGGUCAACUCGGAGGAAGGUGGGGAUGACGUCAAGUCAUCAUGCCCCUUAUGUCCAGGGCUUCACACAUGCUACAAUGGCCGGUACAAAGGGCUGCGAUGCCGCAAGGUUAAGCGAAUCCUUUUAAAGCCGGUCUCAGUUCGGAUCGGGGUCUGCAACUCGACCCCGUGAAGUCGGAGUCGCUAGUAAUCGCAGAUCAGCAACGCUGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACGUCAUGAAAGUCGGUAACACCCGAAGCCAGUGGCCUAACCCUCGGGAGGGAGCUGUCCAAGGUGGGAUCGGCGAUUGGGACGAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGCGGCUGGAUCACCUCCUUUCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.P.pacificensis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.P.pacificensis.seq new file mode 100644 index 0000000..539e3c1 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.P.pacificensis.seq @@ -0,0 +1,2 @@ +>d.16.b.P.pacificensis +AGAGUUUGAUCAUGGCUCAGAUUGAUCGCUGGCGGCAGGCUUAACACAUGCAAGUCGAGCGGAACGAUGAUAGCUUGCUAUCAGGCGUCGAGCGGCGGACGGGUGAGUAAUACUUAGGAAUCUACCUAGUAGUGGGGGAUAGCUCGGGGAAACUCGAAUUAAUACCGCAUACGUCCUACGGGAGAAAGCAGGGGAUCAUUAGACCUUGCGCUAUUAGAUGAGCCUAAGUCGGAUUAGCUAGAUGGUGGGGUAAAGGCCUACCAUGGCGACGAUCAGUAGCUGGUCUGAGAGGAUGAUCAGCCACACCGGGACUGAGACACGGCCCGGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGGACAAUGGGGGGAACCUGAUCCAGCCAUGCCGCGUGUGUGAAGAAGGCCUUUUGGUUGUAAAGCACUUUAAGCAGUGAAGAAGACUCUUCGGUUAAUACCCGGGGACGAUGACAUUAGCUGCAGAAUAAGCACCGGCUAACUCUGUGCCAGCAGCCGCGGUAAUACAGAGGGUGCAAGCGUUAAUCGGAAUUACUGGGCGUAAAGCGAGCGUAGGUGGCUUGAUAAGUCAGAUGUGAAAUCCCCGGGCUUAACCUGGGAACUGCAUCUGAAACUGUUAGGCUAGAGUAGGUGAGAGGGAAGUAGAAUUUCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGAAGGAAUACCGAUGGCGAAGGCAGCUUCCUGGCAUCAUACUGACACUGAGGCUCGAAAGCGUGGGUAGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGUCUACUAGUCGUUGGGUCCCUUGAGGACUUAGUGAUGCAGCUAACGCAAUAAGUAGACCGCCUGGGGAGUACGGCCGCAAGGUUAAAACUCAAAUGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCCGGUCUUGACAUACACAGAAUCUUGUAGAGAUACGAGAGUGCCUUCGGGAAUUGUGAUACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUCCUUAGUUACCAGCGGGUUAAGCCGGGAACUCUAAGGAUACUGCCAGUGACAAACUGGAGGAAGGCGGGGACCACGUCAAGUCAUCAUGGCCCUUACGACCAGGGCUACACACGUGCUACAAUGGUAGGUACAGAGGGCAGCUACACAGCGAUGUGAUGCGAAUCUCAAAAAGCCUAUCGUAGUCCAGAUUGGAGUCUGCAACUCGACUCCAUGAAGUAGGAAUCGCUAGUAAUCGCGGAUCAGAAUGCCGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUUGAUUGCACCAGAAGUGGUUAGCCUAACUUAGUGAGGGCGAUCACCACGGUGUGGUCGAUGACUGGGGUGAAGUCGUAACAAGGUAGCCCGUAGGGGAAACCUGCGGCGGUUGGAUCACCUCCUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.P.vulgaris.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.P.vulgaris.seq new file mode 100644 index 0000000..a0ca78a --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.P.vulgaris.seq @@ -0,0 +1,2 @@ +>d.16.b.P.vulgaris +UAAUUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGGCCUAACACAUGCAAGUCGAGCGGUAACAGGAGAAAGCUUGCUUUCUUGCUGACGAGCGGCGGACGGGUGAGUAAUGUAUGGGGAUCUGCCCGAUAGAGGGGGAUAACUACUGGAAACGGUGGCUAAUACCGCAUGACGUCUACGGACCAAAGCAGGGGCUCUUCGGACCUUGCGCUAUCGGAUGAACCCAUAUGGGAUUAGCUAGUAGGUGAGGUAAUGGCUCACCUAGGCAACGAUCUCUAGCUGGUCUGAGAGGAUGAUCAGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGCAAGCCUGAUGCAGCCAUGCCGCGUGUAUGAAGAAGGCCUUAGGGUUGUAAAGUACUUUCAGCGGGGAGGAAGGUGAUAAAGUUAAUACCUUUAUCAAUUGACGUUACCCGCAGAAGAAGCACCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGUGCAAGCGUUAAUCGGAAUUACUGGGCGUAAAGCGCACGCAGGCGGUCAAUUAAGUCAGAUGUGAAAGCCCCGAGCUUAACUUGGGAAUUGCAUCUGAAACUGGUUGGCUAGAGUCUUGUAGAGGGGGGUAGAAUUCCACGUGUAGCGGUGAAAUGCGUAGAGAUGUGGAGGAAUACCGGUGGCGAAGGCGGCCCCCUGGACAAAGACUGACGCUCAGGUGCGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCUGUAAACGAUGUCGAUUUAGAGGUUGUGGUCUUGAACUGUGGCUUCUGGAGCUAACGCGUUAAAUCGACCGCCUGGGGAGUACGGCCGCAAGGUUAAAACUCAAAUGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCUACUCUUGACAUCCAGCGAAUCCUUUAGAGAUAGAGGAGUGCCUUCGGGAACGCUGAGACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUUGUGAAAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCCUUUGUUGCCAGCGCGUAAUGGCGGGAACUCAAAGGAGACUGCCGGUGAUAAACCGGAGGAAGGUGGGGAUGACGUCAAGUCAUCAUGGCCCUUACGAGUAGGGCUACACACGUGCUACAAUGGCAGAUACAAAGAGAAGCGACCUCGCGAGAGCAAGCGGAACUCAUAAAGUCUGUCGUAGUCCGGAUUGGAGUCUGCAACUCGACUCCAUGAAGUCGGAAUCGCUAGUAAUCGUAGAUCAGAAUGCUACGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUGGGUUGCAAAAGAAGUAGGUAGCUUAACCUUCGGGAGGGCGCUUACCACUUUGUGAUUCAUGACUGGGGUGAAGUCGUAACAAGGUAACCGUAGGGGAACCUGCGGUUGGAUCACCUCCUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.R.erythropolis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.R.erythropolis.seq new file mode 100644 index 0000000..37dd472 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.R.erythropolis.seq @@ -0,0 +1,2 @@ +>d.16.b.R.erythropolis +UCAACGGAGAGUUUGAUCCUGGCUCAGGACGAACGCUGGCGGCGUGCUUAACACAUGCAAGUCGAGCGGUAAGGCCUUCGGGGUACACGAGCGGCGAACGGGUGAGUAACACGUGGGUGAUCUGCCCUGCACUUCGGGAUAAGCCUGGGAAACUGGGUCUAAUACCGGAUAUGACCUCCUAUCGCAUGGUGGGUGGUGGAAAGAUUUAUCGGUGCAGGAUGGGCCCGCGGCCUAUCAGCUUGUUGGUGGGGUAAUGGCCUACCAAGGCGACGACGGGUAGCCGACCUGAGAGGGUGACCGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGAAAGCCUGAUGCAGCGACGCCGCGUGAGGGAUGACGGCCUUCGGGUUGUAAACCUCUUUCAGCAGGGACGAAGCGCAAGUGACGGUACCUGCAGAAGAAGCACCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGAGCAAGCGUUGUCCGGAAUUACUGGGCGUAAAGAGUUCGUAGGCGGUUUGUCGCGUCGUUUGUGAAAACCAGCAGCUCAACUGCUGGCUUGCAGGCGAUACGGGCAGACUUGAGUACUGCAGGGGAGACUGGAAUUCCUGGUGUAGCGGUGAAAUGCGCAGAUAUCAGGAGGAACACCGGUGGCGAAGGCGGGUCUCUGGGCAGUAACUGACGCUGAGGAACGAAAGCGUGGGUAGCGAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGGUGGGCGCUAGGUGUGGGUUCCUUCCACGGAAUCCGUGCCGUAGCUAACGCAUUAAGCGCCCCGCCUGGGGAGUACGGCCGCAAGGCUAAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGCGGAGCAUGUGGAUUAAUUCGAUGCAACGCGAAGAACCUUACCUGGGUUUGACAUAUACCGGAAAGCUGCAGAGAUGUGGCCCCCCUUGUGGUCGGUAUACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCCUAUCUUAUGUUGCCAGCACGUUAUGGUGGGGACUCGUAAGAGACUGCCGGGGUCAACUCGGAGGAAGGUGGGGACGACGUCAAGUCAUCAUGCCCCUUAUGUCCAGGGCUUCACACAUGCUACAAUGGCCAGUACAGAGGGCUGCGAGACCGUGAGGUGGAGCGAAUCCCUUAAAGCUGGUCUCAGUUCGGAUCGGGGUCUGCAACUCGACCCCGUGAAGUCGGAGUCGCUAGUAAUCGCAGAUCAGCAACGCUGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACGUCAUGAAAGUCGGUAACACCCGAAGCCGGUGGCUUAACCCCUUGUGGGAGGGAGCCGUCGAAGGUGGGAUCGGCGAUUGGGACGAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGCGGCUGGAUCACCUCCUUUCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.R.felis.URRWXCal2.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.R.felis.URRWXCal2.seq new file mode 100644 index 0000000..4cea7ad --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.R.felis.URRWXCal2.seq @@ -0,0 +1,2 @@ +>d.16.b.R.felis.URRWXCal2 +GACAGAAUCAAACUUGAGAGUUUGAUCCUGGCUCAGAACGAACGCUAUCGGUAUGCUUAACACAUGCAAGUCGGACGGACUAAUUGGGGCUUGCUCCAAUUAGUUAGUGGCAGACGGGUGAGUAACACGUGGGAAUCUGCCCAUCAGUACGGAAUAACUUUUAGAAAUAAAAGCUAAUACCGUAUAUUCUCUACAGAGGAAAGAUUUAUCGCUGAUGGAUGAGCCCGCGUCAGAUUAGGUAGUUGGUGAGGUAACGGCUCACCAAGCCGACGAUCUGUAGCUGGUCUGAGAGGAUGAUCAGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGGACAAUGGGCGAAAGCCUGAUCCAGCAAUACCGAGUGAGUGAUGAAGGCCCUAGGGUUGUAAAGCUCUUUUAGCAAGGAAGAUAAUGACGUUACUUGCAGAAAAAGCCCCGGCUAACUCCGUGCCAGCAGCCGCGGUAAGACGGAGGGGGCUAGCGUUGUUCGGAAUUACUGGGCGUAAAGAGUGCGUAGGCGGUUUAGUAAGUUGGAAGUGAAAGCCCGGGGCUUAACCUCGGAAUUGCUUUCAAAACUACUAAUCUAGAGUGUAGUAGGGGAUGAUGGAAUUCCUAGUGUAGAGGUGAAAUUCUUAGAUAUUAGGAGGAACACCGGUGGCGAAGGCGGUCAUCUGGGCUACAACUGACGCUGAUGCACGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGAGUGCUAGAUAUCGGAAGAUUCUCUUUCGGUUUCGCAGCUAACGCAUUAAGCACUCCGCCUGGGGAGUACGGUCGCAAGAUUAAAACUCAAAGGAAUUGACGGGGGCUCGCACAAGCGGUGGAGCAUGCGGUUUAAUUCGAUGUUACGCGAAAAACCUUACCAACCCUUGACAUGGUGGUCGCGGAUCGCAGAGAUGCUUUCCUUCAGCUCGGCUGGACCACACACAGGUGUUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUCAUUCUUAUUUGCCAGCGGGUAAUGCCGGGAACUAUAAGAAAACUGCCGGUGAUAAGCCGGAGGAAGGUGGGGACGACGUCAAGUCAUCAUGGCCCUUACGGGUUGGGCUACACGCGUGCUACAAUGGUGUUUACAGAGGGAAGCAAGACGGCGACGUGGAGCAAAUCCCUAAAAGACAUCUCAGUUCGGAUUGUUCUCUGCAACUCGAGAGCAUGAAGUUGGAAUCGCUAGUAAUCGCGGAUCAGCAUGCCGCGGUGAAUACGUUCUCGGGCCUUGUACACACUGCCCGUCACGCCAUGGGAGUUGGUUUUACCUGAAGGUGGUGAGCUAACGCAAGAGGCAGCCAACCACGGUAAAAUUAGCGACUGGGGUGAAGUCGUAACAAGGUAGCCGUAGGGGAACCUGCGGCUGGAUUACCUCCUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.R.prowazekii.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.R.prowazekii.seq new file mode 100644 index 0000000..4768ec6 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.R.prowazekii.seq @@ -0,0 +1,2 @@ +>d.16.b.R.prowazekii +AUCAAACUUGAGAGUUUGAUCCUGGCUCAGAACGAACGCUAUCGGUAUGCUUAACACAUGCAAGUCGAACGGAUUAACUAGAGCUCGCUUUAGUUAAUUAGUGGCAGACGGGUGAGUAACACGUGGGAAUCUACCCAUCAGUACGGAAUAACUUUUAGAAAUAAAAGCUAAUACCGUAUAUUCUCUACGGAGGAAAGAUUUAUCGCUGAUGGAUGGGCCCGCGUCAGAUUAGGUAGUUGGUGAGGUAAUGGCUCACCAAGCCGACGAUCUGUAGCUGGUCUGAGAGGAUGAUCAGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGGACAAUGGGCGAAAGCCUGAUCCAGCAAUACCGAGUGAGUGAUGAAGGCCUUAGGGUUGUAAAGCUCUUUUAGCAAGGAAGAUAAUGACGUUACUUGCAGAAAAAGCCCCGGCUAACUCCGUGCCAGCAGCCGCGGUAAGACGGAGGGGGCUAGCGUUGUUCGGAAUUACUGGGCGUAAAGAGUGCGUAGGCGGUUUAGUAAGUUGGAAGUGAAAGCCCGGGGCUUAACCUCGGAAUUGCUUUCAAAACUACUAAUCUAGAGUGUAGUAGGGGAUGAUGGAAUUCCUAGUGUAGAGGUGAAAUUCUUAGAUAUUAGGAGGAACACCGGUGGCGAAGGCGGUCAUCUGGGCUACAACUGACGCUGAUGCACGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGAGUGCUAGAUAUCGGAGGAUUCUCUUUCGGUUUCGCAGCUAACGCAUUAAGCACUCCGCCUGGGGAGUACGGUCGCAAGAUUAAAACUCAAAGGAAUUGACGGGGGCUCGCACAAGCGGUGGAGCAUGCGGUUUAAUUCGAUGUUACGCGAAAAACCUUACCAACCCUUGACAUGGUGGUUACGGAUUGCAGAGAUGCUUUCCUUCAGUUCGGCUGGGCCACACACAGGUGUUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUUCUUAUUUGCCAGUGGGUAAUGCCGGGAACUAUAAGAAAACUGCCGGUGAUAAGCCGGAGGAAGGUGGGGACGACGUCAAGUCAUCAUGGCCCUUACGGGUUGGGCUACACGCGUGCUACAAUGGUGUUUACAGAGGGAAGCAAUACGGUGACGUGGAGCAAAUCCCUAAAAGACAUCUCAGUUCGGAUUGUUCUCUGCAACUCGAGAGCAUGAAGUUGGAAUCGCUAGUAAUCGCGGAUCAGCAUGCCGCGGUGAAUACGUUCUCGGGCCUUGUACACACUGCCCGUCACGCCAUGGGAGUUGGUUUUACCUGAAGGUGGUGAGCUAACGCAAGAGGCAGCCAACCACGGUAAAAUUAGCGACUGGGGUGAAGUCGUAACAAGGUAGCCGUAGGGGAACCUGCGGCUGGAUUACCUCCUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.acidiscabies.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.acidiscabies.seq new file mode 100644 index 0000000..639b9c2 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.acidiscabies.seq @@ -0,0 +1,2 @@ +>d.16.b.S.acidiscabies +CAUUCACGGAGAGUUUGAUCCUGGCUCAGGACGAACGCUGGCGGCGUGCUUAACACAUGCAAGUCGAACGAUGAAGCCCUUCGGGGUGGAUUAGUGGCGAACGGGUGAGUAACACGUGGGCAAUCUGCCCUUCACUCUGGGACAAGCCCUGGAAACGGGGUCUAAUACCGGAUAUCACUCCUGCCUGCAUGGGCGGGGGUCGAAAGCUCCGGCGGUGAAGGAUGAGCCCGCGGCCUAUCAGCUUGUUGGUGAGGUAAUGGCUCACCAAGGCGACGACGGGUAGCCGGCCUGAGAGGGCGACCGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGGAAGCCUGAUGCAGCGACGCCGCGUGAGGGAUGACGGCCUUCGGGUUGUAAACCUCUUUCAGCAGGGAAGAAGCGAAAGUGACGGUACCUGCAGAAGAAGCGCCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGCGCAAGCGUUGUCCGGAAUUAUUGGGCGUAAAGAGCUCGUAGGCGGCUUGUCGCGUCGGAUGUGAAAGCCCGGGGCUUAACCCCGGGUCUGCAUUCGAUACGGGCAGGCUAGAGUUCGGUAGGGGAGAUCGGAAUUCCUGGUGUAGCGGUGAAAUGCGCAGAUAUCAGGAGGAACACCGGUGGCGAAGGCGGAUCUCUGGGCCGAUACUGACGCUGAGGAGCGAAAGCGUGGGGAGCGAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGGUGGGAACUAGGUGUUGGCGACAUUCCACGUCGUCGGUGCCGCAGCUAACGCAUUAAGUUCCCCGCCUGGGGAGUACGGCCGCAAGGCUAAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCAGCGGAGCAUGUGGCUUAAUUCGACGCAACGCGAAGAACCUUACCAAGGCUUGACAUACACCGGAAACGGCCAGAGAUGGUCGCCCCCUUGUGGUCGGUGUACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUCCUGUGUUGCCAGCGUGCCCUUCGGGGUGACGGGGACUCACAGGAGACCGCCGGGGUCAACUCGGAGGAAGGUGGGGACGACGUCAAGUCAUCAUGCCCCUUAUGUCUUGGGCUGCACACGUGCUACAAUGGCAGGUACAAAGAGCUGCGAAACCGUGAGGUGGAGCGAAUCUCAAAAAGCCUGUCUCAGUUCGGAUUGGGGUCUGCAACUCGACCCCAUGAAGUCGGAGUUGCUAGUAAUCGCAGAUCAGCAUUGCUGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACGUCACGAAAGUCGGUAACACCCGAAGCCGGUGGCCCAACCCCUUGUGGGAGGGAGCUGUCGAAGGUGGGACUGGCGAUUGGGACGAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGCGGCUGGAUCACCUCCUUUCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.aureus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.aureus.seq new file mode 100644 index 0000000..1181b57 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.aureus.seq @@ -0,0 +1,2 @@ +>d.16.b.S.aureus +UUUUAUGGAGAGUUUGAUCCUGGCUCAGGAUGAACGCUGGCGGCGUGCCUAAUACAUGCAAGUCGAGCGAACGGACGAGAAGCUUGCUUCUCUGAUGUUAGCGGCGGACGGGUGAGUAACACGUGGAUAACCUACCUAUAAGACUGGGAUAACUUCGGGAAACCGGAGCUAAUACCGGAUAAUAUUUUGAACCGCAUGGUUCAAAAGUGAAAGACGGUCUUGCUGUCACUUAUAGAUGGAUCCGCGCUGCAUUAGCUAGUUGGUAAGGUAACGGCUUACCAAGGCAACGAUGCAUAGCCGACCUGAGAGGGUGAUCGGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUAGGGAAUCUUCCGCAAUGGGCGAAAGCCUGACGGAGCAACGCCGCGUGAGUGAUGAAGGUCUUCGGAUCGUAAAACUCUGUUAUUAGGGAAGAACAUAUGUGUAAGUAACUGUGCACAUCUUGACGGUACCUAAUCAGAAAGCCACGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGUGGCAAGCGUUAUCCGGAAUUAUUGGGCGUAAAGCGCGCGUAGGCGGUUUUUUAAGUCUGAUGUGAAAGCCCACGGCUCAACCGUGGAGGGUCAUUGGAAACUGGAAAACUUGAGUGCAGAAGAGGAAAGUGGAAUUCCAUGUGUAGCGGUGAAAUGCGCAGAGAUAUGGAGGAACACCAGUGGCGAAGGCGACUUUCUGGUCUGUAACUGACGCUGAUGUGCGAAAGCGUGGGGAUCAAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGAGUGCUAAGUGUUAGGGGGUUUCCGCCCCUUAGUGCUGCAGCUAACGCAUUAAGCACUCCGCCUGGGGAGUACGACCGCAAGGUUGAAACUCAAAGGAAUUGACGGGGACCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAAGCAACGCGAAGAACCUUACCAAAUCUUGACAUCCUUUGACAACUCUAGAGAUAGAGCCUUCCCCUUCGGGGGACAAAGUGACAGGUGGUGCAUGGUUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAAGCUUAGUUGCCAUCAUUAAGUUGGGCACUCUAAGUUGACUGCCGGUGACAAACCGGAGGAAGGUGGGGAUGACAUCAAAUCAUCAUGCCCCUUAUGAUUUGGGCUACACACGUGCUACAAUGGACAAUACAAAGGGCAGCGAAACCGCGAGGUCAAGCAAAUCCCAUAAAGUUGUUCUCAGUUCGGAUUGUAGUCUGCAACUCGACUACAUGAAGCUGGAAUCGCUAGUAAUCGUAGAUCAGCAUGCUACGGUGAAUACGUUCCCGGGUCUUGUACACACCGCCCGUCACACCACGAGAGUUUGUAACACCCGAAGCCGGUGGAGUAACCUUUUAGGAGCCAGCCGUCGAAGGUGGGACAAAUGAUUGGGGUGAAGUCGUAACAAGGUAGCCGUAUCGGAAGGUGCGGCUGGAUCACCUCCUUUCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.bottropensis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.bottropensis.seq new file mode 100644 index 0000000..2548398 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.bottropensis.seq @@ -0,0 +1,2 @@ +>d.16.b.S.bottropensis +CAUUCACGGAGAGUUUGAUCCUGGCUCAGGACGAACGCUGGCGGCGUGCUUAACACAUGCAAGUCGAACGAUGAACCACUUCGGUGGGGAUUAGUGGCGAACGGGUGAGUAACACGUGGGCAAUCUGCCCUUCACUCUGGGACAAGCCCUGGAAACGGGGUCUAAUACCGGAUACAACACUCUCGGGCAUCCGAUGAGUGUGGAAAGCUCCGGCGGUGAAGGAUGAGCCCGCGGCCUAUCAGCUUGUUGGUGAGGUAACGGCUCACCAAGGCGACGACGGGUAGCCGGCCUGAGAGGGCGACCGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGAAAGCCUGAUGCAGCGACGCCGCGUGAGGGAUGACGGCCUUCGGGUUGUAAACCUCUUUCAGCAGGGAAGAAGCGAAAGUGACGGUACCUGCAGAAGAAGCGCCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGCGCGAGCGUUGUCCGGAAUUAUUGGGCGUAAAGAGCUCGUAGGCGGUCUGUCGCGUCGGAUGUGAAAGCCCGGGGCUUAACCCCGGGUCUGCAUUCGAUACGGGCAGACUAGAGUGUGGUAGGGGAGAUCGGAAUUCCUGGUGUAGCGGUGAAAUGCGCAGAUAUCAGGAGGAACACCGGUGGCGAAGGCGGAUCUCUGGGCCAUUACUGACGCUGAGGAGCGAAAGCGUGGGGAGCGAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGGUGGGAACUAGGUGUUGGCGACAUUCCACGUCGUCGGUGCCGCAGCUAACGCAUUAAGUUCCCCGCCUGGGGAGUACGGCCGCAAGGCUAAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCAGCGGAGCAUGUGGCUUAAUUCGACGCAACGCGAAGAACCUUACCAAGGCUUGACAUCGCCCGGAAAGCAUCAGAGAUGGUGCCCCCCUUGUGGUCGGGUGACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUUCUGUGUUGCCAGCAUGCCCUUCGGGGUGAUGGGGACUCACAGGAGACUGCCGGGGUCAACUCGGAGGAAGGUGGGGACGACGUCAAGUCAUCAUGCCCCUUAUGUCUUGGGCUGCACACGUGCUACAAUGGCAGGUACAAUGAGCUGCGAAGCCGUGAGGCGGAGCGAAUCUCAAAAAGCCUGUCUCAGUUCGGAUUGGGGUCUGCAACUCGACCCCAUGAAGUCGGAGUUGCUAGUAAUCGCAGAUCAGCAUUGCUGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACGUCACGAAAGUCGGUAACACCCGAAGCCGGUGGCCCAACCCCUUGUGGGAGGGAGCUGUCGAAGGUGGGACUGGCGAUUGGGACGAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGCGGCUGGAUCACCUCCUUUCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.diastatochromogenes.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.diastatochromogenes.seq new file mode 100644 index 0000000..bc38f32 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.diastatochromogenes.seq @@ -0,0 +1,2 @@ +>d.16.b.S.diastatochromogenes +CAUUCACGGAGAGUUUGAUCCUGGCUCAGGACGAACGCUGGCGGCGUGCUUAACACAUGCAAGUCGAACGAUGAACCACUUCGGUGGGGAUUAGUGGCGAACGGGUGAGUAACACGUGGGCAAUCUGCCCUUCACUCUGGGACAAGCCCUGGAAACGGGGUCUAAUACCGGAUACAACCACUAGGGGCAUCUCUUGGUGGUGGAAAGCUCCGGCGGUGAAGGAUGAGCCCGCGGCCUAUCAGCUUGUUGGUGAGGUAACGGCUCACCAAGGCGACGACGGGUAGCCGGCCUGAGAGGGCGACCGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGAAAGCCUGAUGCAGCGACGCCGCGUGAGGGAUGACGGCCUUCGGGUUGUAAACCUCUUUCAGCAGGGAAGAAGCGAAAGUGACGGUACCUGCAGAAGAAGCGCCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGCGCGAGCGUUGUCCGGAAUUAUUGGGCGUAAAGAGCUCGUAGGCGGUCUGUCGCGUCGGAUGUGAAAGCCCGGGGCUUAACCCCGGGUCUGCAUUCGAUACGGGCAGACUAGAGUGUGGUAGGGGAGAUCGGAAUUCCUGGUGUAGCGGUGAAAUGCGCAGAUAUCAGGAGGAACACCGGUGGCGAAGGCGGAUCUCUGGGCCAUUACUGACGCUGAGGAGCGAAAGCGUGGGGAGCGAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGGUGGGAACUAGGUGUUGGCGACAUUCCACGUCGUCGGUGCCGCAGCUAACGCAUUAAGUUCCCCGCCUGGGGAGUACGGCCGCAAGGCUAAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCAGCGGAGCAUGUGGCUUAAUUCGACGCAACGCGAAGAACCUUACCAAGGCUUGACAUACACCGGAAACGGCCAGAGAUGGUCGCCCCCUUGUGGUCGGUGUACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUUCUGUGUUGCCAGCAUGCCCUUCGGGGUGAUGGGGACUCACAGGAGACUGCCGGGGUCAACUCGGAGGAAGGUGGGGACGACGUCAAGUCAUCAUGCCCCUUAUGUCUUGGGCUGCACACGUGCUACAAUGGCAGGUACAAUGAGCUGCGAAGCCGUGAGGCGGAGCGAAUCUCAAAAAGCCUGUCUCAGUUCGGAUUGGGGUCUGCAACUCGACCCCAUGAAGUCGGAGUUGCUAGUAAUCGCAGAUCAGCAGUGCUGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACGUCACGAAAGUCGGUAACACCCGAAGCCGGUGGCCCAACCCCUUGUGGGAGGGAGCUGUCGAAGGUGGGACUGGCGAUUGGGACGAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGCGGCUGGAUCACCUCCUUUCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.eurythermus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.eurythermus.seq new file mode 100644 index 0000000..8d346c2 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.eurythermus.seq @@ -0,0 +1,2 @@ +>d.16.b.S.eurythermus +CAUUCACGGAGAGUUUGAUCCUGGCUCAGGACGAACGCUGGCGGCGUGCUUAACACAUGCAAGUCGAACGAUGAACCUCCUUCGGGAGGGGAUUAGUGGCGAACGGGUGAGUAACACGUGGGCAAUCUGCCCUUCACUCUGGGACAAGCCCUGGAAACGGGGUCUAAUACCGGAUACGAGCCUCCAAGGCAUCUUGGAGGUUGGAAAGCUCCGGCGGUGAAGGAUGAGCCCGCGGCCUAUCAGCUUGUUGGUGAGGUAAUGGCUCACCAAGGCGACGACGGGUAGCCGGCCUGAGAGGGCGACCGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGAAAGCCUGAUGCAGCGACGCCGCGUGAGGGAUGACGGCCUUCGGGUUGUAAACCUCUUUCAGCAGGGAAGAAGCGAAAGUGACGGUACCUGCAGAAGAAGCGCCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGCGCAAGCGUUGUCCGGAAUUAUUGGGCGUAAAGAGCUCGUAGGCGGCUUGUCACGUCGGUUGUGAAAGCCCGGGGCUUAACCCCGGGUCUGCAGUCGAUACGGGCAGGCUAGAGUUCGGUAGGGGAGAUCGGAAUUCCUGGUGUAGCGGUGAAAUGCGCAGAUAUCAGGAGGAACACCGGUGGCGAAGGCGGAUCUCUGGGCCGAUACUGACGCUGAGGAGCGAAAGCGUGGGGAGCGAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGGUGGGCACUAGGUGUGGGCAACAUUCCACGUUGUCCGUGCCGCAGCUAACGCAUUAAGUGCCCCGCCUGGGGAGUACGGCCGCAAGGCUAAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGCGGAGCAUGUGGCUUAAUUCGACGCAACGCGAAGAACCUUACCAAGGCUUGACAUACACCGGAAAGCAUUAGAGAUAGUGCCCCCCUUGUGGUCGGUGUACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUCCCGUGUUGCCAGCAGGCCCUUGUGGUGCUGGGGACUCACGGGAGACCGCCGGGGUCAACUCGGAGGAAGGUGGGGACGACGUCAAGUCAUCAUGCCCCUUAUGUCUUGGGCUGCACACGUGCUACAAUGGCCGGUACAAUGAGCUGCGAUACCGUGAGGUGGAGCGAAUCUCAAAAAGCCGGUCUCAGUUCGGAUUGGGGUCUGCAACUCGACCCCAUGAAGUCGGAGUUGCUAGUAAUCGCAGAUCAGCAUUGCUGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACGUCACGAAAGUCGGUAACACCCGAAGCCGGUGGCCCAACCCCUUGUGGGAGGGAGCUGUCGAAGGUGGGACUGGCGAUUGGGACGAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGCGGCUGGAUCACCUCCUUUCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.griseus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.griseus.seq new file mode 100644 index 0000000..89dcb68 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.griseus.seq @@ -0,0 +1,2 @@ +>d.16.b.S.griseus +CAUUCACGGAGAGUUUGAUCCUGGCUCAGGACGAACGCUGGCGGCGUGCUUAACACAUGCAAGUCGAACGAUGAAGCCUUUCGGGGUGGAUUAGUGGCGAACGGGUGAGUAACACGUGGGCAAUCUGCCCUUCACUCUGGGACAAGCCCUGGAAACGGGGUCUAAUACCGGAUAACACUCUGUCCCGCAUGGGACGGGGUUAAAAGCUCCGGCGGUGAAGGAUGAGCCCGCGGCCUAUCAGCUUGUUGGUGGGGUAAUGGCCUACCAAGGCGACGACGGGUAGCCGGCCUGAGAGGGCGACCGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGAAAGCCUGAUGCAGCGACGCCGCGUGAGGGAUGACGGCCUUCGGGUUGUAAACCUCUUUCAGCAGGGAAGAAGCGAGAGUGACGGUACCUGCAGAAGAAGCGCCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGCGCAAGCGUUGUCCGGAAUUAUUGGGCGUAAAGAGCUCGUAGGCGGCUUGUCACGUCGGAUGUGAAAGCCCGGGGCUUAACCCCGGGUCUGCAUUCGAUACGGGCUAGCUAGAGUGUGGUAGGGGAGAUCGGAAUUCCUGGUGUAGCGGUGAAAUGCGCAGAUAUCAGGAGGAACACCGGUGGCGAAGGCGGAUCUCUGGGCCAUUACUGACGCUGAGGAGCGAAAGCGUGGGGAGCGAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGUUGGGAACUAGGUGUUGGCGACAUUCCACGUCGUCGGUGCCGCAGCUAACGCAUUAAGUUCCCCGCCUGGGGAGUACGGCCGCAAGGCUAAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCAGCGGAGCAUGUGGCUUAAUUCGACGCAACGCGAAGAACCUUACCAAGGCUUGACAUAUACCGGAAAGCAUCAGAGAUGGUGCCCCCCUUGUGGUCGGUAUACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUUCUGUGUUGCCAGCAUGCCUUCGGGGUGAUGGGGACUCACAGGAGACUGCCGGGGUCAACUCGGAGGAAGGUGGGGACGACGUCAAGUCAUCAUGCCCCUUAUGUCUUGGGCUGCACACGUGCUACAAUGGCCGGUACAAUGAGCUGCGAUGCGCGAGGCGGAGCGAAUCUCAAAAAGCCGGUCUCAGUUCGGAUUGGGGUCUGCAACUCGACCCCAUGAAGUCGGAGUUGCUAGUAAUCGCAGAUCAGCAUUGCUGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACGUCACGAAAGUCGGUAACACCCGAAGCCGGUGGCCCAACCCCUUGUGGGAGGGAGCUGUCGAAGGUGGGACUGGCGAUUGGGACGAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGCGGCUGGAUCACCUCCUUUCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.neyagawaensis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.neyagawaensis.seq new file mode 100644 index 0000000..ea52e53 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.neyagawaensis.seq @@ -0,0 +1,2 @@ +>d.16.b.S.neyagawaensis +CAUUCACGGAGAGUUUGAUCCUGGCUCAGGACGAACGCUGGCGGCGUGCUUAACACAUGCAAGUCGAACGAUGAAGCCCUUCGGGGUGGAUUAGUGGCGAACGGGUGAGUAACACGUGGGCAAUCUGCCCUUCACUCUGGGACAAGCCCUGGAAACGGGGUCUAAUACCGGAUACGACGCGCUCGGGCAUCCGAUGUGCGUGGAAAGCUCCGGCGGUGAAGGAUGAGCCCGCGGCCUAUCAGCUUGUUGGUGAGGUAACGGCUCACCAAGGCGACGACGGGUAGCCGGCCUGAGAGGGCGACCGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGAAAGCCUGAUGCAGCGACGCCGCGUGAGGGAUGACGGCCUUCGGGUUGUAAACCUCUUUCAGCAGGGAAGAAGCGAAAGUGACGGUACCUGCAGAAGAAGCGCCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGCGCGAGCGUUGUCCGGAAUUAUUGGGCGUAAAGAGCUCGUAGGCGGUCUGUCGCGUCGGAUGUGAAAGCCCGGGGCUUAACCCCGGGUCUGCAUUCGAUACGGGCAGACUAGAGUGUGGUAGGGGAGAUCGGAAUUCCUGGUGUAGCGGUGAAAUGCGCAGAUAUCAGGAGGAACACCGGUGGCGAAGGCGGAUCUCUGGGCCAUUACUGACGCUGAGGAGCGAAAGCGUGGGGAGCGAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGGUGGGAACUAGGUGUUGGCGACAUUCCACGUCGUCGGUGCCGCAGCUAACGCAUUAAGUUCCCCGCCUGGGGAGUACGGCCGCAAGGCUAAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCAGCGGAGCAUGUGGCUUAAUUCGACGCAACGCGAAGAACCUUACCAAGGCUUGACAUACGCCGGAAACACCCAGAGAUGGGUGCCCCCUUGUGGUCGGUGUACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUUCUGUGUUGCCAGCAUGCCCUUCGGGGUGAUGGGGACUCACAGGAGACUGCCGGGGUCAACUCGGAGGAAGGUGGGGACGACGUCAAGUCAUCAUGCCCCUUAUGUCUUGGGCUGCACACGUGCUACAAUGGCAGGUACAAUGAGCUGCGAAGCCGUGAGGCGGAGCGAAUCUCAAAAAGCCUGUCUCAGUUCGGAUUGGGGUCUGCAACUCGACCCCAUGAAGUCGGAGUUGCUAGUAAUCGCAGAUCAGCAGUGCUGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACGUCACGAAAGUCGGUAACACCCGAAGCCGGUGGCCCAACCCCUUGUGGGAGGGAGCUGUCGAAGGUGGGACUGGCGAUUGGGACGAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGCGGCUGGAUCACCUCCUUUCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.nodosus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.nodosus.seq new file mode 100644 index 0000000..a046f62 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.nodosus.seq @@ -0,0 +1,2 @@ +>d.16.b.S.nodosus +UUCACGGAGAGUUUGAUCCUGGCUCAGGACGAACGCUGGCGGCGUGCUUAACACAUGCAAGUCGAACGAUGAAGCCCUUCGGGGUGGAUUAGUGGCGAACGGGUGAGUAACACGUGGGCAAUCUGCCCUGCACUCUGGGACAAGCCCUGGAAACGGGGUCUAAUACCGGAUACGAGCCGGGGAGGCAUCUCCCUGGUUGGAAAGCUCCGGCGGUGCAGGAUGAGCCCGCGCCCUAUCAGCUUGUUGGUGAGGUAACGGCUCACCAAGGCGACGACGGGUAGCCGGCCUGAGAGGGCGACCGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGAAAGCCUGAUGCAGCGACGCCGCGUGAGGGAUGACGGCCUUCGGGUUGUAAACCUCUUUCAGCAGGGAAGAAGCGAGAGUGACGGUACCUGCAGAAGAAGCGCCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGCGCGAGCGUUGUCCGGAAUUAUUGGGCGUAAAGAGCUCGUAGGCGGCUUGUCGCGUCGCGUUGUGAAAGCCCGGGGCUUAACCCCGGGUCUGCAGUCGAUACGGGCAGGCUAGAGUUCGGUAGGGGAGAUCGGAAUUCCUGGUGUAGCGGUGAAAUGCGCAGAUAUCAGGAGGAACACCGGUGGCGAAGGCGGAUCUCUGGGCCGAUACUGACGCUGAGGAGCGAAAGCGUGGGGAGCGAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGGUGGGCACUAGGUGUGGGCAACAUUCCACGUUGUCCGUGCCGCAGCUAACGCAUUAAGUGCCCCGCCUGGGGAGUACGGCCGCAAGGCUAAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGCGGAGCAUGUGGCUUAAUUCGACGCAACGCGAAGAACCUUACCAAGGCUUGACAUACACCGGAAAGCAUUAGAGAUAGUGCCCCCCUUGUGGUCGGUGUACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUCCCGUGUUGCCAGCAGGCCCUUGUGGUGCUGGGGACUCACGGGAGACCGCCGGGGUCAACUCGGAGGAAGGUGGGGACGACGUCAAGUCAUCAUGCCCCUUAUGUCUUGGGCUGCACACGUGCUACAAUGGCCGGUACAAUGAGCUGCGAUACCGUGAGGUGGAGCGAAUCUCAAAAAGCCGGUCUCAGUUCGGAUUGGGGUCUGCAACUCGACCCCAUGAAGUCGGAGUCGCUAGUAAUCGCAGAUCAGCAUUGCUGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACGUCACGAAAGUCGGUAACACCCGAAGCCGGUGGCCCAACCCCUUGUGGGAGGGAGCUGUCCAAGGUGGGACUGGCGAUUGGGACGAAAUCGUAACAAGGUAGCCGUACCGGAAGGUGCGGCUGGAUCACCUCCUUUCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.sampsonii.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.sampsonii.seq new file mode 100644 index 0000000..f530e47 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.sampsonii.seq @@ -0,0 +1,2 @@ +>d.16.b.S.sampsonii +CAUUCACGGAGAGUUUGAUCCUGGCUCAGGACGAACGCUGGCGGCGUGCUUAACACAUGCAAGUCGAACGAUGAACCGCUUUCGGGCGGGGAUUAGUGGCGAACGGGUGAGUAACACGUGGGCAAUCUGCCCUGCACUCUGGGACAAGCCCUGGAAACGGGGUCUAAUACCGGAUAUGACUGUCCAUCGCAUGGUGGAUGGUGUAAAGCUCCGGCGGUGCAGGAUGAGCCCGCGGCCUAUCAGCUUGUUGGUGAGGUAGUGGCUCACCAAGGCGACGACGGGUAGCCGGCCUGAGAGGGCGACCGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGAAAGCCUGAUGCAGCGACGCCGCGUGAGGGAUGACGGCCUUCGGGUUGUAAACCUCUUUCAGCAGGGAAGAAGCGAAAGUGACGGUACCUGCAGAAGAAGCGCCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGCGCAAGCGUUGUCCGGAAUUAUUGGGCGUAAAGAGCUCGUAGGCGGCUUGUCACGUCGGUUGUGAAAGCCCGGGGCUUAACCCCGGGUCUGCAGUCGAUACGGGCAGGCUAGAGUUCGGUAGGGGAGAUCGGAAUUCCUGGUGUAGCGGUGAAAUGCGCAGAUAUCAGGAGGAACACCGGUGGCGAAGGCGGAUCUCUGGGCCGAUACUGACGCUGAGGAGCGAAAGCGUGGGGAGCGAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGGUGGGCACUAGGUGUGGGCAACAUUCCACGUUGUCCGUGCCGCAGCUAACGCAUUAAGUGCCCCGCCUGGGGAGUACGGCCGCAAGGCUAAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGCGGAGCAUGUGGCUUAAUUCGACGCAACGCGAAGAACCUUACCAAGGCUUGACAUACACCGGAAACGUCUGGAGACAGGCGCCCCCUUGUGGUCGGUGUACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUCCCGUGUUGCCAGCAGGCCCUUGUGGUGCUGGGGACUCACGGGAGACCGCCGGGGUCAACUCGGAGGAAGGUGGGGACGACGUCAAGUCAUCAUGCCCCUUAUGUCUUGGGCUGCACACGUGCUACAAUGGCCGGUACAAUGAGCUGCGAUACCGUGAGGUGGAGCGAAUCUCAAAAAGCCGGUCUCAGUUCGGAUUGGGGUCUGCAACUCGACCCCAUGAAGUCGGAGUCGCUAGUAAUCGCAGAUCAGCAUUGCUGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACGUCACGAAAGUCGGUAACACCCGAAGCCGGUGGCCCAACCCCUUGUGGGAGGGAGCUGUCGAAGGUGGGACUGGCGAUUGGGACGAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGCGGCUGGAUCACCUCCUUUCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.scabiei.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.scabiei.seq new file mode 100644 index 0000000..1155f53 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.scabiei.seq @@ -0,0 +1,2 @@ +>d.16.b.S.scabiei +CAUUCACGGAGAGUUUGAUCCUGGCUCAGGACGAACGCUGGCGGCGUGCUUAACACAUGCAAGUCGAACGAUGAACCACUUCGGUGGGGAUUAGUGGCGAACGGGUGAGUAACACGUGGGCAAUCUGCCCUUCACUCUGGGACAAGCCCUGGAAACGGGGUCUAAUACCGGAUACGACACUCUCGGGCAUCCGAUGAGUGUGGAAAGCUCCGGCGGUGAAGGAUGAGCCCGCGGCCUAUCAGCUUGUUGGUGAGGUAACGGCUCACCAAGGCGACGACGGGUAGCCGGCCUGAGAGGGCGACCGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGAAAGCCUGAUGCAGCGACGCCGCGUGAGGGAUGACGGCCUUCGGGUUGUAAACCUCUUUCAGCAGGGAAGAAGCGAAAGUGACGGUACCUGCAGAAGAAGCGCCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGCGCGAGCGUUGUCCGGAAUUAUUGGGCGUAAAGAGCUCGUAGGCGGUCUGUCGCGUCGGAUGUGAAAGCCCGGGGCUUAACCCCGGGUCUGCAUUCGAUACGGGCAGACUAGAGUGUGGUAGGGGAGAUCGGAAUUCCUGGUGUAGCGGUGAAAUGCGCAGAUAUCAGGAGGAACACCGGUGGCGAAGGCGGAUCUCUGGGCCAUUACUGACGCUGAGGAGCGAAAGCGUGGGGAGCGAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGGUGGGAACUAGGUGUUGGCGACAUUCCACGUCGUCGGUGCCGCAGCUAACGCAUUAAGUUCCCCGCCUGGGGAGUACGGCCGCAAGGCUAAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCAGCGGAGCAUGUGGCUUAAUUCGACGCAACGCGAAGAACCUUACCAAGGCUUGACAUACACCGGAAACGGCCAGAGAUGGUCGCCCCCUUGUGGUCGGUGUACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUUCUGUGUUGCCAGCAUGCCCUUCGGGGUGAUGGGGACUCACAGGAGACUGCCGGGGUCAACUCGGAGGAAGGUGGGGACGACGUCAAGUCAUCAUGCCCCUUAUGUCUUGGGCUGCACACGUGCUACAAUGGCAGGUACAAUGAGCUGCGAAGCCGUGAGGCGGAGCGAAUCUCAAAAAGCCUGUCUCAGUUCGGAUUGGGGUCUGCAACUCGACCCCAUGAAGUCGGAGUUGCUAGUAAUCGCAGAUCAGCAUUGCUGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACGUCACGAAAGUCGGUAACACCCGAAGCCGGUGGCCUAACCCGUAAGGGAGGGAGCUGUCGAAGGUGGGACUGGCGAUUGGGACGAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGCGGCUGGAUCACCUCCUUUCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.tendae.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.tendae.seq new file mode 100644 index 0000000..8cd1523 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.tendae.seq @@ -0,0 +1,2 @@ +>d.16.b.S.tendae +CAUUCACGGAGAGUUUGAUCCUGGCUCAGGACGAACGCUGGCGGCGUGCUUAACACAUGCAAGUCGAACGAUGAACCACUUCGGUGGGGAUUAGUGGCGAACGGGUGAGUAACACGUGGGCAAUCUGCCCUGCACUCUGGGACAAGCCCUGGAAACGGGGUCUAAUACCGGAUACUGACCCUCGCAGGCAUCUGCGAGGUUCGAAAGCUCCGGCGGUGCAGGAUGAGCCCGCGGCCUAUCAGCUUGUUGGUGAGGUAAUGGCUCACCAAGGCGACGACGGGUAGCCGGCCUGAGAGGGCGACCGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGAAAGCCUGAUGCAGCGACGCCGCGUGAGGGAUGACGGCCUUCGGGUUGUAAACCUCUUUCAGCAGGGAAGAAGCGAAAGUGACGGUACCUGCAGAAGAAGCGCCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGCGCAAGCGUUGUCCGGAAUUAUUGGGCGUAAAGAGCUCGUAGGCGGCUUGUCACGUCGGUUGUGAAAGCCCGGGGCUUAACCCCGGGUCUGCAGUCGAUACGGGCAGGCUAGAGUUCGGUAGGGGAGAUCGGAAUUCCUGGUGUAGCGGUGAAAUGCGCAGAUAUCAGGAGGAACACCGGUGGCGAAGGCGGAUCUCUGGGCCGAUACUGACGCUGAGGAGCGAAAGCGUGGGGAGCGAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGGUGGGCACUAGGUGUGGGCAACAUUCCACGUUGUCCGUGCCGCAGCUAACGCAUUAAGUGCCCCGCCUGGGGAGUACGGCCGCAAGGCUAAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGCGGAGCAUGUGGCUUAAUUCGACGCAACGCGAAGAACCUUACCAAGGCUUGACAUACACCGGAAAGCAUCAGAGAUGGUGCCCCCCUUGUGGUCGGUGUACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUCCCGUGUUGCCAGCAGGCCCUUGUGGUGCUGGGGACUCACGGGAGACCGCCGGGGUCAACUCGGAGGAAGGUGGGGACGACGUCAAGUCAUCAUGCCCCUUAUGUCUUGGGCUGCACACGUGCUACAAUGGCCGGUACAAUGAGCUGCGAUACCGCAAGGUGGAGCGAAUCUCAAAAAGCCGGUCUCAGUUCGGAUUGGGGUCUGCAACUCGACCCCAUGAAGUCGGAGUCGCUAGUAAUCGCAGAUCAGCAUUGCUGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACGUCACGAAAGUCGGUAACACCCGAAGCCGGUGGCCCAACCCCUUGUGGGAGGGAGCUGUCGAAGGUGGGACUGGCGAUUGGGACGAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGCGGCUGGAUCACCUCCUUUCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.Streptomyces.sp.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.Streptomyces.sp.seq new file mode 100644 index 0000000..d849fb4 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.Streptomyces.sp.seq @@ -0,0 +1,2 @@ +>d.16.b.Streptomyces.sp +CAUUCACGGAGAGUUUGAUCCUGGCUCAGGACGAACGCUGGCGGCGUGCUUAACACAUGCAAGUCGAACGAUGAAGCCUUUCGGGGUGGAUUAGUGGCGAACGGGUGAGUAACACGUGGGCAAUCUGCCCUGCACUCUGGGACAAGCCCUGGAAACGGGGUCUAAUACCGGAUAAUACCUUCCCUCGCAUGGGGGUGGGUUCAAAGCUCCGGCGGUGCAGGAUGAGCCCGCGGCCUAUCAGCUUGUUGGUGAGGUAGUGGCUCACCAAGGCGACGACGGGUAGCCGGCCUGAGAGGGCGACCGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGAAAGCCUGAUGCAGCGACGCCGCGUGAGGGAUGACGGCCUUCGGGUUGUAAACCUCUUUCAGCAGGGAAGAAGCGAAAGUGACGGUACCUGCAGAAGAAGCGCCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGCGCAAGCGUUGUCCGGAAUUAUUGGGCGUAAAGAGCUCGUAGGCGGUCUGUCGCGUCGGAUGUGAAAGCCCGGGGCUUAACCCCGGGUCUGCAUUCGAUACGGGCAGACUAGAGUGUGGUAGGGGAGAUCGGAAUUCCUGGUGUAGCGGUGAAAUGCGCAGAUAUCAGGAGGAACACCGGUGGCGAAGGCGGAUCUCUGGGCCAUUACUGACGCUGAGGAGCGAAAGCGUGGGGAGCGAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGGUGGGAACUAGGUGUUGGCGACAUUCCACGUCGUCGGUGCCGCAGCUAACGCAUUAAGUUCCCCGCCUGGGGAGUACGGCCGCAAGGCUAAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCAGCGGAGCAUGUGGCUUAAUUCGACGCAACGCGAAGAACCUUACCAAGGCUUGACAUACACCGGAAACAUCCAGAGAUGGGUGCCCCCUUGUGGUCGGUGUACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUUCUGUGUUGCCAGCAUGCCCUUCGGGGUGAUGGGGACUCACAGGAGACUGCCGGGGUCAACUCGGAGGAAGGUGGGGACGACGUCAAGUCAUCAUGCCCCUUAUGUCUUGGGCUGCACACGUGCUACAAUGGCCGGUACAAUGAGCUGCGAUGCCGUGAGGCGGAGCGAAUCUCAAAAAGCCGGUCUCAGUUCGGAUUGGGGUCUGCAACUCGACCCCAUGAAGUCGGAGUUGCUAGUAAUCGCAGAUCAGCAUUGCUGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACGUCACGAAAGUCGGUAACACCCGAAGCCGGUGGCCCAACCCUUACGGGGAGGGAGCUGUCGAAGGUGGGACUGGCGAUUGGGACGAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGCGGCUGGAUCACCUCCUUUCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.Synechococcus.sp.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.Synechococcus.sp.seq new file mode 100644 index 0000000..0e4a9bb --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.Synechococcus.sp.seq @@ -0,0 +1,2 @@ +>d.16.b.Synechococcus.sp +CAAAAUGGAGAGUUUGAUCCUGGCUCAGGAUGAACGCUGGCGGCGUGCUUAACACAUGCAAGUCGAACGGGCUCUUCGGAGCUAGUGGCGGACGGGUGAGUAACGCGUGAGAAUCUGCCUACAGGACGGGGACAACAGUUGGAAACGACUGCUAAUACCCGAUGUGCCGAGAGGUGAAACAUUUAUGGCCUGUAGAUGAGCUCGCGUCUGAUUAGCUAGUUGGUGGGGUAAGGGCCUACCAAGGCGACGAUCAGUAGCUGGUCUGAGAGGAUGAUCAGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUUUUCCGCAAUGGGCGCAAGCGACGGAGCAACGCCGCGUGGGGGAGGAAGGUUUUUGGACUGUAAACCCCUUUUCUCAGGGAAGAAGAAAGUGACGGUACCUGAGGAAUAAGCCUCGGCUAAUUCCGUGCCAGCAGCCGCGGUAAUACGGGAGAGGCAAGCGUUAUCCGGAAUUAUUGGGCGUAAAGCGCCUGCAGGCGGUUAAUCAAGUCUGUUGUCAAAGCGUGGGGCUCAACCUCAUACAGGCAAUGGAAACUGAUUGACUAGAGUAUGGUAGGGGUAGCGGGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAUAUCUGGAAGAACACCAGCGGCGAAAGCGCGCUACUGGGCCAUAACUGACGCUCAUGGACGAAAGCUAGGGGAGCGAAAGGGAUUAGAUACCCCUGUAGUCCUAGCCGUAAACGAUGAACACUAGGUGUUGCGUGAAUCGACCCGCGCAGUGCCGUAGCCAACGCGUUAAGUGUUCCGCCUGGGGAGUACGCACGCAAGUUGGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGUAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCAGGGUUUGACAUCCCCCGAAUCUCUUGGAAACGAGAGAGUGCCUUCGGGAGCGGGGAGACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCACGUUUUUAGUUGCCAUCAUUCAGUUGGGCACUCUAGAGAAACUGCCGGUGACAAACCGGAGGAAGGUGUGGACGACGUCAAGUCAUCAUGCCCCUUACAUCCUGGGCUACACACGUACUACAAUGCUCCGGACAGCGAGACGCGAAGCCGCGAGGUGAAGCAAAUCUCCCAAACCGGGGCUCAGUUCAGAUUGCAGGCUGCAACUCGCCUGCAUGAAGGCGGAAUCGCUAGUAAUCGCAGGUCAGCAUACUGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGAAGUUGGCCAUGCCCGAAGUCGUUACCCUAACCGUUCGCGGAGGGGGGCGCCGAAGGUAGGGCUGAUGACUGGGGUGAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGUGGCUGGAUCACCUCCUUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.T.maritima.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.T.maritima.seq new file mode 100644 index 0000000..2d0e8e9 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.T.maritima.seq @@ -0,0 +1,2 @@ +>d.16.b.T.maritima +UAUAUGGAGGGUUUGAUCCUGGCUCAGGGUGAACGCUGGCGGCGUGCCUAACACAUGCAAGUCGAGCGGGGGAAACUCCCUUCGGGGAGGAGUACCCAGCGGCGGACGGGUGAGUAACACGUGGGUAACCUGCCCUCCGGAGGGGGAUAACCAGGGGAAACCCUGGCUAAUACCCCAUACGCUCCAUCAACGCAAGUUGGUGGAGGAAAGGGGCGUUUGCCCCGCCGGAGGAGGGGCCCGCGGCCCAUCAGGUAGUUGGUGGGGUAACGGCCCACCAAGCCGACGACGGGUAGCCGGCCUGAGAGGGUGGUCGGCCACAGGGGCACUGAGACACGGGCCCCACUCCUACGGGAGGCAGCAGUGGGGAAUCUUGGACAAUGGGGGAAACCCUGAUCCAGCGACGCCGCGUGCGGGACGAAGCCCUUCGGGGUGUAAACCGCUGUGGCGGGGGAAGAAUAAGGUAGGGAGGAAAUGCCCUACCGAUGACGGUACCCCGCUAGAAAGCCCCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGGGCAAGCGUUACCCGGAUUUACUGGGCGUAAAGGGGGCGUAGGCGGCCUGGUGUGUCGGAUGUGAAAUCCCACGGCUCAACCGUGGGGCUGCAUCCGAAACUACCAGGCUUGGGGGCGGUAGAGGGAGACGGAACUGCCGGUGUAGGGGUGAAAUCCGUAGAUAUCGGCAGGAACGCCGGUGGGGAAGCCGGUCUCCUGGGCCGACCCCGACGCUGAGGCCCGAAAGCCAGGGGAGCAAACCGGAUUAGAUACCCGGGUAGUCCUGGCUGUAAACGAUGCCCACUAGGUGUGGGGGGGUAAUCCCUCCGUGCUGAAGCUAACGCGUUAAGUGGGCCGCCUGGGGAGUACGCCCGCAAGGGUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCGUGUGGUUUAAUUGGAUGCUAAGCCAAGAACCUUACCAGGGCUUGACAUGCCGGUGGUACCUCCCCGAAAGGGGUAGGGACCCAGUCCUUCGGGACUGGGAGCCGGCACAGGUGGUGCACGGCCGUCGUCAGCUCGUGCCGUGAGGUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCCUGCCCCUAGUUGCCAGCGGUUCGGCCGGGCACUCUAGGGGGACUGCCGGCGACGAGCCGGAGGAAGGAGGGGAUGACGUCAGGUACUCGUGCCCCUUAUGCCCUGGGCGACACACGCGCUACAAUGGGCGGUACAAUGGGUUGCGACCCCGCGAGGGGGAGCCAAUCCCCAAAGCCGCCCUCAGUUCGGAUCGCAGGCUGCAACCCGCCUGCGUGAAGCCGGAAUCGCUAGUAAUCGCGGAUCAGCCAUGCCGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACGCCACCCGAGUCGGGGGCUCCCGAAGACACCUACCCCAACCCGAAAGGGAGGGGGGGUGUCGAGGGAGAACCUGGCGAGGGGGGCGAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGCGGCUGGAUCACCUCCUUUCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.T.pallidum.A.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.T.pallidum.A.seq new file mode 100644 index 0000000..23d8958 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.T.pallidum.A.seq @@ -0,0 +1,2 @@ +>d.16.b.T.pallidum.A +AUGAUGGAGAGUUUGAUCCUGGCUCAGAACGAACGCUGGCGGUGCGUUUUAAGCAUGCAAGUCGAACGGCAAGGAAGCGAAUUUUCGUUUCUCUAGAGUGGCGGACUGGUGAGUAACGCGUGGGUAAUCUGCCUUUGAGAUGGGGAUAGCCUCUAGAAAUAGGGGGUAAUACCGAAUACGCUCUUUUGGACGUAGUCUUUGAGAGGAAAGGGGCUGCGGCCUCGCUCAGAGAUGAGCCUGCGACCCAUUAGCUUGUUGGUGGGGUAAUGGCCUACCAAGGCGUCGAUGGGUAUCCGACCUGAGAGGGUGACCGGACACACUGGGACUGAGAUACGGCCCAGACUCCUACGGGAGGCAGCAGCUAAGAAUAUUCCGCAAUGGGCGAAAGCCUGACGGAGCGACACCGCGUGGAUGAGGAAGGUCGAAAGAUUGUAAAGUUCUUUUGCCGACGAAGAAUGAGGACGGGAGGGAAUGCCCGUUUGAUGACGGUAGUCGUGCGAAUAAGCCCCGGCUAAUUACGUGCCAGCAGCCGCGGUAACACGUAAGGGGCGAGCGUUGUUCGGAAUUAUUGGGCGUAAAGGGCAUGCAGGCGGACUGGUAAGCCUGGUGUGAAAUCCCCGAGCUCAACUUGGGAACUGCACUGGGUACUGCUGGUCUAGAAUCACGGAGGGGAAACCGGAAUUCCAAGUGUAGGGGUGGAAUCUGUAGAUAUUUGGAAGAACACCGGUGGCGAAGGCGGGUUUCUGGCCGAUGAUUGACGCUGAGGUGCGAAGGUGUGGGGAGCGAACAGGAUUAGAUACCCUGGUAGUCCACACAGUAAACGAUGUACACUAGGUGUUGGGGCAUGAGUCUCGGCGCCGACGCGAACGCAUUAAGUGUACCGCCUGGGGAGUAUGCUCGCAAGAGUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGAUACGCGAGGAACCUUACCCGGGUUUGACAUCAAGAGGAGCGCCGUAGAAAUGCGGUGGCGUAGCGAUACGCCUCUUGACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGCCGUGAGGUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCCUACUGCCAGUUGCCAGCAAGUGGUGUUGGGGACUCUGGCGGAACUGCCGGUGACAAACCGGAGGAAGGUGGGGAUGACGUCAAGUCAUCAUGGCCCUUAUGUCCGGGGCUACACACGUGCUACAAUGGUUGCUACAGAGCGAUGCGAGGUUGUGAAGUGGAGCAAACCGCAAAAAGGCAAUCGUAGUCCGGAUUGAAGUCUGAAACUCGACUUCAUGAAGUUGGAAUCGCUAGUAAUCGCACAUCAGCAUGGUGCGGUGAAUGUGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUCCGAGUUGGAGAUACCCGAAGUCACUAGCCUAACCCGCAAGGGAGGGCGGUGCCGAAGGUAUGUUUGGUAAGGAGGGUGAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGCGGCUGGAUCACCUCCUUUC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.c.C.caldarium.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.c.C.caldarium.seq new file mode 100644 index 0000000..575befd --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.c.C.caldarium.seq @@ -0,0 +1,2 @@ +>d.16.c.C.caldarium +UAUAAUGGAGAGUUUGAUCCUGGCUCAGGAUUAACGCUGGCGGUAUGCCUAACACAUGCAAGUCGUACGAGAAUUUUAUUCUAGUGGCGGACGGGUGAGUAACACGUGAGAAUCUACCUCUAGGAGGGGGAUAACAGUUGGAAACGAUUGCUAAAACCCCAUAUGCCAUUAUUGGUGAAAAAGAUUUAUCUGCCUGGAGAUGAGCUCGCGGCUGAUUAGCUAGUUGGUAGGGUAAUGGCUUACCAAGGCAACGAUCAGUAGCUGGUCUUAGAGGAUGAUCAGCCACACUGGAACUGAGAUACGGUCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUUUUCCACAAUGGGCGAAAGCCUGAUGGAGCAAUACCGUGUGAGGGAUGAAGGCCUGUGGGUUGUAAACCUCUUUUUUCAGGAAAGAAACUUUGACGGUACCUGAAGAAUAAGCAUCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGAUGCAAGCGUUAUCCGGAAUCACUGGGCGUAAAGCGUCUGUAGGUGGUUUAUCAAGUCUGCUGUUAAAGCUUGAGGCUUAACCUCAAAAAAGCAGUGGAAACUGAUAGACUAGAGAAUGGUAGGGGCAGAGAGAAUUCUCAGUGUAGCGGUGAAAUGCGUAGAUAUUGAGAAGAAUACCGAUAGCGAAGGCGCUCUGCUGGGCCAUUACUGACACUCAGAGACGAAAGCUAGGGGAGCAAAUGGGAUUAGAUACCCCAGUAGUCCUAGCCGUAAACUAUGGAUACUAGAUGUUGUGUGAGUAAAAUUGUGCAGUAUCGAAGCUAACGCGUUAAGUAUCCCGCCUGGGAAGUACGCUCGCAAGAGUGAAACUCAAAGGAAUUGACGGGGACCCGCACAAGCGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCAGGACUUGACAUGUUACUAAUUUCCUUGAAAGAGGAAAGUGCCUUUGGGAAAGUAAACACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUCUUUAGUUACCAUCAUUAAGUUGGGGACUCUAAAGAGACUGCCGGUGAUAAACCGGAGGAAGGUAAGGAUGAGGUCAAGUCAUCAUGCCCCUUAUGUCCUGGGCUACACACGUGCUACAAUGGUUAGGACAAUAAGUCGCAAAUUCGUGAGAACUAGCUAAUCUUAUAAACCUAAUCUCAGUACGGAUUGUAGGCUGCAACUCGCCUACAUGAAGACGGAAUCGCUAGUAAUCGCUGGUCAGCUACACAGCGGUGAAUACGUUCCCGGGUCUUGUACACACCGCCCGUCACACCAUGGGAGCUGGCCAUGUCCGAAAUCAUUACUCUAACCUUAAUGGAGGAGGAUGCUUAAGGCAGGGCUAGUGACUGGGGUGAAGUCGUAACAAGGUAGCCGUACUGGAAGGUGCGGCUGGAUUACCUCCUUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.c.C.fragile.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.c.C.fragile.seq new file mode 100644 index 0000000..b5a551f --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.c.C.fragile.seq @@ -0,0 +1,2 @@ +>d.16.c.C.fragile +UUGAAAUGGAGAGGUUUGAUCCUGGCUCAGGAUGAACGCUGGCGAUAUGCUUAACACAUGCAAGUCGAACGAAUAUUAAGUUUUCUUAAAUUUGUAGAAAUUUAAUAUUAGUGGCGAACGGGUGAGUAACGCGUAAGAAUCUGCUUUUGGGUAAAGAAUAACAAUUGGAAACGAUUGCUAAUACUUUAUAGGCUGAGGAGUUAAAGGUUUUAUUUCCGCCCAGAAAUGAGCUUGCGUCUGAUUAGCUAGUUGGUAAGAUAAAAGCUUACCAAGGCAAUGAUCAGUAGUUGGUCUGAGAGGAUGAUCAACCACACUGGGACUGAGAUACGGCCCAGACCUUUACGGAGGGCAGCAGUGAGGAAUUUUCCGCAAUGGGCGAAAGCCUGACGGAGCAAUAUCGCGUGAAGGAUGACGGCCUGUGGGUUGUAAACUUCUUUUCUUAAGAAAGAAUUCUGACGGUACUUAAGGAAUAAGCAUCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGAUGCAAGCGUUAUCCGAAAUUAUUGGGCGUAAAGAGUUUGUAGGUGGUUUUUUAAGUCUACUGUUAAAUAUCAGAGCUUAACUUUGAACAAGCAGUAUGAAACUAAUUAACUUGAGUUUGGUAGAGGCAGAGGGAACUCUCGAUGUAGUGGUGAAAUACGUAGAUAUCGGGGGGAACACCAGUAGCGAAAGCGCUCUGCUGGGCCAUAACUGACACUGAGAAACGAAAGCUAGGGGAGCAAAUAGGAUUAGAUACCCUAGUAGUCCUAGCUGUAAACGAUGGAUACUAAGUAUUGGGCUUUUUGAAGUUCAGUGUUGAAGCUAACGCGUUAAGUAUCCCGCCUGGGGAGUACGUUCGCAAGAAUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCAGGAAUUGACAUACUCGUUGGUUUUUUAGAAAUAAAAAACUGUUAAAGAGAUACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUCUUUAGUUGUUAUCUAGAGAGACUGCCGGUGAUAAACCGGAGGAAGGUGAGGAUGACGUCAAGUCAGCAUGCCCCUUAAGUCCUGGGCGACACACGUGCUACAAUGGUAUAGACAAAGGGAAGCAAAUCUGCGAAGAGUAGCAAAUCUCAAAAACUAUAUCUCAGUUCGGAUUGCAGGCUGCAACUCGCCUGCAUGAAGUCGGAAUCGCUAGUAAUCGCUGGUCAGCCAUACAGCGGUGAAUAUGUUCUCGGGCCUUGUACACACCGCCCAUCACGCUCGAGAAAUUGGAAAUACCCAAAGUCAUCAUUCUAACCAUAUUUUUUGGAAGAUAAUGCCAAAGGUAGAGCUAGUGACUCAAGCGAAGUUGUAACAAGGUAACCGUACUGGAAGGUGCGGUUGGAUCACCUCCUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.c.C.reinhardtii.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.c.C.reinhardtii.seq new file mode 100644 index 0000000..665ca3f --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.c.C.reinhardtii.seq @@ -0,0 +1,2 @@ +>d.16.c.C.reinhardtii +AUCCAUGGAGAGUUUGAUCCUGGCUCAGGACGAACGCUGGCGGCAUGCUUAACACAUGCAAGUCGAACGAGCAAAGCAAUUUGUGUAGUGGCGAACGGGUGCGUAACGCGUAAGAACCUACCUAUCGGAGGGGGAUAACAUUGGGAAACUGUUGCUAAUACCCCAUACAGCUGAGGAGUGAAAGGUGAAAAACCGCCGAUAGAGGGGCUUGCGUCUGAUUAGCUAGUUGGUGGGGGUAACGGCCUCCCAAGGCCACGAGCAGUAGCUGGUCUGAGAGGAUGAUCAGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGAGGAAUUUUUCGCAAUGGGCGCAAGCGACGGAGCAAUGCCGCGUGCAGGAAGAAGGCCUGUGGGUCGUAAACUGCUUUUCUCAGAGAAGAAGUUCUGACGGUAUCUGAGGAAUAAGCACCGGCUAACUCUGUGCCAGCAGCCGCGGUAAUACAGAGGGUGCAAGCGUUGUCCGGAAUGAUUGGGCGUAAAGCGUCUGUAGGUGGCUCGUAAAGUCUAAUGUCAAAUACCAGGGCUCAACCUUGGACCGGCAUUGGAGUACUCACGAGCUUGAGUACGGUAGGGGCAGAGGGAAUUCCAUGUGGAGCGGUGAAAUGCGUAGAGAUAUGGAGGAACACCAGUGGCGAAGGCGCUCUGCUGGGCCGAAACUGACACUGAGAGACGAAAGCUGGGGGAGCGAAUAGGAUUAGAUACCCUAGUAGUCCCAGCCGUAAACUAUGGAGACUAAGUGCUGCCGCAAGCAGUGCUGUAGCUAACGCGUUAAGUCUCCCGCCUGGGGAGUAUGCUCGCAAGAGUGAAACUCAAAGGAAUUGACGGGACCGCACAAGCGGUGGAUUAUGUGGAUUAAUUCGAUACAACGCGAAGAACCUUACCAGGGUUUGACAUGUCAAGAACCUCUCAGAAAUGGGAGGGUGCCCUAACGGACUUGAACACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGCUGUGAAGUGUAUAGUUAAGUCUCAUAACGAGCGCAACCCUCGUCUUUAGUUGCCAUUUGGUUCUCUAAAGAGACUGCCAGUGUAAGCUGGAGGAAGGUGAGGAUGACGUCAAGUCAGCAUGCCCCUUACAUCCUGGGCUUCACACGUAAUACAAUGGUUGGGACAAUCAGAAGCGACUCGUGAGAGCUAGCGGCUCUGUUAAACCCAACCUCAGUUCGGAUUGUAGGCUGCAACUCGCCUACAUGAAGCCGGAAUCGCUAGUAAUCGCCAGUCAGCUAUAUGGCGGUGAAUACGUUCCCGGGUCUUGUACACACCGCCCGUCACACCAUGGAAGCUGGUUCUGCUCCAAGUCGUUACCCUAACCUUCGGGAGGGGGGCGCCUAAAGCAGGGCUAGUGACUAGGGUGAAGUCGUAACAAGGUAGGGCUACUGGAAGGUGGCCCUGGCUCACCUCCUUC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.c.C.vulgaris.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.c.C.vulgaris.seq new file mode 100644 index 0000000..c5ee178 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.c.C.vulgaris.seq @@ -0,0 +1,2 @@ +>d.16.c.C.vulgaris +UGCCUGCAGAGAGUUYGAUCCUGGCUCAGGAUGAACGCUGGCGGCAUGCUUAACACAUGCAAGUCGUACGCAUGCAAUUUGGCUUGCCAGAUUGCGAUGAGUGGCGGACGGGUGAGUAACACGUAAGAACCUACCUUUUGGAGAGGGAUAACCAUUGGAAACGAUGGCUAAUACCUCGUAUUGCUGAGAAGUGAAAGAUGAAAAUCGCCAAUAGAUGGGCUUGCGGCUGAUUAGCUUGUUGGUGAGGUAAUGGCUUACCAAGGCAAUGAUCAGUAGCUGGUCUGAGAGGAUGAUCAGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGAGGAAUUUUCCGCAAUGGGCGACAGCCUGACGGAGCAAUGCCGCGUGAAGGAUGAAGGCCUAUGGGUUGUAAACUUCUUUUCUCAGAGAAGAAGCAUUGACGGUAUCUGAGGAAUAAGCAUCGGCUAACUCUGUGCCAGCAGCCGCGGUAAGACAGAGGAUGCAAGCGUUAUCCGGAAUGAUUGGGCGUAAAGCGUCUGUAGGUGGCUUAAAAAGUCUCCUGUCAAAGAUCAGGGCUUAACCCUGGGCCGGCAGGAGAAACUCUUAGGCUAGAGUUUGGUAGGGGCAGAGGGAAUUCCCGGUGGAGCGGUGAAAUGCGUAGAGAUCGGGAGGAACACCAAAGGCGAAAGCACUCUGCUGGGCCAUAACUGACACUGAGAGACGAAAGCGAGGGGAGCAAAAGGGAUUAGAUACCCCUGUAGUCCUCGCCGUAAACGAUGGAUACUAGAUGUUGGGUAGGUUAAAUCACUCAGUAUCGUAGCUAACGCGUGAAGUAUCCCGCCUGGGGAGUAUGCUCGCAAGAGUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCAGGACUUGACAUGCCACUUUUUCCCUGAAAGGGGAAGUUCCAGAGUGGACACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCUUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUUUUGAAUUGCCAGUAAUGGGAAAUUCAAAAGACUGCCGGUGACAAGCCGGAGGAAGGUGAGGAUGACGUCAAGUCAGCAUGCCCCUUACGUCCUGGGCGACACACGUGCUACAAUGGCCGGGACAAAGAGAUGCAAACCCGCGAGGGCUAGCCAACCUCAAAAACCCGGUCUCAGUUCGGAUUGCAGGCUGCAACUCGCCUGCAUGAAGUCGGAAUCGCUAGUAAUCGCAGGUCAGCCAUACUGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGCUGGCUAUGCCCAAAGUCGUUACCCCAACCUUUUAGGAGGGGGACGCCUAAGGCAGAGCUAGUGACUAGGGUGAAGUCGUAACAAGGUAGCCGUACUGGAAGGUGWGGYUGGAUCACCUCCUUG diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.c.Cryptomonas.sp.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.c.Cryptomonas.sp.seq new file mode 100644 index 0000000..3b7fc1b --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.c.Cryptomonas.sp.seq @@ -0,0 +1,2 @@ +>d.16.c.Cryptomonas.sp +AAAUCAUGGAGAGUUUGAUCCUGGCUCAGGAUGAACGCUGGCGGUAUGCUUAACACAUGCAAGUCGUACGAAAGUUUUUAACUUUAGUGGCGGACGGGUGAGUAACACGUGAGAAUCUACCCUUAGGAGGAGGGGGAUAACAGCUGGAAACGGCUGCUAAUACUCCAUAUGCUGAAGAGUGAAAGGGAAACCACCUAAGGAAGAGCUCGCGUCUGAUUAGCUAGUUGGUAGGGUAAGGGCCUACCAAGGCGACGAUCAGUAGCUGGUUUGAGAGGACGAUCAGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUUUUCCGCAAUGGGCGCAAGCCUGACGGAGCAAUACCGCGUGAGGGAUGAAGGCCUGUGGGUUGUAAACCUCUUUUCUCAAGGAAGAAGUUCUGACGGUACUUGAGGAAUAAGCAUCGGCUAACUCUGUGCCAGCAGCCGCGGUAAUACAGAGGAUGCAAGCGUUAUCCGGAAUUACUGGGCAUAAAGCGUCUGUAGGUUGUUUAGUAAGUCUGCUGUUAAAGACUAGGGCUUAACCCUAGAAAAGCAGUGGAAACUGCUAGACUUGAGUGUGGUAGAGGUAGAGGGAAUUCCUAGUGUAGCGGUGAAAUGCGUAGAUAUUAGGAAGAACACCAAUGGCGAAAGCACUUUACUGGGCCAUAACUGACACUGAGAGACGACAGCUAGGGGAGCAAAUGGGAUUAGAUACCCCAGUAGUCCUAGCCGUAAACUAUGGAUACUAGAUGUUGUACGUAUUAACCCGUACAGUAUCGUAGCUAAGGCGUUAAGUAUCCCGCCUGGGAAGUACGCUCGCAAGAGUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGUAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCAGGGUUUGACAUGUCACAAAUUUUCUUGAAAAAGAAAAGUGCCUUCGGGAAUGUGAACACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGUAACCCUUGUUUUUAGUUGCCAUCAUUAAGUUGGGCACUUUAAAAAGACUGCCGGUGAUAAACCGGAGGAAGGUGAGGACGACGUCAAGUCAGCAUGCCCCUUACACUCUGGGCUACACACGUACUACAAUGGUCGAGACAAAAAGUCGCAAACUUGUGAAAGUAAGCUAAUCUUAUAAACUCGAUCUCAGUUCGGAUUGCAGGCUGCAACUCGCCUGCAUGAAGUUGGAAUCGCUAGUAAUCGCCGGUCAGCUAUACGGCGGUGAAUCCGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGAAGCUAGUCAUACCCAAAGUCGUUACCUUAACCAUUCGGAGGGGGGCGCCUAAGGUAGGGUUAGUGACUGGGGUGAAGUCGUAACAAGGUAGCCGUACUGGAAGGUGCGGCUGGAUCACCUCCUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.c.E.gracilis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.c.E.gracilis.seq new file mode 100644 index 0000000..6c04b9e --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.c.E.gracilis.seq @@ -0,0 +1,2 @@ +>d.16.c.E.gracilis +UGGAAAUGACGAGUUUGAUCCUUGCUCAGGGUGAACGCUGGCGGUAUGCUUAACACAUGCAAGUUGAACGAAAUUACUAGCAAUAGUAAUUUAGUGGCGGACGGGUGAGUAAUAUGUAAGAAUCUGCGCUUGGGCGAGGAAUAACAGAUGGAAACGUUUGCUAAUGCCUCAUAAUUUACUAGAUCUAUGUGAGUAGCUAGUUAAAGAGAAUUUCGCCUAGGCAUGAGCUUGCAUCUGAUUAGCUUGUUGGUGAGGUAAAGGCUUACCAAGGCGACGAUCAGUAGCUGAUUUGAGAGGAUGAUCAGCCACACUGGGAUUGAGAACGGAACAGACUUCUACGGAAGGCAGCAGUGAGGAAUUUUCCGCAAUGGGCGCAAGCCUGACGGAGCAAUACCGCGUGAAGGAAGACGGCCUUUGGGUUGAAAACCUCUUUUCUCAAAGAAGAAGAAAUGACGGUAUUUGAGGAAUAAGCAUCGGCUAAUUCCGUGCCAGCAGCCGCGGUAAUACGGGAGAUGCGAGCGUUAUCCGGAAUUAUUGGGCGUAAAGAGUUUGUAGGCGGUCAAGUGUGUUUAAUGUUAAAAGUCAAAGCUUAACUUUGGAAGGGCAUUAAAAACUGCUAGACUUGAGUAUGGUAGGGGUGAAGGGAAUUUCCAGUGUAGCGGUGAAAUGCGUAGAGAUUGGAAAGAACACCAAUGGCGAAGGCACUUUUCUAGGCCAAUACUGACGCUGAGAAACGAAAGCUGAGGGAGCAAACAGGAUUAGAUACCCUGUAGUCUUGGCCGUAAACUAUGGAUACUAAGUGGUGCUGAAAGUGCACUGCUGUAGUUAACACGUUAAGUAUCCCGCCUGGGGAGUACGCUUGCACAAGUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAACACGAAGAACCUUACCAGGAUUUGACAGGAUCUAGGAAGUUUGAAAGAACGCAGUACCUUCGGGUAUCUAGACACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUUUUUUUAAUUAACGCUUGUCAUUUAGAAAUACUGCUGGUUAUUACCGGAGGAAGGUGAGGACGACGUCAAGUCAUCAUGCCCCUUAUAUCCUGGGCUACACACGUGCUACAAUGGUUAAGACAAUAAGUUGCAAUUUUGUGAAAAUGAGCUAAUCUUAAAACUUAGCCUAAGUUCGGAUUGUAGGCUGAAACUCGCCUACAUGAAGCCGGAAUCGCUAGUAAUCGCCGGUCAGCUAUACGGCGGUGAAUACGUUCUCGGGCCUUGUACACACCGCCCGUCACACCAUGGAAGUCGGCUGUGCCCGAAGUUAUUAUCUUGCCUGAAAAGAGGGAAAUACCUAAGGCCUGGCUGGUGACUGGGGUGAAGUCGUAACAAGGUAGCCGUACUGGAAGGUGUGGCUGGAACAACUCC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.c.H.africana.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.c.H.africana.seq new file mode 100644 index 0000000..13a55b3 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.c.H.africana.seq @@ -0,0 +1,2 @@ +>d.16.c.H.africana +UCUCAUGGAGAGUUCGAUCCUGGCUCAGGAUGAACGCUGGCGGCAUGCUUAACACAUGCAAGUUGAACGAGAAAUAGAACAACUAUUUCUAGUAGCGAACGGGUGCGUAAUUACAUAAGAACUUAUCCUUUUAAGAAGGAAAUAACAAAUAACAAAUGGAAACAUUUGCUAAUGUCCUAUAAGCUGAAAAGUAAAAGGAUUAAAUCCACUAAAGGUAAGGCUUAUGUCUAGUUAGUUGGUAAGGUAACAGCUUAACAAGACAAUGAUCAGUAAUUGGUCUGAGAGGAUGAUCAAUCACACUGGAACUGAGAUAAGGUCCAGACUCCUACGGGUGGCAGCAGUGGGGAAUUUUCCGCAAUGGGCGAAAGCUGACGGGGCAAUGUUGCGUGAAGGCAGAAGGCCGAUAGGUUGUAAACUUCUUUUGUGAGAAAAUAAGGAAAAUGACAGUAUCUCAAGAAUAAGCAUCGGCUAACUUUGUGCCAGCAGCCGCGGUGAUACAGAGGAUGCGAGCAUUAUCCGGAAUUAUUGGGCGUAAAGUGUUUUAAGGUGGCUUUAUAAGUCUAUCGUUAAAUCUCAGAGCUUAACUCUGAUUAGGCGAUUGACUAUUAAGCUAGAGCUUUGAAUAAAGCAAGGGGAAUUUCUAAUGAAGCGGUUAAAUGCGUUGAGAUUGGAAAGAACACCAAGGGCGAAAGCACUCUGCUGGGCCAAAAUUGACACUGAUAAACGAAAGCUAGGGUAGCGAGAGGGAUUAGACACCCCAAUAGUCCUAGCUGUAAACAAUGGAUACUUAGCAUUACUAUAUGAAAAGAUAGCUAAGCUUAAAGCUAACGCAAUAAGUAUCCCGCCUGGGAAGUACGUUCGCAAGAAUGAAACUCAAAGGAAUUGGCGGGGGUUCACGCAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAAAGCGAAGAACCUUACCAGGGAUUGUAUGUCGUAAUCUUUCUGAAAAAGUAAGAUACGUAUUUAUUUAAUAAAUAAAUACGUAGACACAGGUGGUGCAUGGCUGUCGUCAGCCCGUGCUGUCAAGCGUAGGGUUAACUCCCAUAACGGGCGCAACUCCCAUGUUUAGUUACCAAUUUAUGGUACUCUAAACAAACAGCUAAUGAUAAAUACUAAAUUAGAGGAAGGUGGGGAAGACGUCAAGUCAUCAUGCCCUUUAUACUCUGGGCUACACGCGUGCUACAAUGGCUGGGACAAAAUGUUGCAAUUCUGUAAAGAUAUAGCAAAACAUAAAACCCAGUCUCAGUUCGGAUUCGGGCUGCAACUCGCCCGCAUGAAGUCGGAAUCGCUAGUAAUCGCUGGUCAGCAAUACAGCGGUGAAUAAGUCACCGGACCUUGUACACACCGCCCGUCACACUCAGGAAAUUGGUCAUGCCCUAACUCAUUUUAAUAUAAUGAUAAAGGUGAGGCUGGUAACUAGAGUGAAGUCGUAACAAGGUAGCCGUACUGGAAGGUGCGGCUGGAUCACCUCCUUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.c.H.akashiwo.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.c.H.akashiwo.seq new file mode 100644 index 0000000..7f1d3dd --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.c.H.akashiwo.seq @@ -0,0 +1,2 @@ +>d.16.c.H.akashiwo +UUUUAGGAUAUAAUUGAGAGUUUGAUCCUGGCUCAGGAUGAACGCUGGCGGUAUGCUUAACACAUGCAAGUCGAACGAGAGGUUUUUAAAGAUUUUUCUUAAAAAACUGAAAGUGGCGGACGGGUGAGUAACACGUGAGAAUCUGCCUUUAGGAAAGGGACAACAUUUGGAAACGAAUGCUAAUACCUUAUAUGCCUAUUAUAACUUGUAUAAUUAAUAGGUGAAAAGUUUUCUGCCUAGAGAGGAGCUCGCGGCUGAUUAGCUAGUUGGUGGGGUAAUGGCCUACCAAGGCGACGAUCAGUAACUGAUUUGAGAGGAUGAUCAGUCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUUUUCUGCAAUGGGCGAAAGCCUGACAGAGCAAUACCGCGUGAGGGAUGACAGUCCUAUGGAUUGUAAACCUCUUUUUUCAGGGAGGAAGUUCUGACGUUACCUGAAGAAUAAGCAUCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGAUGCAAGUGUUAUCCGGAAUCACUGGGCGUAAAGCGUCUGUAGGUGGUUUAAUGUGUCUGUUGUUAAAUCUUAAGGCUCAACCUUAAACCAGCAAUGGAAACUAUUAUGACUUGAGUGUGGUAGAGGUAGAGGGAAUUUCCAGUGGAGCGGUGAAAUGCGUAGAUAUUGGAAAGACCACCAAUGGCGAAGGCACUCUACUGGGCCAUUACUGACACUGAGAGACGAAAGCUAGGGGAGCAAAUGGGAUUAGAUACCCCAGUAGUCCUAGCUGUAAACGAUGGAUACUAGAUGUCGCAUGUAUCGACCCAUGCGGUAUUAUAGCUAACGCGUUAAGUAUCCCGCCUGGGAAGUAUGCUCGCAAGAGUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCAGGGUUUGACAUAGUACGAAGUUUUUUGAAAAAAAAACCACCUUCGGGAACGUACAUACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGUAACCCUUGUUUUUAGUUGCCUUUCGAGGAUAUUUAGAAAGACUGCCGAUUAUAAAUCGGAGGAAGGUAAGGACGACGUCAAGUCAUCAUGCCCCUUACACUCUGGGCUACACACGUGCUACAUUGGGUAGAACAAUAAGUUGCUAAGUUGCGAAACCAAGCGAAUCUUCAAAUCUACUCUAAGUUCGGAUUGUAGGCUGCAACUCGCCUACAUAAAGAUGGAAUCGCUAGUAAUCGCUGGUCAGCUACACAGCGGUGAAUCGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGAAGCUGGUCACACCCAAAGUCGUUAUUCUAACCGUUUGGAGGAAGGCGCCUAAGGUAGGAUUGGUGACUGGGGUGAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGCGGCUGGAUCACCUCCUUAUAAAGGUUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.c.M.polymorpha.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.c.M.polymorpha.seq new file mode 100644 index 0000000..516122e --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.c.M.polymorpha.seq @@ -0,0 +1,2 @@ +>d.16.c.M.polymorpha +UCUCAUGGAGAGUUUGAUCCUGGCUCAGGAUGAACGCUGGCGGCAUGCUUAACACAUGCAAGUCGUACGGGAAGGAUCCUAGUGGUGUUUCCAGUGGCGGACGGGUGAGUAACGCGUAAGAACCUGCCCUUGGGAGGGGGACAACAGCUGGAAACGGUUGCUAAUACCCCAUAGGCUGAGGAGCAAAAGGAGGAAUCCGCCUAAGGAGGGGCUUGCGUCUGAUUAGCUAGUUGGUGAGGUAAUAGCUUACCAAGGCGACGAUCAGUAGCUGGUCUGAGAGGAUGAUCAGCCACACUGGGACUGAGACACGGCCCAGACUCUUACGGGAGGCAGCAGUGGGGAAUUUUCCGCAAUGGGCGAAACGUGACGGAGCAAUGCCGCGUGGAGGUAGAAGGCUCACGGGUCGUAAACUCCUUUUCUCAGAGAAGAUGCAAUGACGGUAUCUGAGGAAUAAGCAUCGGCUAACUCUGUGCCAGCAGCCGCGGUAAGACAGAGGAUGCAAGCGUUAUCCGGAAUGAUUGGGCGUAAAGCGUCUGUAGGUGGCUUUUUAAGUCCGCCGUCAAAUCCCAGGGCUCAACCCUGGACAGGCGGUGGAAACUACCAAGCUGGAGUACGGUAGGGGCAGAGGGAAUUUCCGGUGGAGCGGUGAAAUGCGUAGAGAUCGGAAAGAACACCAAUGGCGAAAGCACUCUUCUGGGCCGACACUGACACUGAGAGACGAAAGCUAGGGGAGCAAAUGGGAUUAGAUACCCCAGUAGUCCUAGCCGUAAACGAUGGAUACUAAGCGCUGUGCUAUCGACCCGUGCAGUGCUGUAGCUAACGCGUUAAGUAUCCCGCCUGGGGAGUACGUUCGCAAGAAUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCAGGGCUUGACAUGCCGUGAAUCUUUUUGAAAGAAAAGAGUGCCUUCGGGAACGCGGACACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGCCGUAAGGUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUCUUGUUUAGUUGCCAUCAUUAAGUUUGGAACCCUAAACAGACUGCCGGUGAUAAGCCGGAGGAAGGUGAGGAUGACGUCAAGUCAGCAUGCCCCUUACGCCCUGGGCGACACACGUGCUACAAUGGCCGGGACAAAGGGUCGCGACCUCGCGAGAGAAAGCUAACCUCAAAAACCCGGCCUCAGUUCGGAUUGCAGGCUGCAACUCGCCUGCAUGAAGCCGGAAUCGCUAGUAAUCGCCGGUCAGCCAUACGGCGGUGAAUCCGUUCCCGGGCCUUGUACACACCGCCCGUCACACUAUGGGAGCUGGCCAUGCCCGAAGUCGUUACUCUAACCGUAAGGAGGGGGGUGCCGAACAGGGGCUAGUGACUGGAGUGAAGUCGUAACAAGGUAGCCGUACUGGAAGGUGCGGCUGGAUCACCUCCUUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.c.P.falciparum.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.c.P.falciparum.seq new file mode 100644 index 0000000..09f3dac --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.c.P.falciparum.seq @@ -0,0 +1,2 @@ +>d.16.c.P.falciparum +UUAUAUUGCGAGUUUGAUCCUAGCUCAGAAUUAACGCUAGAAAUAUACAUUACACAUGCAAAUUAAUGAUAAUAUCAUAGUGUAUAGGUGAGGAUAUAUAAAUUUUUAAUUUUAAAUAGAUUAUAAAUUUUAUUAAAUAAUAAUCUAUAAGCGCAAAAAUAUAUGUACUAUAUUAAAAAUUAAUAUUAUUUAAAAUAAAAUUUAUAUUUGAUUAACUAGUUGGUAAUUUAAAAGACUACCAAGGUUAUUAUCAAAAAUUGGUUUGAAAGAAUGUACAAUCACAUUAGGAUUGAAAUAAAGCCUAAAUUUUUAUAAAAAAUCAGCAGUGAGGAAUAUUUUACAAUAAGUGUAAGCUUGAUAAAGUAAUAUUUCUUUUAGGAAGACAGUAUUAUUAAAAUAUUGUAAACUUUUUAUUUUAUUUUUAAAUAUUGAUAAAAAUAAAAAAUAGUAUUUGCUAUUUCUGUGCCAGCAGCAGCGGUAAUACAGAAAAUGCAAGCGUUAUUCAUUUUAUUAGGCGUAAAGCGUUUUAAGGUUUUAUAUUAAUUUUAUGUUUAAAUAUUUAAAUUAAAUUUAAAAUAAAUUAAUAAAUAAUAAUAUAAUAGAGUAUUAUAAAAGUAUUAAGAAUUUUUUGAGAAGUAGUGAAAUACAAUGAUACAAAAAAGAAUAUCAAAGGCGGAAGCAUAAUACUAUAUAAUUACUGACACUUAAAAACGAAAGCUAAGGUAGCAAAUAGGAUUAGAUACCCUAGUAGUCUUAGCUGUAAACUAUGAAUAUUUUAUAUUUAUAUUUUAUAAAUAUAAUAACUAACGUGAUAAAUAUUCCGCCUGAGUAGUAUAUUCGCAAGAAUGAAAUUCAAAGGAAUUGACGGGAGCUUAUACAAGUGGUGGAACAUGUGGCUUAAUUCGAUGCAACACGAUAAACCUUACCAAAAUUUAACAAUAUUUUUAAUAUUAAGAAAUUAAUAUUUUAAUAAAAUAUAUAGGUAGUGCAUGGCUGUCGUCAGUUCGUGCUGUGAAGUGUUAAUUUUAGUAUUAUAACGAACGUAACCUUUUAUAAAAAAAAUUUUUAUAAUAAAUAAUAAUAAAGAUUACGUCAAGUCAUUAUGCUCCUUAUAUUUUGGGCUGCUCACGUGUUACAUAAAAUAUUACAAUAUUUUAUUAUAUGUUAAAUAUAAUAAUUAAAAUAUAUUUAUAGUUCAGAUUAUAAAUUGAAACUCAUUUAUAUAAAGAUGGAAUCACUAGUAAUCGCUAAUCAGAAUUAUAGCGGUGAAUAAGUUCUUAAGCUUUGUACACACCGCCCGUCACAUCUAAAAAGUAUCAUAUUAUAUAAAAAUUAUUGUUAAAUAAUAAUAUAUAAUUAUAUAAUUUAGAUGAAGUCGUAACAAGGUAGCCGUACUGGAAGGUGCGGCUGGAUAAUAAAAUAAAUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.c.P.littoralis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.c.P.littoralis.seq new file mode 100644 index 0000000..6a92f4d --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.c.P.littoralis.seq @@ -0,0 +1,2 @@ +>d.16.c.P.littoralis +AAACUAUCGAGAGUUUGAUCCUGGCUCAGGAUGAACGCUGGCGGUAUGCUUUACACAUGCAAGUCGUACGAAAGUGUUAAAACUUUAGUGGCGGACGGGUGAGUAACACGUGAGAAUUUACCUUUAGGAGGGGAAUAACAGUUGGAAAUGACUGCUAAUGCCGCAUAUCGUAAUUAUGAGACAUAUCAUAACUAUGAAAGAAGAAAUUCGCCUAAAGAAAAGCUUGCGUCUGAUUAGCUAGUUGGUAAGGGUAAAGGCUACAAGGCGACGAUCAGUAGCUGGUUUGAGAGGACGACCAGUCACACUGGACUGAGACACGGUCCAGACUACUACGGGAGGCAGCAGUGGGGAAUUUUCUGCAAUGGGCGAAACUGAACAGAGCAAUACCGCGUGAGGGAAGAAAGCCCACAGGGUUGUAAACCUCUUUUGUCAAGGAAGAAGAUUCUGACGUUACUUGACGAAUAAGCAUCGGCUAACUCCGUGCCAGCAGCCGCGGUAAGGACGGGGGAUGCAAGUGUUAUCCGGAAUUACUGGGCGUAAAGCGUUUGUAGGUGGUUUAGUAAGUCUAUUGUUAAAGCUUGAAGCUUAACUUCAAAAGUGUAAUAGAAACUACUAGACUUGAGGAUAGUAGGGGUAAAGGGAAUUUCCAGUGGAGCGGUGAAAUGCGUAGAGAUUGGAAGGACCACCGAUGGCGAAGGCACUUUACUGGGCUAUUUCUGACACUAAGAGACGAAAGCUAGGGUAGCAAAUGGGAUUAGAUACCCCAGUAGUCCUAGCUGUAAACGAUGAAUACUAGAUGUUGCGUGUAUCGAUCCAUGCAGUAUCGUAGCUAACGCGUUAAGUAUUCCGCCUGGGAACUAUGCUCGCAAGAGUGAAACUCAAAGGAAUUGACGGGGACCCGCACAAGCGUGGCAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCAGGGUUUGACAUUAUGUAAAUCUAUUUGAAAGAACAGAGUGCCCUCGGGAAUACAUAAACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUUUCUAGUUGCUUUACAAAAGGAAUCUUGAAGACUGCCGGUUAUAAACCGGAGGAAGGUGAGGAUGACGUCAAGUCAUCAUGCCCCUUAUACCCUGGGCUACACACGUGCUACAUUGGAUAAGACAAAAAGUUGCGAAUUUGUGAAAAUAAGCUAAUCUUUAAACUUAUUCCUAAGUUCGGAUUGAAGGCUGCAACUCGCCUUCAUGAAGAUGGAAUCGCUAGUAAUCGCUGGUCAGCUAUACAGCGGUGAAUCCGUUCCCGGGUCUUGUACACACCGCCCGUCACACCAUGGAAGCUGGUUAUACCCGAAGUCGUUUUCUUAACCUUUUUGGAGAGAGGCGCCUAAGGUAAGGCUAGUGACUGGGGUGAAGUCGUAACAAGGUAGCCGUACGGGAACGUGCGGCUGGAUCACCUCCUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.c.P.minor.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.c.P.minor.seq new file mode 100644 index 0000000..42ff17e --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.c.P.minor.seq @@ -0,0 +1,2 @@ +>d.16.c.P.minor +AUUUUUGGAGAGUUUGAUCCUGGCUCAGGAUGAACGCUGGCGGUAUGCCUAACACAUGCAAGUCGAACUAGCUCUAGCGCAAGUUAGAGUGGGUGGCGGACGGGUGAGGAACACGUAAGAACCUACCCUUUGGAGGAGGAUAACUGUUGGAAACGGCAGCUAAUACUCCAUAUGCUGAGGAGUAAAAGGUCGAAAGGCCGCCAAGGGAUGGGCUUGCGUCUGAUUAGCUAGUUGGUGAGGUAAAUGCUUACCAAGGCGACGAUCAGUAGCUGGUCUGAGAGGAUGAUCAGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGAGGAAUUUUCCGCAAUGGGCGAAAGCCUGACGGAGCAAUACCGCGUGAAGGAUGAAGGCCUGUGGGUUGUAAACUUCUUUUCUCAGAGACGAAUAAAUGACGGUAUCUGAGGAAUAAGCAUCGGCUAACUCUGUGCCAGCAGCCGCGGUAAGACAGAGGAUGCAAGCGUUAUCCGGAAUGAUUGGGCGUAAAGCGUCUGUAGGUGGCUUUCCAAGUCUUUUGUCAAAUCCCAGAGCUUAACUUUGGAUCGGCACGAGAAACUCGAGAGCUUGAGUAUGGUAGGGGCAGAGGGAAUUCCCGGUGUAGCGGUGAAAUGCGUAGAGAUCGGGAAGAACACCGAUGGCGAAAGCACUCUGCUGGGCCAUUACUGACACUGAGAGACGAAAGCUAAGGGAGCGAAUAGGAUUAGAUACCCUAGUAGUCUUAGCCGUAAACGAUGGAAACUAAGUGCUUGGGCCGCGAGUAAUCGCUGCUUGAGUCCUGUAGCUAACGCGUUAAGUUUCCCGCCUGGGAAGUAUGCUCGCAAGAGUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCAGGGCUUGACAUGCCACUCUUUCGGGAGGUCAUGGUGAAAGCCAGUUUAGGACACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUCUCUUGUUGCAACUUUGUUGUUAUCGAGAGAGACUGCCGGUGAUAAGUCGGAGGAAGGUGGGGAUGACGUCAAGUCAGCAUGCCCCUUACGCCCUGGGCAACACACGUGCUACAAUGGCCAGGACAAAGAGAUGCAACCUCGCAAGAGCAAGCCAACCUCAAAAACCUGGUCUCAGUUCGGAUUAGUCUCUGCAACCCGAGACUAUGAAGCCGGAAUCGCUAGUAAUCGCUGGUCAGCUAUACAGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCACGGGAGCUGGCUAUGCCCAAAGUCGUUACCCCAACCGUUUGGAGGGGGAUGCCUAAGGCAGAGCUAGUGACUGGGGUGAAGUCGUAACAAGGUAGCCGUACUGGAAGGUGCGGCUGGAUCACCUCCUUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.c.P.palmata.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.c.P.palmata.seq new file mode 100644 index 0000000..69f34fd --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.c.P.palmata.seq @@ -0,0 +1,2 @@ +>d.16.c.P.palmata +ACACCAUGGAGAGUUUGAUCCUGGCUCAGGAUGAACGCUGGCGGUAUGCUUAACACAUGCAAGUCGAACGAAGGUUUUACCUUAGUGGCGGACGGGUGAGUAACACGUGAGAAUCUACCCUUGGGAGGGGAAUAACAGUUGGAAACGAUUGCUAAUGCCCCAUAAGCUGAAAAGUAAAAUGAUUUUUCGCCCAGGGAUGAGCUCGCGCCUGAUUAGCUAGUUGGUAAGAUAAAAGCUUACCAAGGCAACGAUCAGUAGCUGGUUUGAGAGGACGAUCAGCCACACUGGGACUGAGACACGGCCCAGACUUCUACGGGAGGCAGCAGUGGGGAAUUUUCCGCAAUGGGCGAAAGCUGACGGAGCAAUACCGCGUGAGGGAAGAAUGCCCGUGCGUUGUAAACCUCUUUUCUUAGGGAAGAAGCUCUGACGGUACCUAAAGAAUAAGCAUCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGAUGCAAGCGUUAUCCGGAAUCACUGGGCGUAAAGUGUAGUAGGUGGCUUAUAAAGUCCGCUGUUAAAUCUUAGGGCUCAACCCUAAGCCAGCAGUAGAAACUUCUAGGCUAGAGUAUGGUAGGGGCAGAGGGAAUUCCCAGUGUAGCGGUGAAAUGCGUAGAUAUUGGGAAGAACACCAGAGGCGAAAGCGCUCUGCUAGGCCAUUACUGACACUCAGAGACGAAAGCUAGGGGAGCAAAUGGGAUUAGAUACCCCAGUAGUCCUAGCCGUAAACGAUGGAUACUAGAUGUUGCGCGUAUCGAUCCGUGCAGUAUCGUAGCUAACGCGUUAAGUAUCCCGCCUGGGGAGUAUGCUCGCAAGAGUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCAGAGCUUGACAUGUCACGAAUUUUUUCGAGAGAAAAAAGUGCCUUAGGGAACGUGAACACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUCUUUAGUUGCCAUCAUUUAGUUGGGCACUCUAGAGAGACUGCCGGUGACAAACCGGAGGAAGGUAAGGAUGACGUCAAGUCAGCAUGCCCCUUACGCUCUGGGCUACACACGUGCUACAAUGGUCGCGACAAAGAGUUGCCAGUCUGCAAAGACGCGCUAAUCUCAUAAACGUGGCCUCAGUUCGGAUUGUAGGCUGAAACUCGCCUACAUGAAGGUGGAAUCGCUAGUAAUCGCCGGUCAGCUACACGGCGGUGAAUCCGUUCCCGGGCCUUGUACACACCGCCCGUCACACCACGGAAGCUGGCCACGCCCAAAGUCGUUACCCUAACCUUUUGGAGGGGGGCGCCUAAGGCAGGGCUAGUGACUGGGGUGAAGUCGUAACAAGGUAGCCGUACUGGAAGGUGCGGCUGGAUCACCUCCUUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.c.P.wickerhamii.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.c.P.wickerhamii.seq new file mode 100644 index 0000000..6ae32f5 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.c.P.wickerhamii.seq @@ -0,0 +1,2 @@ +>d.16.c.P.wickerhamii +UGUGAAAACGAAGAGUUUGAUCCUGGCUCAGGAUAAACGCUGGCGGCAUGCUUAACACAUGCAAGUUGUACGAAGGUAUUUAUCUUUCGAGCUAAAUAUACUGAGUAGCGGACGGGUGAGUAACACGUAAGAAUCUACCUUUUGGAGAGGGAUAACUACUGGAAACGGUAGCUAAUACCUUAUAUUGCUGAGAAGUGAAAAAUGUAAAUUGCCAGAAGAUGAGCUUGCGCCUGAUUAGCUAGUUGGUGUGGUAACUGCAUACCAAGGCAAUGAUCAGUAGCUGUUCUGAGAGGAUGAUCAGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGAGGAAUUUUCCGCAAUGGGCGAAAGCCUGACGGAGCAAUGCCGCGUGAAGGAUGACGGCCUAUGGGUUGUAAACUUCUUUUCUCAGAAAAGAUUAAUGACGGUAUCUGAGGAAUAAGCAUCGGCUAACUCUGUGCCAGCAGCCGCGGUAAGACAGAGGAUGCAAGCGUUAUCCGGAAUGAUUGGGCGUAAAGCGUCUGUAGGUUGUUUAAAAAGUAUUCUGUCAAAAAUUAGGGCUUAACCCUAUACAGGCAGAAUAAACUUUUAAGCUAGAGUUUGGUAGAGGCAGAGGGAAUUCCCGGUGGAGCGGUGAAAUGCGUAGAUAUCGGGAGGAACACCAAAGGCGAAGGCACUCUGCUGGGCCAAUACUGACACUGAGAGACGAAAGCGAGGGGAGCAAAUGGGAUUAGAUACCCCAGUAGUCCUCGCUGUAAACGAUGGAUACUAGGUGUUGGGUGUAUCAAAAACAUUCAGUAUCGUAGCUAACGCAUUAAGUUUCCCGCCUGGGGAGUAUGCUCGCAAGAGUGAAACUCAAAGGAAUUGACGGGAACCCGCACAAUUGGUGGGGUACGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCAGGAUUUGACAUGUCAUUUGUUUCUUCAACUUAAUACUUUAAUUUGUUUUAAGUAGAAACAUAAAAAAAUGAACACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCUUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUUUUUUGAAUUGCUUGGGGCAUUAUAUGCCUUUUUACAGAGGAAAUUCAAAAGACUGCCGGUGAUAAGCCGGAGGAAGGUGAGGAUGACGUCAAGUCAGCAUGCCCCUUAUAUCCUGGGCGACACACGUGCUACAAUGGACGUAACAAAGAGAAGCUACUUCGCGAGAACAAGCUAAUCUCAAAAAUACGUUCUCAGUUCGGAUUGCAGGCUGCAACUCGCCUGCAUGAAGUUGGAAUCAAUAGUAAUCGCAGGUCAGCCACACUGCGGUGAAUACGUUUCCGGGUUUUGCACACACCGCCCGUCACACCACGGAAAUUGGCUACGCCCUAAAUCAUUACCCUAACCAUUCUGUGGAGGGGGAUGCCUAAGGCGGGGCUGGUAACUGGGGUGAAGUCGUAACAAGGUAGCCGUACUGGAAGGUGCGGCUGGAUCACCUCCUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.c.S.oleracea.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.c.S.oleracea.seq new file mode 100644 index 0000000..8de7320 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.c.S.oleracea.seq @@ -0,0 +1,2 @@ +>d.16.c.S.oleracea +UCUCAUGGAGAGUUCGAUCCUGGCUCAGGAUGAACGCUGGCGGCAUGCUUAACACAUGCAAGUCGGACGGGAAGUGGUGUUUCCAGUGGCGGACGGGUGAGUAACGCGUAAGAACCUGCCCUUGGGAGGGGAACAACAGCUGGAAACGGCUGCUAAUACCCCGUAGGCUGAGAAGCAAAAGGAGGAAUCCGCCCGAGGAGGGGCUCGCGUCUGAUUAGCUAGUUGGUGAGGUAAUAGCUUACCAAGGCGAUGAUCAGUAGCUGGUCCGAGAGGAUGAUCAGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUUUUCCGCAAUGGGCGAAAGCCUGACGGAGCAAUGCCGCGUGGAGGCAGAAGGCCCACGGGUCGUGAACUUCUUUUCCCGGAGAAGAAGCAAUGACGGUAUCCGGGGAAUAAGCAUCGGCUAACUCUGUGCCAGCAGCCGCGGUAAGACAGAGGAUGCAAGCGUUAUCCGGAAUGAUUGGGCGUAAAGCGUCUGUAGGUGGCUUUUUAAGUCCGCCGUCAAAUCCCAGGGCUCAACCCUGGACAGGCGGUGGAAACUACCAAGCUGGAGUACGGUAGGGGCAGAGGGAAUUUCCGGUGGAGCGGUGAAAUGCGUAGAGAUCGGAAAGAACACCAACGGCGAAAGCACUCUGCUGGGCCGACACUGACACUGAGAGACGAAAGCUAGGGGAGCGAAUGGGAUUAGAUACCCCAGUAGUCCUAGCCGUAAACGAUGGAUACUAGGCGCUGUGCGUAUCGACCCGUGCAGUGUUGUAGCUAACGCGUUAAGUAUCCCGCCUGGGGAGUACGUUCGCAAGAAUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAAAGCGAAGAACCUUACCAGGGCUUGACAUGCCGCGAAUCCUCUUGAAAGAGAGGGGUGCCUUCGGGAACGCGGACACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGCCGUAAGGUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUCGUGUUUAGUUGCCAACGUUGAGUUUGGAACCCUGAACAGACUGCCGGUGAUAAGCCGGAGGAAGGUGAGGAUGACGUCAAGUCAUCAUGCCCCUUAUGCCCUGGGCGACACACGUGCUACAAUGGCCGGGACAAAGGGUCGCGAUCCCGCGAGGGUGAGCUAACCCCAAAAACCCGUCCUCAGUUCGGAUUGCAGGCUGCAACUCGCCUGCAUGAAGCCGGAAUCGCUAGUAAUCGCCGGUCAGCCAUACGGCGGUGAAUUCGUUCCCGGGCCUUGUACACACCGCCCGUCACACUAUGGGAGCUGGCCAUGCCCGAAGUCGUUACCUUAACCGCAAGGAGGGGGAUGCCGAAGGCAGGGCUAGUGACUGGAGUGAAGUCGUAACAAGGUAGCCGUACUGGAAGGUGCGGCUGGAUCACCUCCUUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.c.T.gondii.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.c.T.gondii.seq new file mode 100644 index 0000000..b37e535 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.c.T.gondii.seq @@ -0,0 +1,2 @@ +>d.16.c.T.gondii +AAAUUAUUACGAGUUUGAUCCUGGCUCCGGAAGAACGCAAGAGAUGUGCUUAACACAUGCUAAUUGAAUGGUAUUAAUAUAUCAUAGUGUAAUAGUGAGUAAUGUAUGAGAAUUUAUUUUUAGAAUAUAAUAAAAAUUUAAUAAUUUAUAAUAAACGCAAUAGUGUUUUAAAAGAUAAUUAUUGUCUAAAAAAAAGCUCAUAUCUAAUUAGCUAGUUGGUGAAGUAAUAGUUUUACCAAGGCGAAGAUUAGUAGCUGCCUUGAGAGGGGAAACAGCCACAUAGAGAUUGAAAUACAGCUCUAACUCCUAAGGGGGGCAGCAGUGGGGAAUUUUCUGCCAAUAAGCGCAAGCUUGACAGAGCGUCAUCACAUGAAGGAGGAAGGCCUAUAAAGGUUGUAAACUUCUUUUGCUUAAAAAAAUAAUACUGACGUUUAAGUUUAAAAAGUAUCGGCUAACUCCGUGCCAGCAGCCGCGGUCAUACGGGGGAUACAAGCGUUUUCCAAAAUUACUGGGCGUAAAGUGUAUGUAGGUGGAUUGGUAUGUUCUUCCUUAAAUACUAUUUGAUAAAUUUAGAAAAAGGAAGAAAACUAUUAAUCUUGAGUUCGAUAAGGGUAAGAGGAAUUUUUUGAGGAGUAGUGAAAUGCGAAGAUACAAAAAAGAAGAUCAACAGCGAAAGCAUCUUACUGGGUCGAUACUGACACUGAGAUACGAAAGUUAAGGUAGCAAAUGGGAUUAGAUACCCCAGUAGUCUUAACUGUAAACAAUGGAUACUCGGUACUGGAGACAUUAAAUAUAUAAAUUCAGUACCCUAGCUAACGCGUUAAGUAUUCCGCCUGAGUAGUACGCUCGCAAGGGUGAAACUCAAAGGAAUUGACGGGGGCUCGUACAAGCGGUGGAGCACGUAAUUUAAUUCGAUGUAACGCGAUAAACCUUACCAGAACUAGACUAAAUUUAUUUUAAAUUAUUAAUAUUAAUUAAUAAAAAAUUUACAGGAGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCUACGAGCGCUACCCUUAUUUAAAGUUUUUUAUAUCUUUAAAAACAGACUAUAUAAAUUUUUGUACUAAAUUAGUAGGAAGGAGAGGAAAACGUCAAGUCUUUAUGCCCUUUAUGUUCUGGGCUACAUACGUGCUACAAUAGAUGGUACAAUAAUUUUUAAAAAUAAAUACAAUAUCAAUUUAUUUUUAAUUUAUUUGUGAAAAUAAAUGUAAUAAUUGAAAACCAUUUUUAGUUCGGAACAUAAACUGCAAUUUGUUUAUGUAAAGUUGGAAUCGCUAGUAAUCGCCGGUCAGCAUUACGGCGGUGAAUAAGUCUUCGAGCCUUGUACACACCGCCCGUCACGCCACGGAAAUUGAUUAUUUUUUAAAACUUUUGAUAAAAGGAUAAAUAAUAAUAAAUAACUGGGGUGAAGUCGUAACAAGGUAGCUGUACUGGAAGGUGCUGCUGGAUAAUUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.c.Z.mays.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.c.Z.mays.seq new file mode 100644 index 0000000..9bffa4d --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.c.Z.mays.seq @@ -0,0 +1,2 @@ +>d.16.c.Z.mays +CUCAUGGAGAGUUCGAUCCUGGCUCAGGAUGAACGCUGGCGGCAUGCUUAACACAUGCAAGUCGAACGGGAAGUGGUGUUUCCAGUGGCGAACGGGUGAGUAACGCGUAAGAACCUGCCCUUGGGAGGGGAACAACAACUGGAAACGGUUGCUAAUACCCCGUAGGCUGAGGAGCAAAAGGAGAAAUCCGCCCAAGGAGGGGCUCGCGUCUGAUUAGCUAGUUGGUGAGGCAAUAGCUUACCAAGGCGAUGAUCAGUAGCUGGUCCGAGAGGAUGAUCAGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUUUUCCGCAAUGGGCGAAAGCCUGACGGAGCAAUGCCGCGUGGAGGUGGAAGGCCUACGGGUCGUCAACUUCUUUUCUCGGAGAAGAAACAAUGACGGUAUCUGAGGAAUAAGCAUCGGCUAACUCUGUGCCAGCAGCCGCGGUAAGACAGAGGAUGCAAGCGUUAUCCGGAAUGAUUGGGCGUAAAGCGUCUGUAGGUGGCUUUUCAAGUCCGCCGUCAAAUCCCAGGGCUCAACCCUGGACAGGCGGUGGAAACUACCAAGCUGGAGUACGGUAGGGGCAGAGGGAAUUUCCGGUGGAGCGGUGAAAUGCAUUGAGAUCGGAAAGAACACCAACGGCGAAAGCACUCUGCUGGGCCGACACUGACACUGAGAGACGAAAGCUAGGGGAGCAAAUGGGAUUAGAGACCCCAGUAGUCCUAGCCGUAAACGAUGGAUACUAGGUGCUGUGCGACUCGACCCGUGCAGUGCUGUAGCUAACGCGUUAAGUAUCCCGCCUGGGGAGUACGUUCGCAAGAAUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAAGGCGAAGAACCUUACCAGGGCUUGACAUGCCGCGAAUCCUCUUGAAAGAGAGGGGUGCCCUCGGGAACGCGGACACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGCCGUAAGGUGUUGGGUUAAGUCUCGCAACGAGCGCAACCCUCGUGUUUAGUUGCCACUAUGAGUUUGGAACCCUGAACAGACCGCCGGUGUUAAGCCGGAGGAAGGAGAGGAUGAGGCCAAGUCAUCAUGCCCCUUAUGCCCUGGGCGACACACGUGCUACAAUGGGCGGGACAAAGGGUCGCGAUCUCGCGAGGGUGAGCUAACUCCAAAAACCCGUCCUCAGUUCGGAUUGCAGGCUGCAACUCGCCUGCAUGAAGCAGGAAUCGCUAGUAAUCGCCGGUCAGCCAUACGGCGGCGAAUCCGUUCCCGGGCCUUGUACACACCGCCCGUCACACUAUAGGAGCUGGCCAGGUUUGAAGUCAUUACCCUUAACCGUAAGGAGGGGGAUGCCUAAGGCUAGGCUUGCGACUGGAGUGAAGUCGUAACAAGGUAGCCGUACUGGAAGGUGCGGCUGGAUCACCUCCUUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.ambigua.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.ambigua.seq new file mode 100644 index 0000000..53be3ef --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.ambigua.seq @@ -0,0 +1,2 @@ +>d.16.e.A.ambigua +NAACCUGGUUGAUCCUGCCAGUAGUGAUACGCUGUCAUUAAGACUAAGCCAUGCAUGUGUAAGUAUAAGAAGUACUCGAGACUGCGAAUGGCUCAUUAUAUCAGUUAUAGUUUAUUUGAUAGUCCCUUACUACUUGGAUAACCGUAGUAAUUCUAGAGCUAAUACAUGCGUCAAGAUCCGACUUCGGGAGGAUUGUAUUUAUUAGGUUACAAAACCAACCCUCUCUCGGGAGGUUCUUUGGGUGAGUCAUGAUAAGCAUGCGGAUCGCAGGGCUUUACGCCGGCGACGGAUCAUGUAAGUUCCUGCCCUAUCAGCUUCGGAUGGUAGGGUAUUGGCCUACCAUGGCAUUAACGGGUAACGGGAGAUCAGGGUUUGACUCCGGAGAGGGAGCCUGAGAGACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGACACAGGGAGGUAGUGACGAUAAAUAACAAUGCCGGGCCUUUCUAGGUCUGGCAAUUGGAAUGAGAACGAUGCAAASACCCUAUCGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGAAUUUCUGGUGGAGUCGGUCUGUCCUUCACUUGGUGUUGGUACGUGACUGUAUCUCUGCCCUCCUUGGUUGGAUCCAGUGCUGGCAUUUGGUUGUCGGUCUGGGGACGGCCAUCGUUUACUGUGAAGAAAUUAGAGUGUUCAAAGCAGGCUUAGGCCUUGAAUACAUUAGCAUGGAAUAAUGAAAUAGGGUUUUGGCACUAUUUCGUUGGUUUGCGCGCCGAAACAAUGAUUAAUAGGGACAGUUUGGGGAUAUUCCUAUUCAAUUGUCAGAGGUGAAAUUCUUGGAUUUCUGGAAGACGAACGACUGCGAAAGCAUUUAUCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGAUGAUUAGAUACCAUCGUAGUCUUAACCAUAAACCAUGCCGACUAGGGAUUUGCGGUUGUUCUUGUAGACUCCGUAAGCACCUUAUGAGAAAUCAAAGUGUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGAAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGBGAAAACUUACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCCCCGCCUGCUAAAUAGUCCGGUGAAUGAGUUUUCAUUGACCUGGUCUUCUUAGAGGGACUUUCGGUGACUAACCGAAGGAAGUUGGGGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGAUCUGGGCCGCACGCGCGCUACACUGAUGCAUUCAACGAGUCUAGAACCUUGGCCGAGAGGCCUGGGUAAUCUUGUGAACGUGCAUCGUGAUAGGGAUUGAAUAUUGCAAUUAUUAUUCAUGAACGAGGAAUUCCUAGUAAACGCAGAUCAUCAAUCUGCAUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCACCUACCGAUUGAAUGGUCCGGUGAAGCCUCGGGAUUGCGGUCCGUUCCUUUACUGGGAUGUGGCUGUGAGAACUUGUCUAAACCUUAUCAUUUAGAGGAAGGUGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAANNN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.baicalensis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.baicalensis.seq new file mode 100644 index 0000000..6dbbac3 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.baicalensis.seq @@ -0,0 +1,2 @@ +>d.16.e.A.baicalensis +NAACCUGGUUGAUCCUGCCAGUAGUGAUACGCUGUCAUUAAGGACUAAGCCAUGCAUGUGUAAGUAUAAGAACUUUCGAGACUGCGAAUGGCUCAUUAUAUCAGUUAUAGUUUAUUUGAUAGUCCCUUACUACUUGGAUAACCGUAGUAAUUCUAGAGCUAAUACAUGCGUCAAGAUCCGACUUCGGGAGGAUCGUAUUUAUUAGGUUACAAAACCAACCCUCUUUCGGGAGGUUCUCUGGGUGAGUCAUGAUAAGCAUGCGGAUCGCACGGCUUUAUGCCGGCGUCGGAUCAGGUAAGUUCCUGCCCCAUCAGCUUCGGAUGGUAGAGUAUUGGCCUACCAUGGCGUUAACGGGUAACGGGAGAUCAGGGUUUGACUCCGGAGAGGGAGCCUGAGAGACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGAUACAGGGAGGUAGUGACGAUAAAUAACAAUGCCGGGCCUUUUUAGGUCUGGCAAUUGGAAUGAGAACGAUGCAAAUACCCUAUCGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGAAUUUCUGGUGGAGUCGGUCUGUCCUUCACUUGGUGUUGGUUCGUGACUGUAUCUCUGCCCUCCUUGGUUGGAGCCAGUGUUGGCAUUCAGUUGUUGGGCUGGGGACAAUCAUCGUUUACUGUGAAGAAAUUAGAGUGUUCAAAGCAGGCUUAGGCCUUGAAUACAUUAGCAUGGAAUAAUGAAAUAGGGUUUUGGCACUAUUUUGUUGGUUUGCGCGCCAAAAUAAUGAUUAACAGGGACAGUUUGGGGAUAUUCGUAUUCAAUUGUCAGAGGUGAAAUUCUUGGAUUUCUGGAAGACGAACGACUGCGAAAGCAUUUAUCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGAUGAUUAGAUACCAUCGUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUUUGCGGUUGUUCUUGUAGACUCCGUAAGCACCUUAUGAGAAAUCAAAGUGUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGAAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACAGGAAAACUUACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCCCCGCCUGCUAAAUAGUCCGGUGAAUGAGUUUUCAUUGACCUGGUCUUCUUAGAGGGACUUUCGGUGACUAACCGAAGGAAGUUGGGGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGAUCUGGGCCGCACGCGCGCUACACUGAUGCAUUCAACGAGUCUAGAACCUUGGCCGUGAGGCCUGGGUAAUCUUAUGAACGUGCAUCGUGCUAGGGAUUGAAUAUUGCAAUUAUUAUUCAUGAACGAGGAAUUCCUAGUAAACGCAGAUCAUCAAUCUGCAUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCACCUACCGAUUGAAUGGUCCGGUGAAGCCUCGGGAUUGUGGUCCGUUCCUUCAGUGGGAUGUGGCUGUGAGAACUUGUCUAAACCUUAUCAUUUAGAGGAAGGUGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAANNN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.bongranii.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.bongranii.seq new file mode 100644 index 0000000..bd0b78d --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.bongranii.seq @@ -0,0 +1,2 @@ +>d.16.e.A.bongranii +NAACCUGGUUGAUCCUGCCAGUAGUCAUACGCUCGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUAUAACUCUUUUACUUGAAAACUGCGAACGGCUCAUUAUAUCAGUUAUAGUUUAUUGGAUAGUCCCUUACUACUUGGAUAACCGUAGUAAUUCUAGAGCUAAUACAUGCGUCGAUACCCUUCUGGGGUAGUAUUUAUUAGAUAGAAACCAACCCCUUCGGGGUGAUGUGGUGAUUCAUAAUAAGUUUACGAAUCGCAUGCCUUCGGGCGGCGAUGGAUCUUUCAAGUUUCUGCCCUAUCAGCUUUGGAUGGUAGGGUAUUGGCCUACCAUGGCUUUAACGGGUAACGGGAAAUUAGGGUUUGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUUCUGACACAGAGAGGUAGUGACAAUAAAUAACAAUGCCGGGCCUUUGUAGGUCUGGCAAUUGGAAUGAGAACAAUUUAAAUCCCUUAUCGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGAAUUUGUGGCUGUUGCGGGAGGCCUGGCACGUGCCAGCGCUCUUCCUGCGACGCCAUCCUUGGGUUGAAAGUGGGUGGCAUUAGGUUGUCGCCUAUGGGAAGCCCAUCGUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCAGGCUUACGCCGUUGAAUAGAUUAGCAUGGAAUAAUAAGAUAGGACCUGGGUACUAUUUUGUUGGUUUGCGUACUUAGGUAAUGAUUAACAGGGACAGUUGGGGGUAUUCGUAUUCCAUUGUCAGAGGUGAAAUUCUUGGAUUUCUGGAAGACGAACUACUGCGAAAGCAUUUACCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGAUGAUUAGAUACCAUCGUAGUCUUAACCAUAAACUAUGCCGACAAGGGAUUGGCGGAGUUUCUUUAUGUCUCCGUCAGCACCUUAUGAGAAAUCACAAGUCUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGAAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAGAGUUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCCCUGCCUGCUAAAUAGCUUGGUUAGUGAAUCUUCACUGGCUGAAGCUUCUUAGAGGGACGUGCAUUCUAUCAGAUGCAGGAAGAUAGGGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCCGCACGCGCGCUACACUGAUGCAUUCAACGAGUUUUUCCUUGGCCGAGAGGCCUGGGCAAUCUUCUGAACGUGCAUCGUGAUAGGGAUAGAUUAUUGCAAUUAUUAAUCUUGAACGAGGAAUUCCUAGUAAACGCAGAUCAUCAUUCUGCAUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCACCUACCGAUUGAAUGGUCCGGUGAAGCCUCGGGAUUGUGGCUAGCUCCCUUCAUUGUGGGUUGGCCGCGAGAACUUGUCUAAACCUUAUCAUUUAGAGGAAGGUGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAANNN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.bracteata.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.bracteata.seq new file mode 100644 index 0000000..ddb3562 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.bracteata.seq @@ -0,0 +1,2 @@ +>d.16.e.A.bracteata +CACCAGGUUGAUUCUGCCUGACACACACGCUCGUCCCAAAGAUUAAGCCAUGCAUGCUUGUGAAGGAAGCGGAACGGCGUACGGCUCAGUAGGACGGACCUAAUCUAUCCAGCACGGGAGGGAUAACCACGGGAAACUGUGGCUAAGACCGGGAUCUGCCGUGCCCUCGGGUGCUGAAGAGCGGCGGUGUGCUGGGCGAGAGUCUGACCUAUUAGCUUGAUGGCGCGGUAAGGGCGGGCCAUGGCGACGAUGGGUGACGGGGAAUCGGGGUUUGAUUCCGGAGAAGGAGGCUGAGAGACGGCUCCUACGUCCAAGGACGGCAGCAGGCGCGAAACUUACCCACUCGAGCGGAGGUAGUGACGGGACGUCUAUGGGGAGCUCUUGAUAACUGCGAGGGGCCUCUACUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAGGAGCGUGUGUGGUGAUUGCUGCAGUUAAAAGGUCCGUAGUCGACGUGUCUGGCGGGGUCUUGAGGUGCGCUCAACGUGCUAGGACCUCCGCGAGUUGCGUUCCGGAGCACUUGGGGGUGAGGGUAUUCCUGCGUGAGAGGUGAAAUUCGGUGAUCGCGGGGGGACCGACGGGGGCGCAGGCGCUCAUCCAGACUGUGUCCUAUGAUCAAGGGCGGAAGCCGUGGUAGCGAAGGUGAUUAGUGACCACUGUAGUCGCGGCCGCAAACGAUGCGUUCCCGCCUGCUGGGCGGAGGGAAACCGAGAGAGCUCUGGGGAUAGUACGAGCGCAAGCCUGAAACUUGAAGAAAUUGACGGAAGGACACCACCAGGAGUGGAUCAUGCGGGUUAAUUUGACUCAACGCGGGGCAGCUUACCAGGGCACGCGCGGGUGCGAUCGCGAUGCGAGAUUCUGCGGCGAGUGGUGCAUGGCCGUUUCUAACACGUGGGGUGACCAGUCUGGUUAAGUCCGAUAACGCGUGCCGCCCCGGCCCUGUGCGAAUGGGGGACGACUGCCGACGAGGCAGGGGAAGAGGGGCGAAAACAGGUCCGUAAUGCCCUCCGAAGCCCUGGGCGCCACGCGUGAUACAAUAGCUGCGUCGCGGUUGGGGUCGGGACUGCGGGCUGCGAGGCCAGCACGAACGCGGAAUUCCUAGUAAGCGUGCGUCACCAUUGCGUGCUGAAUGCGUCCCUGUCCUUUGUACACACCGCCCGUCGUUAUUUGAGAUGGUAGUGCGGCCGAGCGGCUGUCCUCGGGCGGCCGCGAGUCCGCCCUGCUAGAUCGAAUACAAGUCGUAACAAGGUAACCANNNNNNNNNNNNNNNNNNNNNNNNNN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.capitellata.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.capitellata.seq new file mode 100644 index 0000000..3de621e --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.capitellata.seq @@ -0,0 +1,2 @@ +>d.16.e.A.capitellata +NAACCUGGUUGAUCCUGCCAGUAGUCAUACGCUCGUCUCAAAGACUAAGCCAUGCAAGUCUAAGUAUAAAUCUUUUACUUUGAAACUGCGAAUGGCUCAUUAUAUCAGUUAUAGUUUAUUUGAUAGUCCCUCACUACUUGGAUAACCGUAGUAAUUCUAGAGCUAAUACAUGCGUCAAUACCCUUCUGGGGUAGUAUUUAUUAGAUGGAAACCAACCCCUUCGGGGUGAUGUGGUGAAUCAUAAUAAGCUUGCGGAGYCCGGUGGCGAUGGAUCAUUCAAGUUUCUGCCCUAUCAGCUUUGGACGGUAAGGUAUUGGCUUACCGUGGCUUUAACGGGUAACGGGGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCUUGACACAAGGAGGUAGUGACAAUAAAUAACAAUGCCGGGCCUUUAUAGGUCUGGCAAUUGGAAUGAGAACAAUUUAAACCCCUUAUCGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUGUGGCGGUUCCUGUGGUCCGAUUUCGGUACUUUCUGGGACUGCCAUCCUUGGGUGGAUCCUGUGUGGCAUUAGGUUGUCGUGCAGGGGAUGCCCAUCGUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCAGGCUUACGCCGUUGAAUAUAUUAGCAUGGAAUAAUGAGAUAGGACCUUGGUACUAUUUUGUUGGUUUGCGCACCGAGGUAAUGAUUAAUAGGGACAGUUGUGGGUAUUCGUAUUCCAUUGUCAGAGGUGAAAUUCUUGGAUUUCUGGAAGACGAACUAAUGCGAAAGCAUUUACCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGAUGAUUAGAUACCAUCGUAGUCUUAACCAUAAACUAUGCCGACAAGGGAUUGGCGGGUUUCGUUACGUCUCCGUCAGCACCUUAUGAGAAAUCACAAGUUUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGAAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCCCUGCCUGCUAAAUAGUCCUUUGAGUGAUUUUCACUGAUUCGGGCUUCUUAGAGGGACGUGCAUUCUAUUAGAUGCAGGAAGAUAGGGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAUGCAUUCAACGAGUUUCCUUGGCCGAGAGGCCUGGGCAAUCUUUUGAACGUGCAUCGUGAUAGGGAUAGAUUAUUGCAAUUAUUAAUCUUGAACGAGGAAUUCCUAGUAAACGCAGAUCAUCAAUCUGCAUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCACCUACCGAUUGGAUGGUCCGGUGAAGCCUCGGGAUUGUGACCGGUGCCUUUAUUGGUGUCGGUCGCGAGAACUUGUCUAAACCUUAUCAUCUAGAGGAAGGUGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAANNN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.castellanii.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.castellanii.seq new file mode 100644 index 0000000..aee7873 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.castellanii.seq @@ -0,0 +1,2 @@ +>d.16.e.A.castellanii +CGACUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAGCUUGUUUAUACGGCGAGACUGCGGAUGGCUCAUUAAAUCAGUUAUAGGUUAUUUGAUGGUCUCUUUUGUCUUUUUUUACCUACUUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCGCAAGGUCCCGAGCGCGGGGGGCGGGGCUUCACGGCCUCGUCCUCGCAUGCGCAGAGGGAUGUAUUUAUUAGGUUAAAAACCAGCAGCCGGCAACGGCUUCAACUCCUGGUGAUUCAUAGUAACUCUUUCGGAUCGCAUUCAUGCCCUCCUUGUGGGGGCGGCGACGAUUCAUUCAAAUUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGAGGCCUACCAUGGUCGUAACGGGUAACGGAGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAAUGGCUACCACUUCUAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCCGACACGGGGAGGUAGUGACAAUAAAUAACAAUACAGGCGCUCGAUAAGAGUCUUGUAAUUGGAAUGAGUACAAUUUAAACCCCUUAACGAGUAACAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUCUAGGGACGCGCAUUUCAAGCGCCCGUGUCGUCGGGUCAAACCGGCGACUGCGUUGGCGUUGCGGGCUCGGUCCGUCGGUGCCCCACAAAGGGCUACUGGCGUGUCAACCGGCCCGCCCGUCCCCUCCUUCUGGAUUCCCGUUCCUGCUAUUGAGUUAGUGGGGACGUCACAGGGGGCUCAUCGUCGUGCGGCGUCAAAACCGUGGCGGCGGUGGGUCCCUGGGGCCCAGAUCGUUUACCGUGAAAAAAUUAGAGUGUUCAAAGCAGGCAGAUCCAAUUUUCUGCCACCGAAUACAUUAGCAUGGGAUAAUGGAAUAGGACCCUGUCCUCCUAUUUUCAGUUGGUUUUGGCAGCGCGAGGACUAGGGUAAUGAUUAAUAGGGAUAGUUGGGGGCAUUAAUAUUUAAUUGUCAGAGGUGAAAUUCUUGGAUUUAUGAAAGAUUAACUUCUGCGAAAGCAUCUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUAACCAUAAACGAUGCCGACCAGCGAUUAGGAGACGUUGAAUACAAAACACCACCAUCGGCGCGGUCGUCCUUGGCGUCGGUCCUUCACGGGGCCGGCGCGAGGGCGGCUUAGCCCGGUGGCACCGGUGAAUGACUCCCCUAGCAGCUUGUGAGAAAUCAUAAGUCUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCGGACAUAGUAAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAACCUGCUAAAUAUGCCGCGCUAGCCCGUCCAUCAAAACCCAUGCGUGGCUCACGCGGUCCGCUGCGGGGUGGUGUCACUUCGCGGCGACGUCAUCCCGCCGGCAGGGCCCGGGUCCGUGUGGGCGGUAGGGUUCGGCGUCCGUGCUUCUUAGAGGGACUGCUGCGCGCCUAGCCAGCGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAUUAAUCCAACGAGUCCGCUUCAAUCGAGGCGCGAUGCCGUUGGGGUCAAACCCAACUGCGUCGCUGUCCUCGAUCGCGCCUGGGCCGAUAGGUCCGGGUAAUCUUUGCAAAUUUAAUCGUGCUGGGGAUAGAUCAUUGUAAUUAUUGAUCUUCAACGAGGAAUUCCUAGUAAGCGCGAGUCAUCAGCUCGCGUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAAUGGUCCGGUGAAAUCCUCGGAGCCGUGGCCUCUACGCAAUCCGGGCAACCGGGUUGUGAGGUCUCCCCUUUUGGCGGCGAAGUCGAUUGAACCUUACCAUUUAGAGGAAGGAGAAGUCGUAACAAGGUCUCCGUAGGUGAACCUGCGAAAGGAUCAGGA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.connecticus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.connecticus.seq new file mode 100644 index 0000000..accfe21 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.connecticus.seq @@ -0,0 +1,2 @@ +>d.16.e.A.connecticus +CACCAGGUUGAUUCUGCCUGACGUGGACGCUAGCCUUGAAGAUUAAGCCAUGCAAGCUUGUGAAUAUUAUAUAUGAAACAGUGAACGGCUCAGUAUAACACGUCUAUCUACCCCAUAUUAUUUAUAACCACGGGAAACUGUGGCUAAGUAUUAGGAUGAGGAUGUGACCUAUCAGCUUGACGGUACGGUAAGUGCGUACCGUGGCUAUAACGGGUAACGGGGAAUAUGGGUUUUAUUCCGGAGAGGGAGCCUGAGAGAUGGCUGCCACGUCCAAGGACGGCAGCAGGCGCGAAACUUACCCAAUGAACAUUGAGGUAGUUACGAGGCGUAUUAUUAGUGUAUAUGGUGUGUAUAAACAGCACACCGAAGUACUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUACCAGCUCCAGUAGCGUCUGUGUUUAUUGCUGCGGUUAAAAUGUGCGUAGUCUGGUUAGUGGUCUGGAGUAAAUCUUUUGUAUCUAACAACAGGGUAUUCUAGAGACUUAUACCUUGAGACAGGGAAGAGGCGAUGAUAUUUGGUAGCGAGAGGUGAAAAUCGAUGACCUACCAAGGAGCACCGGAGGCGAAAGCGAUCGCCGAGAACUGUUCUGACGAUCAAGCGCGUGAGCAGGAGUAUCGAAGAGGAUUAGAGACCCACGUAGUUCCUUGCAGUCAACGAUGCCAACGCUGUGGUGGUAUUUACCAUUGCAGAGGCGAAAGCUAGUGUAUGGGCUCCGGGGAUAGUACGGACGCAAGUUUGAAACUUGAAGAAAUUGACGGAAGGACACCACAAGGAGUGGAGUGUGCGGGUUAAUUUGACUCAACGCGGGAAAACUUACCCGGGCAGGCAAUUGUCGAGGGAAGCUAUUGUAGCUGAUGAUAUUGCGCGUGGUGCAUGGCCGUUCUUAACACGUGGAGUGAUCUGUCUGGUCAAAUCUGAUAACGCGUGAGAGGUGAGUGGUUGCUUUUGUGACUAGACGGUGUCUGUAAAGACAAGGAAGCGACACCCAAUAACAGGUCUGUGAUGCCCGUAGAUGUCCGGGGCUCCACGCGCACUACAAUGGGUGGUAGUAUUAGUAAAGUGUAGCUAGCCGUAGUUGGGAUUGACAUAUGUAAUUAUGUCAUGAACGUGGAAUUCCUAGUAGUUGGUAGUCACUAACGACUAACGAAUGUGUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCUAAGAUGGAAGUGCGGGUGAAGAUGCGAGCAGUCAGGUGAUGGGGAUAAGUGUUUGUGAGUAAUGAAUGCUUGGAACUGUUGCUGGUAAAUGAUUGUGAGUGUAAGAACCCGUGCAGCUAAAUUGGAUGUAAGUCGUAACAAGGUAACCNNNNNNNNNNNNNNNNNNNNNNNNNNN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.dasyae.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.dasyae.seq new file mode 100644 index 0000000..c3ebfab --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.dasyae.seq @@ -0,0 +1,2 @@ +>d.16.e.A.dasyae +CAACCUGGUUGAUCCUGCCAGUGGUAUAUGCUUGUCUCAAGGACUAAGCCAUGCAAGUGUAAGUAUAAGUAAUUUUUACGACGAAACUGCGAAUGGCUCGGUAAAACAGCUAUAGUUUCUUCGAUGGUACCUACUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCCACAACGCGAGGUAACUCGUGGUACCAAUCAGAUAUCAAACCAAUGUGUGGUGAUUCAUGAUUUUUUUUCUGAUCGCUCGUAAGAGCGACGCAUCGUUCAAAUUUCUGACCUAUCAACUUUCGAUGGUAAGGUAUUGUCUUACCAUGGUUGUGACGGGUAACGGACCGUGGGUGCGGGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUUCUGACACAGAGAGGUAGUGACAAGAAAUAUCAAUAGAGGGCGUUUAUACGUCUUCUAAUUGGAAUGAGAACAAGGUAAACAGCUUAUCGAGGAUCCAGCAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUGUAAGCGUAUACCAAAGUUGUUGCAGUUAAAACGCUCGUAGUCGGAUUUUGGGGCAGCCCGUGCUGUGCGCGUAGUGCGUGCGGCGCUGGGAUGUUCUUUUGUGGAGGGCGGCGCGUCGUGGCUUCACUGUCGCGGCGUGUCGGCGCCACCGUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCAGGCGUUUGCCGUGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUUGGUUUCUAUUUUGUUGGUUUGUGAGAGCCGAGUAAUGAUUAAGAGGGACGGUUGGGGGCAUUUGUAUUCCAGCGUCAGAGGUGAAAUUCUUGGAUUGCUGGAAGACAAACCGCUGCGAAAGCGUCUGCCAAGGACGUUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACUAUAAACGAUGAGAACUGGGGAUCGGGCGGGCAUUAUGAUGACCCGUCCGGAACCCUCCGGGAAACCAAAGUGUUUGCUUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUUACCAGGUCCGGACAUAGUGAGGAUUGACAGAUUGGGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAGCGAGACCUGGGCGUGCUAAAUAGGAGCCGUUACCAUUGUGUAGCUGUUGCUCCUUCUUAGACGGACUGCGGGCGUCUAGUCCGCGGAAGCUCCAGGCAAUAACAGGUCUGAGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAACGGACCAACGGGUGAGGAUGCGCGAAAGCGUUUCCCAAUCCCUAAAUCCGUUCGUGCUGGGGAUAGAGGCUUGCAAUUUUCCCUCUUGAACGAGGAAUACCUUGUAAGCGUGGGUCAUCAGCCCGCGCUGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGAUCCGGUGAGGCUUUGGGACUGCUGCGAUCGGAGCGUUUACGCUCCUGGCCGCGGUGGGAACUUAUCCGAACCUUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAGAAN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.ferocious.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.ferocious.seq new file mode 100644 index 0000000..4352cb6 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.ferocious.seq @@ -0,0 +1,2 @@ +>d.16.e.A.ferocious +CACCAGGUUGAUUCUGCCUGACGUGGACGCUUGCCUUGAAGAUUAAGCCAUGCAAGCCUGUGAAUACUUGAAACAGUGAACGGCUCAGUAUAACACGUCUAUCUACCCACNAACCCUAAUAACCACGGUAAACUGUGGCUAAGGUAGUGGAUGAGGAUGUGACCUAUCAGCUUUGUCGGUACGAUAAGUGCGUACCGUGGCUAUAACGGGUAACGGGGAAUAUGGGUUUUAUUCCGGAGAGGGAGCCUGAGAGAUGGCUGCCACGUCCAAGGACGGCAGCAGGCGCGAAACUUACCCAAUGAACAUUGAGGUAGUUACGAGGCGUAAGUUAUAUUGAGUGAAUAAAAUACACUCAUAAAUAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUACCAGCUCCAAUAGCGUCUGUGUUUAUUGCUGCGGUUAAAACGUGCGUAGUCUGGUUUAUAGCCUGAGUUAAAUACGUGUGCUUUAAGCAUGAAGUAUGUCAGGGACUUAGACCUUGGGAUAGGGACGGGGCAAUGAUAUUCGGCAGCGAGAGGUGAAAAUCGAUGACCUGCUGAGGAGCAACAGAGGCGAAAGCGGUUGUCCAGAACUAGUCCGACGAUCAAGCACGUGAGCAGGAGUAUCGAAGGCGAUUAGAGACCGUCGUAGUUCCUAGCAGUAAACGAUGCCAACACUGUGGUGGAAUGUCACUGCAGAAGCGAAAGCUAGUGUGUAGGCUCCGGGGAUAGUACGGACGCAAGUUUGAAACUUGAAGAAAUUGACGGAAGGACACCACAAGGAGUGGAGUGUGCGGGUUAAUUUGACUCAACGCGGGAAAACUUACCUGAGGCAGGCUGUUAGUAGGAGAUUGCUUAGCAAGAUACUGCAGCGCGUGGUGCAUGGCCGUUCUUAACACGUGGGGUGACCUGUCUGGUCAAAUCUGAUAACGCGUGAGAGGUGGAUUCUAUUGUAAAAGGUAGAGACGGUGUAUGUAAGUACAAGGAAGCACCACCCAAUAACAAGUCUGUGAUGCCCGUAGAUGUCCAGGGCUCCACGCGCACUACAGUUUAGUGAAGUGUGUGGAGAGUGAUUUGCUAGGUAGUUGGGAUUGAUGUAUGUAAUUAUGUCAUGAACGUGGAAUUCCUAGUAGUUGGUAGUCACUAACGACCAACGAAUAUGUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCUAAGAUGGAAGUGUGGGUNAANUCCAUAGCGAGCUUAGCGAGGUAGUGAUUAUGCACGAGUUAGGUUAGUUAUGGAAAGAACCCAUGCAGCUAGAUUGGAUGUAAGUCGUAACAAGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.flavus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.flavus.seq new file mode 100644 index 0000000..b35efec --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.flavus.seq @@ -0,0 +1,2 @@ +>d.16.e.A.flavus +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAGCACUUUAUACUGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUCGUUUAUUUGAUAGUACCUUACUACAUGGAUACCUGUGGUAAUUCUAGAGCUAAUACAUGCUAAAAACCUCGACUUCGGAAGGGGUGUAUUUAUUAGAUAAAAAACCAAUGCCCUUCGGGGCUCCUUGGUGAUUCAUAAUAACUUAACGAAUCGCAUGGCCUUGCGCCGGCGAUGGUUCAUUCAAAUUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGUGGCCUACCAUGGUGGCAACGGGUAACGGGGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCCGACACGGGGAGGUAGUGACAAUAAAUACUGAUACGGGGCUCUUUUGGGUCUCGUAAUUGGAAUGAGUACAAUCUAAAUCCCUUAACGAGGAACAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGAACCUUGGGUCUGGCUGGCCGGUCCGCCUCACCGCGAGUACUGGUCCGGCUGGACCUUUCCUUCUGGGGAACCUCAUGGCCUUCACUGGCUGUGGGGGGAACCAGGACUUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCAGGCCUUUGCUCGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACGUGCGGUUCUAUUUUGUUGGUUUCUAGGACCGCCGUAAUGAUUAAUAGGGAUAGUCGGGGGCGUCAGUAUUCAGCUGUCAGAGGUGAAAUUCUUGGAUUUGCUGAAGACUAACUACUGCGAAAGCAUUCGCCAAGGAUGUUUUCAUUAAUCAGGGAACGAAAGUUAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUCGGGCGGUGUUUCUAUGAUGACCCGCUCGGCACCUUACGAGAAAUCAAAGUUUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGAAAUUGACGGAAGGGCACCACAAGGCGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUCACCAGGUCCAGACAAAAUAAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUCUUUUGGAUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGCUUAAUUGCGAUAACGAACGAGACCUCGGCCCUUAAAUAGCCCGGUCCGCGUUUGCGGGCCGCUGGCUUCUUAGGGGGACUAUCGGCUCAAGCCGAUGGAAGUGCGCGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGACAGGGCCAGCGAGUACAUCACCUUGGCCGAGAGGUCCGGGUAAUCUUGUUAAACCCUGUCGUGCUGGGGAUAGAGCAUUGCAAUUAUUGCUCUUCAACGAGGAAUGCCUAGUAGGCACGAGUCAUCAGCUCGUGCCGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGAAUGGCUCGGUGAGGCCUUCGGACUGGCCCAGGAGGGUUGGCAACGACCCCCCAGGGCCGGAAAGUUGGUCAAACCCGGUCAUUUAGAGGAAGUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.fundyense.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.fundyense.seq new file mode 100644 index 0000000..cd73918 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.fundyense.seq @@ -0,0 +1,2 @@ +>d.16.e.A.fundyense +AACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUUAGUAUAAGCUUCAAUUUUGUGAAACUGCAAAUGGCUCAUUAAAACAGUCACAAYGCAUUUGGCGAUCAAUUCUAAAUGGAUAUCUGUGGRAAUUCUAUAGUUAAUACAUGCACUAAAACUUAUCUUUGGGGAAAGGUUGUGGUCGUUAGUUACAGAACCAAUUCAAGCUAUGCUUGGACACUUGAAUGAUUCACAAUGACAAAUGAAUUACAUGGCAACAGCUGGUGAUAAUUCAUUCCAGUUUCUGACCUAUCAGCUUUCGACGGUAAGGUAUUGGCUUACCGUGGCAAUGACAGGUGACGGAGGAUUAGGGUUUGAUUCCGGAGAGGGAGCUUGAGAAAUGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGGCACAGGGAGGUAGUGACAAGAAAUAACAAUACAAGGCAUCCAUGUCUUGUACUUGGAAUGAAUGGAUUUUAAACCUUUCUAUAAGUAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCGGUUAAAAAGCUCGUAGUUGGAUUUCUGCUGAGGAUGGCUGGUCCGCCCUCUGGGUGAGUAUUUGGCACAGCCUGAGCAUUUAUCUUGAAAGUACAACUGCACUUGACUGUGUGGUGUGUUAUUGAGAACAUUUACUUUGAGGAAAUCAGAGUGUUUCAAGCAGGUGUUUGGCCUUGAAUACAUUAGCAUGGAAUAAUAAUCAAGAUCGUGGUUCUUUUUUGUUGGUUUCUAGAAUUGAGGUAAUGAUUAAUAGGGAUAGUUGGGGGCAUUCGUAUUUGAUUGUCAGAGGUGAAAUUCUUGGAUUUGUUAAAGACGGACUACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUGAUCAAGAACGAAAGUUAAGGGAUCGAAGACGAUCAGAUACCGUCCUAGUCUUAACCAUAAACCAUGCCAACUAGAGAUUGGAGGUUGUUACUUGUAUGACUUUUUCAGCACCCUAUGCGAAAUCAAAGUGUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCAGACAUAAUGAGGAUUGACAGAUUGAUAGCUUUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAACCUGCUAAAUAGUUACAUGUAAUUUCGAUUAUGUGGGCAACUUCUUAGAGGGACKUUGUGUGUAUAAUGCAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCUGCACGCGCGCUACACUGAUGUGUUCAACGAGUUUUCAACCUUGCCUGGAAAGGUUUGGUAAUUCUUGAACAGGCAUCGUGAUGGGGAUUGUUUAUUGCAAUUAUUAACCUUCAACGAGGAAUUCCUAGUAAGCUUGAGUCAUCAGCUUGUGCUGAUUAUGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGARUGAUCCGGUGAAUAAUUUGGACUGUAGCAAUGUUCAGUUCUUGAACAAUGCAAUGGCAAAUUUAAUGAACCUUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCUGUAGGUGAACCUGCAGAAGGAUCAAGC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.hermannii.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.hermannii.seq new file mode 100644 index 0000000..1eb2af9 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.hermannii.seq @@ -0,0 +1,2 @@ +>d.16.e.A.hermannii +CACCUGGUUGAUCCUGCCAGUGGUAUAUGCUUGUCUCAAGGACUAAGCCAUGCAAGUGUAAGUAUAAGUAAUUUUUACGACGAAACUGCGAAUGGCUCGGUAAAACAGCUAUAGUUUCUUCGAUGGUACCUACUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCCACAACGCGGGGCAACCCGUGGUACCAAUCAGAUAUCAAACCAAUGUGUGGUGAUUCAUGAUUUUUUUUCUGAUCGCACGCAAGUGCGACGCAUCGUUCAAAUUUCUGACCUAUCAACUUUCGAUGGUAAGGUAUUGUCUUACCAUGGUUGUGACGGGUAACGGACCGUGGGUGCGGGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACAGGGAGGUAGUGACAAGAAAUAUCAAUAGAGGGCAUUUAUAUGUCUUCUAAUUGGAAUGAGAACAAGGUAAACAGCUUAUCGAGGAUCCAGCAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUGUAAGCGUAUACCAAAGUUGUUGCAGUUAAAACGCUCGUAGUCGGAUUUUGGCGUGGCCCGUGCUGUGCGCGUAGUGCGUGCGGCGCUGGGGCGCGCUUUUGUGGAGGGCGGCGCGUCGUGGCUUCACUGUCGCGGCGUGUCGGCGCCACCGUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCAGGCGUUUGCCGUGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUUGGUUUCUAUUUUGUUGGUUUGUGAGAGCCGAGUAAUGAUUAAGAGGGACGGUUGGGGGCAUUUGUAUUCCAGCGUCAGAGGUGAAAUUCUUGGAUUGCUGGAAGACAAACCGCUGCGAAAGCGUCUGCCAAGGACGUUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACUAUAAACGAUGAGAACUGGGGAUCGGGCGGGCAUUACGAUGACCCGUCCGGAACCCUCCGGGAAACCAAAGUGUUUGCUUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUUACCAGGUCCGGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAGCGAGACCUGGGCGUGCUAACUAGGGGCCGCUACCAUUGUGUAGCUGCUUGUCCCUUCUUAGACGGACUGCGGGCGUCUAGCCCGCGGAAGCUCCAGGCAAUAACAGGUCUGAGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAGCGGACCAACGGGUGAGGAUGCGCGAGAGCGUUUCCCAAUCCCCAAAUCCGCUCGUGCUGGGGAUAGAGGCUUGCAAUUUUCCCUCUUGAACGAGGAAUACCUUGUAAGCGUGGGUCAUCAGCCCGCGCUGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGAUCCGGUGAGGCUUUGGGACUGCUGCGAUCGGAGCGUUUACGCUCUGGCCGCGGUGGAAACUUAUCCGAACCUUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAAGCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.invadans.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.invadans.seq new file mode 100644 index 0000000..52c4664 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.invadans.seq @@ -0,0 +1,2 @@ +>d.16.e.A.invadans +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAACAACUUUGUACUGUGAAACUGCGAAUGGCUCAUUAUAUCAGUUAUAGUCUACUCGACAGUACCUUACUACUUGGAUAACCGUAGUAAUUCUAGAGCUAAUACAUGCAUAAAUACCCAACUGCUUGUCGGACGGGUAGCAUUUAUUAGAUUGAAACCAAUUCACUUCGGUGAUUUUGUGUUGAAUCAUAAUAACUGUGCUGAUCGCUCUAAGCGAUAAGUCGAUUGAGUUUCUGCCCUAUCAGCUUUGGAUGGUAGGAUAUGGGCCUACCAUGGCGUUAACGGGUAACGGGGAAUUAGGGUUUGAUUCCGGAGAGGGAGCCUUAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGACACAGGGAGGUAGUGACAAUAAAUAACAAUGCCGGGCUAAUUUAGUCUGGCAAUUGGAAUGAGAACAAUUUAAAUCCCUUAACGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCUGGUUUGAGCGUCCGGUCGACGAAAUGUCAGUACUAUGGAUGUUUGGGCCAUAUUUUGUGAGGAUGCCUUUCUGCCAUUGAGUUGGUGGUUGGGUGGACUUGCAUCGUUUACUGUGAAAAAAUUAGAGUGUUUAAAGCAGGCGUUUGCUCAUUUGAAUACAUUAGCAUGGAAUAAUAAGAUACGACCUUGGUGGUCUAUUUUGUUGGUUUGCACGCCAGGGUAAUGAUUAAUAGGGACAGUUGGGGGUAUUCAUAUUUCAACGUCAGAGGUGAAAUUCUUGGAUCGUUGAAAGAUGAGCUUAGGCGAAAGCAUUUACCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUCAGGGGAUCGAAGAUGAUUAGAUACCAUCGUAGUCUUGACCAUAAACUAUGCCGACUCGGGAUUGGCAGUCGUUUAAUUAGAAUGACCUUGUCAGCACCGUAUGAGAAAUCAAAGUCUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCAGACAUAGUAAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUCCGCGUGCUAAAUAGUCCUGCUUACCAAUUUGGUAGGUAAGGACUUCUUAGAGGGACUUUCAGUGACUAACUGAAGGAAGUUGGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGGUACGCUCAACGAGUAUAUAACCUUGAUCGAUAGGUCUGGGUAAUCUUUUGAAUACGUAUCGUGCUAGGGAUAGAUUAUUGCAAUUAUUAAUCUUGAACGAGGAAUUCCUAGUAAACGCAAGUCAUCAGCUUGCAUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCACCUACCGAUUGAAUGACUCGGUGAGAAAUUGGGACCGCUGUUUCGCUUGCUUCAUUGUGAGUGAAACGGUGGGAACUUUUUCUAACCUCGCCAUUUAGAGGAAGGUGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.kariana.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.kariana.seq new file mode 100644 index 0000000..9e4029d --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.kariana.seq @@ -0,0 +1,2 @@ +>d.16.e.A.kariana +NAACCUGGUUGAUCCUGCCAGUAGUCAUACGCUCGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAAUCUUUUACUUUGAAACUGCGAAUGGCUCAUUAUAUCAGUUAUAAUUUAUUUGAUAGUCCCUUACUACUUGGAUAACCGUAGUAAUUCUAGAGCUAAUACAUGCAUCAAUACUCGACUCACGAAGAGUAGUAUUUAUUAGAUUGAAACCAACCGCUUCGGCGUGAUGUGGUGAUUCAUAAUAACUUUGCGAAUCGCAUGGUUUAACACCGGCGAUGGAUCAUUCAAGUUUCUGCCCUAUCAGCUUUGGAUGGUAGGGUAUUGGCCUACCAUGGCUUUAACGGGUAACGGGAAAUUAGGGUUUGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGACACAGGGAGGUAGUGACAAUAAAUAACAAUGCCGGGCCUUUAUAGGUCUGGCAAUUGGAAUGAGAACAAUUUAAAUCCCUUAUCGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUGUGGUUGGAGAGCUCCUCCGUUCGCUUAGSUUCGUGCUGGAGCUUCUCCGUCCAUCCUUGGGUGGAUCCUGUGUGGCAUUCAGUUGUCGUGCAGGGGAUGCCCAUCGUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCAGGCUUACGCCUUGAAUAUAUUAGCAUGGAAUAAUGAGAUAGGACCUGGGUACUAUUUUGUUGGUUUGCGCACCGAGGUAAUGAUUAAUAGGGACAGUUGGGGGUAUUCGUAUUCCAUUGUCAGAGGUGAAAUUCUUGGAUUUUUGGAAGACGAACUACUGCGAAAGCAUUUACCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGAUGAUUAGAUACCAUCGUAGUCUUAACCAUAAACUAUGCCGACAAGGGAUUGGCGGUUGUUCGUUUUGACUCCGUCAGCACCUUAUGAGAAAUCACAAGUCUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGAAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCCCUGCCUGCUAAAUAGUUGGGUGAAUGACUCGUUCAUUGACUACAGCUUCUUAGAGGGACGUUCAUCUCUUAAGAUGAAGGAGGAUAGGGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCCGCACGCGCGCUACACUGAUGCAUUCAACGAGUUUGUUCCUUGGCCGAGAGGCCUGGGGAAUCUUGUUAACGUGCAUCGUGAUAGGGAUAGAUUAUUGCAAUUAUUAAUCUUGAACGAGGAAUUCCUAGUAAACGCAGAUCAUCAAUCUGCAUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCACCUACCGAUUGAAUGGUCCGGUGAAGCCUCGGGAUUGUGACUGUUCUGCUUUAUUGUGGUCGGUUGCGAGAACUUGUCUAAACCUUAUCAUUUAGAGGAAGGUGAAGUCGUAACAAGGUCUCCGUAGGUGAACCUGCAGAAGGAUCAANNN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.khaliulini.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.khaliulini.seq new file mode 100644 index 0000000..e28f2e8 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.khaliulini.seq @@ -0,0 +1,2 @@ +>d.16.e.A.khaliulini +UCCACCAGGUUGAUUCUGCCUGACGUGGACGCUUGCCUCGAAGAUUAAGCCAUGCAAGUCUGUGAAUCUUUAUAGAGAAACAGUGAACGGCUCAGUAUAACACGUCUAUCUACCCAUCGUGUGAACAUAACCAUGGUAAACUAUGGCUAAAUUGAUGGAUGAGGAUGUGACCUAUCAGCUUGACGGUACGGUAAGUGCGUACCGAGGCGAUAACGGGUAACGGGGAAUAUGGGUUUUAUUCCGGAGAGGGAGCCUGAGAGAUGGCUGCCACGUCCAAGGACGGCAGCAGGCGCGAAACUUACCCAAUGAACAUUGAGGUAGUUACGAGGCGUAGCAUUUAUAUGUGGUAUGUUUAAAUAGCAUAUCGAAGUAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUACCAGCUCCAAUAGCGUCUGUGUUUAUUGCUGNGGUUAAAACGUGCGUAGUCUGGUUAAUGGCCUGAAGGUAACAUGCAUUUUCAUAGUGUAGGAUAUUUCAGGAACUUAUGCCUUGAGANAGGGAAGGGGUAAUGUUAUUUGGUAGCGAGAGGUGACAAUCGAUGACCUACCAAGGAGCGACAGAGGCGAAAGCGAUUACCAAUAACUGAUCUGACGAUCAAGCACGUGAGCAGGAGUAUCGAAGAGGAUUAGAGACCCACGUAGUUCCUUGCAGUCAACGAUGCCAACGCUGUGGUGAUACUUGUCAUUGCAGAGGCGAAAGCUAGUGUAUGGGCUCCGGGGAUANUACGGACGCAAGUUUGAAACUUGAAGAAAUUGACGGAAGGACACCACAAGGAGUGGAGUGUGCNGGUUAAUUUGACUCAACGCGGGAAAACUUACCCGGGCAGGCAAUUGUCGUGAGAAGCUAUUGUAGCUGAUGAUAUUGCGCGUGGUGCAUGGCCGUUCUUAACACGUGGAGUGAUCUGUCUGGUCAAAUCUGAUAACGCGUGAGAGGUGAGUAUUUGGUUGAGAGACCAAAUAGACGGUGUCUGUAAAGACAAGGAAGCGACACCCAAUAACAGGUCUGUGAUGCCCGUAGAUGUCCGGGGCUCCACGCGCACUACAAUGGAUGGUAGUUUUUAUAAGCGGUAACCAUUCGUAGUUGGGAUUGACAUAUGUAAUUAUGUCAUGAACGUGGAAUUCCUAGUAGUUGGUAGUCACUAACGACUAACGAAUGUGUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCUAAGAUGGAAGUGCGGGUGAAGAUGUGAGUGUAGACCAAUGGGAGGAUCAGUAUACUUGUGUGAGUUGAUUACGCUUGUGUAUUGUGACUGUUGUUAGCAUGAGCAUAAGAACCCGUGCAACUAGAUUGGAUGUAAGUCGUAACAAGGUAANCAUNNNNNNNNNNNNNNNNNNNNNNNNN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.macrogynus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.macrogynus.seq new file mode 100644 index 0000000..cd1bf7e --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.macrogynus.seq @@ -0,0 +1,2 @@ +>d.16.e.A.macrogynus +UACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUAAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAACUGUUUAUACAAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUAAUUUAUUUGAUAGUACCCUUUUACUACUUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCACAAAAGUCCUGACCUUUACGGAAGGGAUGCAGUUAUUAGAUACAAAACCAACCCGGGCAACCGGUUUUUUGGUGAUUCAUGAUAACUUUGCGGACCGCAUGGCCCUGCCGGCGGCGGGUCAUUCAAAUUUCUGCCCUAUCAACUGUCGAUGGUAGGAUAGAGGCCUACCAUGGUGAUAACGGGUAACGGGGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGAUACAGGGAGGUAGUGACAAUAAAUAACGAUGCAGGACCUUUUGGUCUUUGCAAUUGGAAUGAGUACAAUUUAAAUCCCUUAACGAGGAACAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGAAUUUCAAGGGUUUUUUUCGUAGCUAGCCAUUGUUCCCUUUGCGGUCAAUGUGCAUUUGGCUACAGGCCCUUUUUUUCUGCUAGGAGAUGCGGCUCUUCUGCUUGUCAGCGGGGCUGCAGUUUUCCUAGCACUUUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCUUUUUCUUUGCCUGAAUAUCUUAGCAUGGAAUAAUAGAAUAGGACUUUGGUUCUAUUUUGUUGGUUUCUAGGACUAGAGUAAUGAUUAAUAGGGAUAGUUGGGGGCAUUAGUAUUUAAUUGUCAGAGGUGAAAUUCUUGGAUUUAGGAAAGACUAACUUCUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAAGGGAUCGAAGAUGAUUAGAUACCAUCGUAGUCUUAACCAUAAACGAUGCCGACCAGGGAUCGGGCGCUUGUAGUUUUUCCAAAAAGACACGCCCGGCACCUUUUGAGAAAUCAAAGUUUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUCACCAGGUCCAGACAUGGUAAGGAUUGACAGAUUGAAAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUCGUGGAUUGAUUUGUCUGGUUAAUUCCGAUAACGAACGAGACCUUUUCCUACUCGUUACUUGCUCAUGGGUUUUAUCUCAUGGCACGCAAGUUCUUAGCGGGACUGCUGGCGUUUAGCCAGAGGAAGUUCGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCGCACGCGCGCUACACUGAUGCAGUCAGCAAGUUUUUUAACUGGCUGUAGUUCUUUCGGGAGCUAUGGUCGAUUUCCUUGCCCGAAAGGGUUGGGUAAUCUUUUGAAACUGCAUCGUGAUGGGGAUCGACCUUUGUAAUUAUCGGUCGUGAACGAGGAAUUCCUAGUAAGUGUGGGUCAUCAGCCCACGCUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGGAUGGCUUAGUGAGAUUUUUGGAUUGUUGAGCGAUUGCAGCAAUGUGAACGCCCGACGAGAAAUUGAUCAAACUUGGUCAUCUAGAGGAAGUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.majus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.majus.seq new file mode 100644 index 0000000..8d7d7a0 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.majus.seq @@ -0,0 +1,2 @@ +>d.16.e.A.majus +NNNNNNNNNNNNNNNNNNNNNNNUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUGUAAGUAUGAACUAAUUCAGACUGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUAGUUUGUUUGAUGGUACCUGCUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCAACAAACCCCGACUUCUGGAAGGGACGCAUUUAUUAGAUAAAAGGUCGACACGGGCUCUGCCCGUUGCUGCGAUGAUUCAUGAUAACUUGACGGAUCGCACGGCCUUCGUGCCGGCGACGCAUCAUUCAAAUUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGUGGCCUACUAUGGUGGUGACGGGUGACGGAGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACGGGGAGGUAGUGACAAUAAAUAACAAUACCGGGCUCUACGAGUCUGGUAAUUGGAAUGAGUACAAUCUAAAUCCCUCAACGAGGAUCCAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUUAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGACUUUGGGUUGGGCCGGCCGGUCCGCCUCUGGUGUGCACCGGUCGUCUCGUCCCUUCUGCCGGCGAUGCGCUCCUGGCCUYAAUUGGCCGGGUCGUGCCUCCGGCGCUGUUACUUUGAAGAAAUUAGAGUGCUCAAAGCAAGCCUACGCUCUGUAUACAUUAGCAUGGGAUAACAUUAUAGGAUUUCGGUCCUAUUACGUUGGCCUUCGGGAUYGGAGUAAUGAUUAACAGGGACAGUYGGGGGCAUUCGUAUUUCAUAGUCAGAGGUGAAAUUCUUGGAUUUAUGAAAGACGAACAACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUGGGGGCUCGAAGACGAUCAGAUACCGUCCUAGUCUCAACCAUAAACGAUGCCGACCAGGGAUCGGCGGAUGUUGCUUUUAGGACUCCGCCGGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCAGACAUAGUAAGGAUUGACAGACUGAGAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUCAGCCUGCUAACUAGCUAUGCGGAGGUAUCCCUCCGCGGCCAGCUUCUUAGAGGGACUACGGCCUUUUAGGCCGCGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAUGUAUUCAACGAGUUUAUAGCCUUGGCCGACAGGCCCGGGUAAUCUUUGAAAUUUCAUCGUGAUGGGGAUAGAUCAUUGCAAUUGUUGGUCUUCAACGAGGAAUUCCUAGUAAGCGCGAGUCAUCAGCUCGCGUUGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAAUGGUCCGGUGAAAUGUUCGGAUCGCGGCGACGUGGGCGGUUCGCUGCCCGCGACGUCGCGAGAAGUCCAUUGAACCUUAUCAUUGAGAGGAAGGANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.michaelis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.michaelis.seq new file mode 100644 index 0000000..8870493 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.michaelis.seq @@ -0,0 +1,2 @@ +>d.16.e.A.michaelis +NNNNNGGUUGAUUCUGCCUGACGUAGAACGCUAGUCUCACAGAUUCAGCCAUGCAAGUAGUAUGUAUGUAAUACACAAUGGCUCAGUAUCGAGUAUAGCUUUGCUCUCCAAGAUGUGAUACUUUCAGGAAACAGAAAAUAAAGCAUCUAUCUUCUAAAGUUUUUUAGAGGAGAGGAGAAGAAGCACUCACCUAUCAGUUAGUAGGUAUGGUAAGGGCAUACCUAGACGAAGACGGGUACGGGGAAGGCAACUUCGAUUCCGGAGAGGGCGCCUUUAGAGAUGGCGACCAGUUCUAAGGAGUGCAGCAGGCUCGAAACUUACCGAAUUAUAGAAUAGAGGUAGUGAUGGAAACGUUUAUAUAGAAAUACUGGUAAAGCAAGUAUUAUUAACUGAGGAAAGCUGGUGCCAGCAGCCGCGGUAAUACUUGCUCCAGGAGCUUAUUCGAUAUGUUGCGGUUAAAACGUCCGUAGUCGCGGCUGGGACUGACCUGUAAUCUAUUUGGUCAACAGAUAGAUAGGGGCAGUAGCAAGUUGGAAAAGAGCAAUUUGGUGUCAGCUAAUGGUAUGGGGAGGGGUAAAGUCUGAGGAUCCUGCAGGAGGAGCAAAGGCGUAAGCACUGACAAAGAUUGAUUCUGUUGAUCAAGGACAGAGGCUAGAGGAUCGAAUACGAUUAGAUACCGUAGUAGUUCUAGCAGUGACCGAUGAUGAUUUUGCCUUAUGCAAUAGAGAAAUCAAAAUAGAUCUCCGGGGAGUACAUGCGCACAGGAACUUAAGAAUUGACGGAAGCUAGCCACAAGGGUUGGAUUGUGCGGCUUAAUUUGACUCAAAGCGGAAAAGCUUACCAAGCUUAUUUAUUCAACGAGUAUUUAUCCGAGAGUAAAAUGGUGUGCAUGGCCGUUCCUAACACAUGGAGUGAUUUUGUGAUUAACCUUCCGUAAUCUGUGUAAAUCCUCAUAAUAGCUUGUUUGAAAAGAACAAUUCGAGCAAGAACAGGUCAGUGAUGUCCUUUGAUAGCUUGGGCUGCACGCGCAAUACAAUUUUUAUGUAGUAAGAUAUAGAUAGGGAUUGAGGGCUGAAAGCGCUCAUGAACACGGAAUAGCUAGUAACGUGAGUUCAAUAUACGGCGAUGAAUAUGUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCGAAGAUGGAGUGAUUUUUGAGUCAAUUAUAAUUGGCUACUUGAAUGAGUUAUUCUAAAACCGGUACAAGUCGUAACAAGGCUACGGUUGAAGAAUCAGCAGUAGGAUUAGCG diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.plicata.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.plicata.seq new file mode 100644 index 0000000..f9edb71 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.plicata.seq @@ -0,0 +1,2 @@ +>d.16.e.A.plicata +CAACCUGGUUGAUCCUGCCAGUGGUAUAUGCUCGUCUCAAGGACUAAGCCAUGCAAGUGUAAGUAUAAGUGAAUUGUACAACGAAACUGCGAAUGGCUCGGUAAAACAGCUAUAGUUUCUUCGAUGAUACCUACUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCCGCAACGCGGGGUAACCCGUGGUACAAGUUAGAUAACAGGCCGACGCUUGACGAUUCAUAACUUUUUUUCUGAUCGCGCCUUGUGCGCGACGCAUCGUUCAAAUUUCUGACCUAUCAACUUUGACGUGAAGGUAUUGUCUUCACGUGGUUGUGACGGGUAACGGACCGUGGGUGCGGGACUCCGGAGAGGGAGCCUGAGAGACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACAGGGAGGUAGUGACAAGAAAUAGCAAUAGAGGGCCCAAUGGGUUUUCUAAUUGGAAUGAGAACAAGGUAAAUAGCUUAUCGAGGAUCCAGCAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUGCUUGCGUAUGUCACCGAUGAUGCGGUUAAAACGCUCGUAGUCGGAGGUUGGCGGGGGCGUCUGGCGGAGAGUAAAUCUUUGUCGGUCGCGCCUGCUUUUGUGGAGGGCGCGAGCGGGCGGCUUUACUGUCGCGCGUUCGCGGCGCCACCGUUUACUGUGAAUAAAUUAGAGUGUUCAAAGCAGGCGUUUGCCGUGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACCUUGUCCUUUUUGUUGGUUUGUGAGGCCGAGGUAAUGAUUAAGAGGGACGGUUGGGGGCAUUUGUAUUCCGGCGUCAGAGGUGAAAUUCUUGGAUUGCCGGAAGACAGACCGCUGCGAAAGCGUCUGCCAAGGACGUUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACUAUAAACGAUGAGAACUGGGGAUCGGGCGGGACUGAAUUUGGCCCGCCCGGGACCCUCCGGGAAACCAAAGUGUUUGCUUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCGGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAGCGAGACCUGGGCGUGCUAGCUAGGGCGGGCUAUCGCUUGAUAGUACUGACCUUCCUAGACGGACUGUGGGCGUCUAGUCCACGGAAGCUCCAGGCAAUAACAGGUCUGAGAUGCCCUUAGAUGUUCUGGGCCGCACGCGUGCUACACUGAGCGGGUCAACGGGUGAGGAUGUGCGAGAGCGCUUCCCAACCCCCAAACCCGCUCGUGCUGGGGAUCGAGGCUUGCAAUUAUCCCUCUUGAACGAGGAAUACCUUGUAGGCGUGGGUCAUCAUCCCGCGCCGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGGUCCGGUGAGGACUCGGGACCGCGCCGACUAGCGCGUCUAACGCGUUGGUUGUUGUGGAAACUUGUCCAAACCUUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAAGC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.scoticae.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.scoticae.seq new file mode 100644 index 0000000..88f7469 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.scoticae.seq @@ -0,0 +1,2 @@ +>d.16.e.A.scoticae +CACCAGGUUGAUUCUGCCUGACGUGUGUGCUAGUCUUGGGGACUUAGCCAUGCAAGCUAGCGAAGCGGAGCGGAGCGGCGGACGGCUCAGUAGGACGGCGAUAAUUCACCCGCGGCAGAAGAGGGAUAACCGCGGCAAGCUGCGGCUAAGACAAGGGAGGCUGUGUUGCGGGGAGGCGCACGCAGCGGACACGGCGGCGAAGAUGCCGACCUAUCAGCUAGUAGGUAGGGUAAGGGCCUACCUAGGCGACGACGGGUGACGGGGGGUGAGAGCCUGAUACCGGAGAGGGAGCCUGAGAAACAGCUCCCACGUCCAAGGACGGCAGCAGGCGCGAAACUUGCCCAAUCCCUACGGGGGGAGGCAGCUACAAGACGUGGGGAAGCCCCGGAAAGCACGGCAAAGGAGUGCGUAGCGACUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAGGAGCGCACAUGUGUGUUGCUGCAGUUAAAACGUCCGUAGUCGGCCAUGAGGGGCAGUGAGGAAAGGGCUGUGCUCAAGGCGGUGUGCAGCGCGGGACCCGGGGCGAGAGGAACGGACGACGGGCGCGGGAUCUGGGGGCGAGAGGUGAAAAUCGGGGACCCUCUGGGGACGAGCGGAAGCGAAGGCGGCGCCCGAGGACGUGUCCGUUGAUCAAGGACGAAGGCCGGAGGAUCAAAGAUGAUUAGAGACCGUCGUAGUUCCGGCAGUAAACGAUGCCAACGGGGCGAAGCCAAGGGGCUGUGUCCGGGAGAAAUUGGAGUGUUUAGGCUCUGGGGAUAGUACGGUCGCAAGACAGAAACUUAAAGAAAUUGACGGAAGGACACCACAAGGAGUGGAGUGUGCGGCUUAAUUUGACUCAACGCGGGGCAGCUUACCAGUGCCGCAUGCGCGGGAGAUUGGCGGCGGAGCGCCCCCGAGAUUGCGCAGGGAGUGGUGCAUGGCCGUUUGCAACACGUGGGGUGACCUGUCUGGUUGAUUCCGACAACGCGUGAGGCCUAGGGCGCAGGGCUGUGCGACGGGCCGCGGCAAGCGGCAGGAAGGGAGGCGAUAACAGGUCAGUGAUGCCCUCAGAUGCACUGGGCUGCACGCGCACUACAAUGGCGGGGCGAGACGGAGUGCCGAGAGGUGCGAAGGAGGCCUGGCUGCAGCGGGGAUGGGUGCCUGGAAGGGCGCCCUGAACGAGGAAUUCCUAGUAGCCGCGGGUCACCAAGCCGCGGCGAAUGUGUCCCUGUUCUUUGUACACACCGCCCGUCACUACCUAAGAUGGAUGUGCAGGCGAGGUGGCUGGAGGGAAGGCAGCCGAGCCGGUGCAACUAGAUAAGGUAUAAGUCGUAACAAGGCUACGGUUGANNNNNNNNNNNNNNNNNNNNN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.thaliana.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.thaliana.seq new file mode 100644 index 0000000..54b1917 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.thaliana.seq @@ -0,0 +1,2 @@ +>d.16.e.A.thaliana +UACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUGUAAGUAUGAACGAAUUCAGACUGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUAGUUUGUUUGAUGGUAACUACUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCAACAAACCCCGACUUAUGGAAGGGACGCAUUUAUUAGAUAAAAGGUCGACGCGGGCUCUGCCCGUUGCUCUGAUGAUUCAUGAUAACUCGACGGAUCGCAUGGCCUCUGUGCUGGCGACGCAUCAUUCAAAUUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGUGGCCUACCAUGGUGGUAACGGGUGACGGAGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACGGGGAGGUAGUGACAAUAAAUAACAAUACUGGGCUCUUUCGAGUCUGGUAAUUGGAAUGAGUACAAUCUAAAUCCCUUAACGAGGAUCCAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUUAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGAACCUUGGGAUGGGUCGGCCGGUCCGCCUUUGGUGUGCAUUGGUCGGCUUGUCCCUUCGGUCGGCGAUACGCUCCUGGUCUUAAUUGGCCGGGUCGUGCCUCCGGCGCUGUUACUUUGAAGAAAUUAGAGUGCUCAAAGCAAGCCUACGCUCUGGAUACAUUAGCAUGGGAUAACAUCAUAGGAUUUCGAUCCUAUUGUGUUGGCCUUCGGGAUCGGAGUAAUGAUUAACAGGGACAGUCGGGGGCAUUCGUAUUUCAUAGUCAGAGGUGAAAUUCUUGGAUUUAUGAAAGACGAACAACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUGGGGGCUCGAAGACGAUCAGAUACCGUCCUAGUCUCAACCAUAAACGAUGCCGACCAGGGAUCAGCGGAUGUUGCUUAUAGGACUCCGCUGGCACCUUAUGAGAAAUCAAAGUUUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCAGACAUAGUAAGGAUUGACAGACUGAGAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGUUAAUGAACGAGACCUCAGCCUGCUAACUAGCUACGUGGAGGCAUCCCUUCACGGCCGGCUUCUUAGAGGGACUAUGGCCGUUUAGGCCAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAUGUAUUCAACGAGUUCACACCUUGGCCGACAGGCCCGGGUAAUCUUUGAAAUUUCAUCGUGAUGGGGAUAGAUCAUUGCAAUUGUUGGUCUUCAACGAGGAAUUCCUAGUAAGCGCGAGUCAUCAGCUCGCGUUGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAAUGAUCCGGUGAAGUGUUCGGAUCGCGGCGACGUGGGUGGUUCGCCGCCCGCGACGUCGCGAGAAGUCCACUAAACCUUAUCAUUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUG diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.verticilliflorum.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.verticilliflorum.seq new file mode 100644 index 0000000..2598366 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.verticilliflorum.seq @@ -0,0 +1,2 @@ +>d.16.e.A.verticilliflorum +NNNNNNNNNGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUGUAAGUAUGAACUAAUUAAGAUGGUGAUACUGUGAAUGGCUCAUUAAAUCAGUUAUAGUUUGUUUGAUGGUUUUUUCUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCAAUAAAUCUUGACUUUUGGAAGAGGAGCAUUUAUUAGAUAAGAGGUCAAUGCAAGCUUUGCUUGUUGCACUGAUGAUUCAUGAUAAUAGACGGAUCGCAUGGCCCCUGUGUCGGCGAUGCAUCAUUCAAGUUUCUGCCCUAUNAACUUUCGAUGGUAAGAUAUUGGCCUACUAUGGUGUUGACGGGUGACGGAGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUAAUGCGGGGAGGUAGUGACAAAAAAUAACAAUACCGGGCUUUAACGAGUUUGGUAAUUGGAAUGAGUACAAUCUAAAUCCCUUAAUGAGGAUCCAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGAUAUUUAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUUGGGUUGGGUUUGAUCGGUCUACCUUUGGGUGUGUACCGGUUACCUCGUCCCUCCUACCCAUGAUGCGCUUCUGGCCUUAAUUGGUCGGGUCGUGCCUUGGGUGCUGUUACUUUGAAGAAAUUAGUGUGCUCAAAGCAAGUUUGUGCUCUGGAUACAUUAGCAUGGGAUAACGUCAUAGGAUUUUGAUCCUAUUUGGUUGGCCUUCGGGAUCGGAGUAAUGAUUAAUAGGGACAGUCGUGGGCAUUCGUAUUUCAUAGUCAGAGGUGAAAUUCUUGGAUUUAUGAAAGACGAACAACUGCGAAAGCAUUUGUCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUGGGGGCUCGAAGACGAUCAGAUACCGUCCUAGUCUCAACCAUAAACGAUGCCGACCAGGGAUCAGCGGAUGUUACUUUUAGGACUCCGUUGGUACCUUAUGAGAAAUCAAAGUUUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCAGACAUAGUAAGGAUUGACAGAUUGAGAGCUCUUUCGUUAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUCAGCCUGCUAACUAGCUAUGUGGAGGUACACCUUCAUGGGUAGCUUCUUAGAGGGACUAUGCCAACUAGGCCACGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAUGUAUUCAACGAGUUUAUAGCCUUGACUAUUAGGUCUGGGUAAUCUUUGAAAUUUCAUCGUGAUGGGGAUAGAUCAUUGCAAUUGUUGGUCUUUAACGAGGAAUUCCUAGUAAGCGUGAGUCAUCAGCUCGCGUUGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAAUGGUCCGGUGAAGUGUUCGGAUUAUGGCGACGUNNNNGCUUUGCUGUCGGCGAUGUUGUGAGAAGUUCAUUAAACCUUAUCAUUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUG diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.bigemina.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.bigemina.seq new file mode 100644 index 0000000..f2d9e72 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.bigemina.seq @@ -0,0 +1,2 @@ +>d.16.e.B.bigemina +UGAAUAGCAACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUUAAAGAUUAAGCCAUGCAUGUCUAAGUACAAGCUUUUUACGGUGAAACUGCGAAUGGCUCAUUACAACAGUUAUAGUUUCUUUGGAGUUCGUUUUCCAUGGAUAACCGUGCUAAUUGUAGGGCUAAUACAAGUUCGAGGCCUUUUGGCGGCGUUUAUUAGUUCGUUAACCACUUUUUCUGGUGAUUCAUAAUAAACUUGCGAAUCGCUUUUGCGAUGUUCCAUUCAAGUUUCUGCCCCAUCAGCUUGACGGUAGGGUAUUGGCCUACCGAGGCAGCAACGGGUAACGGGGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACAGGGAGGUAGUGACAAGAAAUAACAAUACAGGGCUUUCGUCUUGUAAUUGGAAUGAUGGUGAUGUACAACCUCACCAGAGUACCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAACUUGUUGCAGUUAAAAAGCUCGUAGUUGUAUUUCAGCCUCGCGUUUUUUCCCUUUUGUUGGGUCUUUUCGCUGGCUUUUUUUUUACUUUGAGAAAAUUAGAGUGUUUCAAGCAGACUUUUGUCUUGAAUACUUCAGCAUGGAAUAAUAGAGUAGGACCUUGGUUCUAUUUUGUUGGUUUUGAGCCUUGGUAAUGGUUAAUAGGAACGGUUGGGGGCAUUCGUAUUUAACUGUCAGAGGUGAAAUUCUUAGAUUUGUUAAAGACGAACCACUGCGAAAGCAUUUGCCAAGGACGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCCUAACCAUAAACUAUGCCGACUAGGGAUUGGAGGUCGUCAUUUUCCGACUCCUUCAGCACCUUGAGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGUCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGCGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAACCUCACCAGGUCCAGACAGAGUAAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUUUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAACCUGCUAACUAGCUGCUUGGAUGUUGUCCUCGUUUGCUUCUUAGAGGGACUCCUGUGCUUCAAGCGUGGGGGAAGUUUAAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCUGCACGCGCGCUACACUGAUGCAUCCAUCGAGUUUGUCCUGUCCCGAAAGGGUUGGGUAAUCUUUAGUGUGCAUCGUGUCGGGGAUUGAUUUUUGCAAUUCUAAAUCAUGAACGAGGAAUGCCUAGUAUGCGCAAGUCAUCAGCUUGUGCAGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUCGAGUGAUCCGGUGAAUUAUUCGGACCGUGGCUUUUCCGAUUCGUCGGUUUUGCCUAGGGAAGUUUUGUGAACCUUAUCACUUAAAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.bovis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.bovis.seq new file mode 100644 index 0000000..2c3855a --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.bovis.seq @@ -0,0 +1,2 @@ +>d.16.e.B.bovis +NNNNNNNNNNNNNNNNNNNNNNNNNNNNUAGUCAUAUGCUUGUCUUAAAGACUAAGCCAUGCAUGUCUAAGUACCAGCUUGUUACGGUGAGACUGCGAAUGGCUCAUUACAACAGUUAUAGUUUCUUUGGAGUUCACUUUGCUAUGGAUAACCGCGCUAAUUGUGUGGCUAAUACACGUUUGAGGUUAUUACCGCGUUUACUGGUCUUGUGAUUUACAGUAACCUGCGACUCGCUUUUUGCGAUAUUCCAUUCAAGUUUCUGACCCAUCAGCUUGACGGUAGGGUAUUGGCCUCCCGAGGCAUCGACGGGUAACGGGGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGCGAGACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACAGGGAGGUAGUGACAAGAAAUACCAAUACGGGGCUACUGCUCUGUAAUUGGCAUGGGGGCGACCUUCACCCUCGCCCGAGUACCCAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAACUUGUUGCAGUUAAAAAGCUCGUAGUUGUACUUCACGUCCCCCGCUUGGUCCUUUCCUCGCCGGGACGCCUCGUUACUUUGAGAAAAUUAGAGUGUUUCAAGCAGGUUUCGCCUGUAUAAUUGAGCAUGGAAUAACCUUGUAUGACCCUGUCGUACCGUUGGUUGACUUUGGGUAAUGGUUAAUAGGAACGGUUGGGGGCAUUCGUACUCGACUGUCAGAGGUGAAAUUCUUAGAUUUGUCGAUGACGCACGACUGCGAAAGCAUUUGCCAAGGACGCUUCCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCCUAACCUUAAACUAUGCCGACUAGGGAUUGGUGGUCGUCGCCUCGACUCCGUCAGCACCUUGAGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGUCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGCGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAACCUCACCAGGUCCAGACAGCGUAAGGAUUGACAGGUUGAUUGUCCUUUCUUGAUUCUCUGGGUAGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAACCUGCUAUUUAGUCGCUCGGUCUCCGUCCGUGCGCACUUCAUAGAGGGACUCUGCGGCGUCAAGCUGCGGUGAGGUUUAAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCUGCACGCGCGCUACACUGAUGCUUGCCUCGUGUUUACCCUCGGCCGAUAGGCCUGGUAACCCCUAGUCUGCAUCGUGUUUGGGAUUGAUCUUUGCAAUUCUAGAUCAUGAACGAGGAAUGCCUAGUAUGCGCAAGUCAUCAGCUUGUGCAGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUCGAGUGAUCCGGUGAAUUAUUCGGAACCUGCUUGCGCGAUCCGUCGCCGCUCGCGGCCAGGUUUUGUGAACCUUAUCACUUAAAGGAAGGAGAAGUCGUAACAAGGUUUCCNNNNNNNNNNNNNNNNNNNNNNNNNNN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.canis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.canis.seq new file mode 100644 index 0000000..2699b8a --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.canis.seq @@ -0,0 +1,2 @@ +>d.16.e.B.canis +NNNNNNNNAACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUACAAGCUUUUUACGGUGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGGUAUUCUUUUUCCAUGGAUAACCGUGCUAAUUGUAGGGCUAAUACACGUUGGAGGCCUUUUGGCCGCGUUUAUUAGUUGUAAACCUCCGCUUGGUUUUCGGUGAUUCAUAAUAAACUUGCGAAUCGCUUUUAGCGAUGGACCAUUCAAGUUUCUGACCCAUCAGCUUGACGGUAGGGUAUUGGCCUACCGAGGCAGCAACGGGUAACGGGGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCCGACACGGGGAGGUAGUGACAAGAAAUAACAAUACAGGGCUAAUGUCUUGUAAUUGGAAUGAUGGUGACUUAAACCCUCACCAGAGUAGCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAACUUGUUGCAGUUAAAAAGCUCGUAGUUGUAUUUUUGCUUGGCGGUUUGUUGCCUUUGUGGCUUGAUUCCGCUUGGCUUUUGGCUUUUUGCCUUAUUACUUUGAGAAAAUUAGAGUGUUUCAAGCAGACUUUUGUCUUGAAUACUGUAGCAUGGAAUAAUAGAGUAGGACUUUGGUUCUAUUUUGUUGGUUUGGGAACCUUGGGUAAUGGUUANUAGGAACGGUUGGGGGCAUUCGUAUUUAACUGUCAGAGGUGAAAUUCUUAGAUUUGUUAAAGACGAACUACUGCGAAAGCAUUUGCCAAGGACGUUUCCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCCUAACCAUAAACUAUGCCGACUAGUGAUUGGAGGUCGUCGUUUGUUUGACCCCUUCAGGAGCUUGAGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGCGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUCACCAGGUCCAGACAAACGGUAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUUUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAACCUGCUAACUAGCGCUGGUUACUUGGUUUCCCGCUGCUUCUUAGAGGGACUUUGGGGCUUGAAGCUCCAAGGAAGAUUAAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCUGCACGCGCGCUACACUGAUGCAUUCAUCGAGUGUUGCCCCUGGCCGAGAGGUCUGGGUAAUCUUUAGUAUGCAUCGUGACGGGGAUUGAUUUUUGUAAUUCUAAAUCAUGAACGAGGAAUGCCUAGUAUGCGCAAGUCAUCAGCUUGUGCAGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUCGAGUGAUCCGGUGAAUUAUUCGGACCGUGGCUAUUCCGAUUCGUCGGUUUUGCCGUGGAAAGUUUUGUGAACCUUAUCACUUAAAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCNNNN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.coli.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.coli.seq new file mode 100644 index 0000000..dc4b931 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.coli.seq @@ -0,0 +1,2 @@ +>d.16.e.B.coli +AACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGACUAAGCCAUGCAUGUCUAAGUAUAAAUAACUACACAGUAAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUACAUUAAAUGGAUAACUGUAGAAAAACUAGAGCUAAUACAUGCCGAGGCCGUAAGGUCGUAUUUAUUAGAUAUUCCAAUUAAGGUGAAUCAUAAUAACUUCGCAAAUCGCGAUUUUGUCGCGAUAAAUCAUCCAAGUUUCUGCCCUAUCAUGCUUUCGAUGGUAGUGUAUUGGACUACCAUGGCUUUCACGGGUAACGGGGAAUUAGGGUUCGAUUCCGGAGAAGGAGCCUGAGAAACGGCUACUACAUCUACGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGACUCAGGGAGGUGGUGACAAGAUAUAACGACGCAAUUUAUUUUGUGAUUGUAGUGAGGGUAUUCCAAACCGAACCACUAGUACGAUUAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCAAGGCGUGUAUACUCUUUUUGAGUAUGCUACCUACUAGUCUCUGACUGUUACUGUGAGAAAAUUAGAGUGUUUCAAGCAGGCUUUUGCAAGAAUACAUUAGCAUGGAAUAACGAAUGUGUCUAGAAUCUUGGUUAAUUCUAGAUUGCGAUUAAUAGGGACAGUUGGGGGCAUUAGUAUUUAAUUGUCAGAGGUGAAAUUCUUGGAUUUGUUAAAGACUAACGUAUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGAUAGGGGAUCAAAGACAAUCAGAUACUGUCGUAGUCCUAUCUAUAAACUAUGCCGACUAGGGAUUGGAAUGGUUAUAACGCCGUUUCAGUACCUUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGACUGAAACUUAAAGAAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCAGACAUAGUAAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGAUAACGAACGAGACCUUAACCUGCUAACUAGUCUAAUCCAUUUUAUGGAAUAUGACUUCUUAGAGGGACUAUGUAUUUAAAUACAUGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAUAUGUCCUGGGCUGCACGCGUGCUACACUGAUGCAUACAACAAGUGCCUAGCCCGCCAGGGUAUGGCAAUCUCGAAUAUGCAUCGUGAUGGGGAUAGAUCUUUGCAAUUAUAGAUCUUGAACGAGGAAUUCCUAGUAAGUGCAAGUCAUCAUCUUGCAUUGAUUAUGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUACCGGGUGAUCCGGUGAACCUUUUGGACCGCGAUGCGGAAAAAUAAGUAAACCAUAUCACCUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCANNN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.emersonii.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.emersonii.seq new file mode 100644 index 0000000..16f916b --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.emersonii.seq @@ -0,0 +1,2 @@ +>d.16.e.B.emersonii +UACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUAAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAACUGCUUUAUACAAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUAAUUUAUUUGAUAGUACCCCAUUACUACUUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCACUCAAGUCCUGACCGCUUGUCGGAAGGGAUGCAGUUAUUAGAUACAAAACCAGCCCCGGGCAACCGGGUUUUCUGUUGGUGAUUCAUGCUAACUUUGCGGAUCGCAUAGCCUUUGUGCUGGCGACGGGUCAUUCAAAUUUCUGCCCUAUCAACUUUCGACGGUAGGAUAGAGGCCUACCGUGGUGAUAACGGGUAACGGGGAAUAAGGGUUUGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGAUACAGGGAGGUAGUGACAAUAAAUAACGAUGCGGGGCCUUUUGGCCAUCGCAAUUGGAAUGAGUACAAUUUAAAUCCCUUAACGAGGAACAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGAAUUUCAGGGCUGUCUUUGUCACCUGGCCACUGAGCCUUURCGGCCAGUGUUGCUUUCGGGUGCGGGCCCUUUAUUUCUGCUGGGUGCUCCUUUGGGUUGGCUUUUGCUAGCUCGGGGGAUGUCUGCCCAGCACGUUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCUUUUUUUAAGCUUGAAUAUCUUAGCAUGGAAUAAUAGAAUAGGACUCUGGUUCUAUUUUGUUGGUUUCUGGGACUGGAGUAAAUGAUUAAUAGGGAUAGUUGGGGGCAUUAGUAUUUAAUUGUCAGAGGUGAAAUUCUUGGAUUUAGGAAAGACUAACUUCUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAAGGGAUCGAAGAUGAUUAGAUACCAUCGUAGUCUUAACCAUAAACGAUGCCGACCAGGGAUCGGGCGUCAUGUAGUUAUUCACAUAAAAGACGCGCCCGGCACCUUUUGAGAAAUCAAAGUUUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUCACCAGGUCCAGACAUGGUAAGGAUUGACAGAUUGAAAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUCGUGGAUUGAUUUGUCUGGUUAAUUCCGAUAACGAACGAGACCUUGAUCUGCUAAUUAGUUGGGCUUGCAUUUAUGCAAGUAAUCCAACUUCUUAGAGAGACUGCUGGCGUUUAGCCAGAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAUAAGGUCAGCGAGUUUCAACUUGCUGGCUUAAGUUGAGUUUCGGCUCGGCUUAAGCUGGGAUUCCUUGGCCGUGAGGUCUGGGUAAUCUUUUGAAACCUUAUCGUGAUGGGGAUUGACCUUUGUAAUUAUCGGUCAUGAACGAGGAAUACCUAGUAAGUGUGGGUCAUCAACCCACGCUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGGAUGGCUUAGUGAGAUUUUUGGAUUGCCGGGUGAUUGCAGCAAUGCGAACACUUGGCGAGAAAUUGCUCAAACUUGGUCAUCUAGAGGAAGUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.gelatinosum.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.gelatinosum.seq new file mode 100644 index 0000000..3c16027 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.gelatinosum.seq @@ -0,0 +1,2 @@ +>d.16.e.B.gelatinosum +CACCUGGUUGAUCCUGCCAGUGGUAUAUGCUUGUCUCAAGGACUAAGCCAUGCAAGUGUAAGUAUAAGUAAUUUUACGACAAAACUGCGAAUGGCUCGGUAAAACAGCUAUAGUUUCUUCGAUGGUACCUACUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCCAAAACGCGGGGUAACCCGUGGUACCAAUCAGAUAUCAAACCAAUGUGUGGUGAUUCAUGAUUUUUUUUCUGAUCGCACGCAAGUGCGACGCAUCGUUCAAAUUUCUGACCUAUCAACUUUCGAUGGUAAGGUAUUGUCUUACCAUGGUUGUGACGGGUAACGGACCGUGGGUGCGGGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACAGGGAGGUAGUGACAAGAAAUAUCAAUAGGGGGCGUUUAUACGUCUUCUAAUUGGAAUGAGAACAAGGUAAACAGCUUAUCGAGGAUCCAGCAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUGUAAGCGUAUACCAAAGUUGUUGCAGUUAAAACGCUCGUAGUCGGAUUUUGGUGCGCGCCGGGCUGUGCGCGUAAUGCGUGUGGCGCGGGGCGUGCUUUUGUGGAGGGCGGCCGCUCGUGGCUUAACUGUUGCGGGUGUGCCGGCGCCACCGUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCAGGCGUUUGCCGUGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUCGUACCUAUUUUGUUGGUUUGUGAGGGCCGAGUAAUGAUUAAGAGGGACGGUUGGGGGCAUUUGUAUUCCGGCGUCAGAGGUGAAAUUCUUGGAUUGCCGGAAGACAAACCGCUGCGAAAGCGUCUGCCAAGGACGUUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACUAUAAACGAUGAGAACUGGGGAUCGGGCGGGCAUUAUGAUGACCCGUCCGGGACCCUCCGGGAAACCAAAGUGUUUGCUUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUUACCAGGUCCGGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAGCGAGACCUGGGCGUGCUAACUAGGGGCCGUUACCAUUGGUAGCUGUCGCCCCUUCUUAGACGGACUGCGGGCGUCUAGUCCGCGGAAGCUCCAGGCAAUAACAGGUCUGAGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAGCGGACCAACGGGUGAGGAUGCGCGAGAGCGUUUCCCAAUCCCUAAAUCCGCUCGUGCUGGGGAUAGAGGCUUGCAAUUUUCCCUCUUGAACGAGGAAUACCUUGUAAGCGUGGGUCAUCAGCCCGCGCUGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGGUCCGGUGAGGACUUGGGACUGCUGCGAUCGGGGUUCAUUCUCUGGCCGCGGUGGGAACUUGUCCAAACCUUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAAGCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.gibsoni.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.gibsoni.seq new file mode 100644 index 0000000..76f7cfc --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.gibsoni.seq @@ -0,0 +1,2 @@ +>d.16.e.B.gibsoni +NNNNNNNNNNNNNNNNNNNNNNNNNCAGUAGUCAUAUGCUUGUCUUAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAACUUUUAUAUGGUGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAAAUUCGUUUCUACAUGGAUAACCGUGCUAAUUGUAGGGCUAAUACAUGAUCGAGGUCCUUCUGGACUGCGUUUAUUAGACUCGAAACCUUCCCGCUUCGGCGGUUCCCGGUGAUUCAUAAUAAACAGCGAAUCGCAUGGCUUUUGCCGGCGAUAAUUCAUUCAAGUUUCUGACCUAUCAGCUUUGGACGGUAGGGUAUUGGCCUACCGGGGCAGCGACGGGUAACGGGGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUACGGACACCGUGAGGUAGUGACAAGAAAUAACAAUACAGGGCUUUAAGCUUUGUAAUUGGAAUGAUGGGAAUCCAAACCCCUUCCAGAGUAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAUUUGUUGCAGUUAAAAAGCUCGUAGUUGAACUUCUGCCGCCGGGACUUCGUUCCCUUCGGGCUUCGUUUUCUCGGUGGCAUCCCUCUGGUUAAUUUGGGCCUCGGCCCUCUUUUUCCAGUUUUUACUUUGAGAAAAUUAGAGUGUUUCAAGCAGGCUUUUGCCUUGAAUACUUCAGCAUGGAAUAAUAAAGUAGGACUUUGGUUCUAUUUUGUUGGUUUCAGGACCAAAGUAAUGGUUAAUAGGAGCAGUUGGGGGCAUUCGUAUUUAACUGUCAGAGGUGAAAUUCUUAGAUUUGUUAAAGACGAACUACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGCUCGAAGACGAUCAGAUACCGUCGUAGUCCUAACUAUAAACUAUGCCGACUAGAGAUUGGAGGUCGUCAUUUUAAACGACUCCUUCAGCACCUUGAGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGCGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAACCUCACCAGGUCCAGACAUAGUUAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUAGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAACCUGCUAAAUAGCAGCUGAGAAUAAACUUUGUUGUUUCAGCAUUGCUUCUUAGAGGGACUUUGCGGUCAUAAAUCGCAAGGAAGUUUAAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCUGCACGCGCGCUACACUGAUGCAUUCAUCGAGUUUUAUCCUUGCCCGAAAGGGUUAGGUAAUCUUUAGUAUGCAUCGUGAUGGGGAUUGAUUAUUGCAAUUAUUAAUCAUGAACGAGGAAUGCCUAGUAGGCGCGAGUCAUCAGCUCGUGCCGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUCGAGUGAUCCGGUGAAUUAUUCGGACCGUGACGUUUCUAAUUCGUUAGCAACGUCUAGGGAAGUUUUGUGAACCUUAUCACUUAAAGGAAGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.hamifera.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.hamifera.seq new file mode 100644 index 0000000..ee77a35 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.hamifera.seq @@ -0,0 +1,2 @@ +>d.16.e.B.hamifera +CAACCUGGUUGAUCCUGCCAGUGGUAUAUGCUUGUCUCAAGGACUAAGCCAUGCAAGUCUAAGUAUGAGUGAACUGUACAACGAAACUGCGAAUGGCUCGGUAAAACAGCUAUAAUUUCUUCGAUGGUAAUACUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCCGGAACGCCGUGGUACAAAUUGGAUAUACAAACCAAUGUUUGGUGAUUCACAAUUUAUUUUCUGAUCGCACUUAUGUGCGACGCAUCGUUCAAAUUUCCGACCUAUCAACUUUGGAUGGUAAGGUAUUGUCUUACCAUGGUUGUGACGGGUAACGGACCGUGGGUGCGGGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCCAUCCGGACUCCGGGAGGUAGUGACAAGAAAUAGCAAUAGAGGGCCCGAUGGGCUUUCUAAUUGGAAUGAGAACAAGGUAAACAGCUUAUCGAGGAGCCAGCAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUGUAAGCGUAUACCAAAGUUGUUGCAGUUAAAACGCUCGUAGUCGGAGGUUGGCGGGCGGCGCGGGGCGUCCUCACGGACGGUUCUGCGGCGGCCGCCUUUGUGGAUGGGGGCUAGAGCGAUGUUUCAUUACAUUGCACUAGUCGCUGCCACCGUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCGGGCGUUUGCCAUGAGUAAAUUAGCAUGGAGUAAUAGAAUAGGACCUGUGUUCUGUUUUGUUGGUUUGUGAGGCGCGGGUAAUGAUUAAGAGGGACGGUUGGGGGCAUUUGUAUUCCGGCGUCAGAGGUGAAAUUCUUGGAUUGCCGGAAGACAAACAGCUGCGAAAGCGUCUGCCAAGGACGUUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACUAUAAACGAUGAGGACUGGGGAUCGGGCGGGGCUGUUUUUGGCCCGCCCGGCACCCUUCGGGAAACCAAAGUGUUUGCUUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCGGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUCUGUCUGGUUAAUUCCGUUAACGAGCGAGACCUGGGCGUGCUAGCUAGGCGCGGUUACCGAUUUCUGGUAGCCAGGCUUGCCUUCCUAGACGGACUGCGGGCGUCUAGUCCGCGGAAGCUCCAGGCAAUAACAGGUCUGAGAUGCCCUUAGAUGUUCUGGGCCGCACGCGUGCUACACUGAGCGGGUCAACGGGUGAGGAUGGGCGAAAGCUUUUCCUAAUCUCUAAAUCCGCUCGUGCUGGGGAUCGAGGCUUGCAAUUUUCCCUCUUGAACGAGGAAUACCUUGUAAGCGCGGGUCAUCAUCCCGUGCUGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGGUCCGGUGAGGCCUUGGGAGGGCUAGACAGACUGUGUUUCACGGACUGUCUGGCCCGAACUUGGUCAAACCUUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAGAAN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.investiens.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.investiens.seq new file mode 100644 index 0000000..f71fd58 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.investiens.seq @@ -0,0 +1,2 @@ +>d.16.e.B.investiens +NNNNNNNNNNNNNNNNNNNNNNNUAUAUGCUUGUCUAAAGGACUAAGCCAUGCAAGUGUAAGUAUAAGUAAUCUUUACGACGAAACUGCGAAUGGCUCGGUAAAACAGCUAUAGUUUCUUCGAUGGUACCUACUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCCGCAACGCGGGGUAACCCGUGGUACAAAUCAGAUAUCAAACCAAUGUGUGGUGAUUCAUGAUUUUUUUUCUGAUCGAACGCAAGUUCGACGCAUCGUUCAAAUUUCUGACCUAUCAACUUUCGAUGGUAAGGUAUUGUCUUACCAUGGUUGUGACGGGUAACGGACCGUGGGUGCGGGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUAACACAGGGAGGUAGUGACAAGAAAUAUCAAUAGAGGGCGUUUAUACGUCUUCUAAUUGGAAUGAGAACAAGGUAAACAGCUUAUCGAGGAUCCAGCAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUGUAAGCGUAUACCAAAGUUGUUGCAGUUAAAACGCUCGUAGUCGGAUUUUGGCGGGCCCGGUGCUGUGCGCGUAAUGCGUGCGGCGCUUGGGCGCGCUUUUGUGGAGGGCGGCGCGUCGUGGCUUUGCUGUCGCGGUGUGUCGGCGCCACCGUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCAGGCGUUUGCCGUGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUUGGUGUCUAUUUUGUUGGUUUGUGAGGGCCGAGUAAUGAUUAAGAGGGACGGUUGGGGGCAUUUGUAUUCCAGCGUCAGAGGUGAAAUUCUUGGAUUGCUGGAAGACAAACCGCUGCGAAAGCGUCUGCCAAGGACGUUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACUAUAAACGAUGAGAACUGGGGAUCGGGCAGGCAUUACGAUGACCUGUCCGGAACCCUCCGGGAAACCAAAGUGUUUGCUUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUUACCAGGUCCGGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAGCGAGACCUGGGCGUGCUAACUAGGGGCCGUUACCAUUGGUAGCUGCUUGCCCCUUCUUAGACGGACUGCGGGCGUCUAGUCCGCGGAAGCUCCAGGCAAUAACAGGUCUGAGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAGCGGACCAACGGGUUUUAGGAUGCGCGAAAGCGUUUCCCAAUCCCCAAAUCCGCUCGUGCUGGGGAUAGAGGCUUGCAAUUUUCCCUCUUGAACGAGGAAUACCUUGUAAGCGUGGGUCAUCAGCCCGCGCUGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGGUCCGGUGAGGAUUUGGGACUGCUGCGAUCGGAGCGUUUACGCUCUGGCCGCGGUGGGAACUUAUCCGAACCUUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.macrosporum.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.macrosporum.seq new file mode 100644 index 0000000..d4c4c9b --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.macrosporum.seq @@ -0,0 +1,2 @@ +>d.16.e.B.macrosporum +CACCUGGUUGAUCCUGCCAGUGGUAUAUGCUUGUCUCAAGGACUAAGCCAUGCAAGUGUAAGUAUAAGUAAUCUUACGACGAAACUGCGAAUGGCUCGGUAAAACAGUUAUAGUUUCUUCGAUGUUACCUACUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCCAUCACGCGGGGCAACCCGUGGUACGAAUCAGAUAUCAAACCAAUGUAUGGUGAUUCAUGAAUAUUUUUCGGAUCGCACUGUAUGGUGCGACACAUCGUUCAAAUUUCUGACCUAUCAACUUUCGAUGGUAAGGUAUUGUCUUAUCAUGGUUGUGACAGGUGACGGACCGUGGGUGCGGGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAACUUACCCAAUCCUAACACAGGGAGGUAGUGACAAGAAAUAUCAAUAGAGGGCGCAUAUGCGUCUUCUAAUUGGAAUGAGAACACGGUAAACAGCUUAUCGAGGAUCCAGCAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUGUAAGCGUAUACCAAAGUUGUUGCAGUUAAAACGCUCGUAGUCGGAUGUUGGCACGGGCCGGGCUGUGCGCGUCAUGCGUGCGGCCACGGGACGUGCUUUUGUGGAUGGCGGCCGCACGUGGCUUAAUUGUUGCGGGCGUGCCGGCGCCACCAUUUACUGUGAAGAAAUUAGAGUGUUCAAAGCAGGCGUUUGCCGUGAAUACGUUAGCAUGGAAUAAUAGAAUAGGACUCGUUUCUAUUUUGUUGGUUUGUCAGUGGCGAGUAAUGAUUAAGAGGGACGGUUGGGGGCAUCUGUAUUCCGGCGUCAGAGGUGAAAUUCUUGGAUUGCCGGAAGACAAACUGCUGCGAAAGCGUUUGCCAAGGACGUUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACUAUAAACGAUGAGAACUGGGGAUCGGGCGGGCAUUAUGAUGACCCGCCCGGCACCCUCCGGGAAACCAAAGUGUUUGCUUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUUACCAGGUCCGGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAGCGAGACCUGGGCGUGCUAACUAGGGGCGGGUACCCGUGUGGUAGCUGCUGCCCCUUCUUAGACGGACUGCGGGCGUCUAGCCCGCGGAAGCUCCAGGCAAUAACAGGUCUGAGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAGCGGGCCAACGGGUGAGGAUACGCGAGAGCGUUUCCCAAUCCCCAAAUCCGCUCGUGCUGGGGAUAGAGGCUUGCAAUUUUCCCUCUUGAACGAGGAAUACCUUGUAAGCGCGGGUCAUCAGCCCGCGCUGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGGUCCGGUGAGGCUUUGGGACCGCCACGACCGGGGUUUACUCUCUGGCCGCAGUGGAAACUUAUCCAAACCUUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAAGCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.mandrillaris.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.mandrillaris.seq new file mode 100644 index 0000000..2225903 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.mandrillaris.seq @@ -0,0 +1,2 @@ +>d.16.e.B.mandrillaris +NNNNNNNNNNNNNNNNNNNNNNNUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAGCUUUUAUACGGCGAGACUGCGGAUGGCUCAUUAAAUCAGUUAUAGUUUAUUUGAUGGUUCCUUUAUUUUUACUACUUGGAUAACCGUAGUAAUUCUAGAGCUAAUACAUGCCCAAAGUCCCGACUGGGGGUCGCAAGGCUCUCUGGAAGGGAUGUAUUUAUUAGAUAAAAAACCGAUGCAGGGUGGCUUGCUGCCCUGACCCAACGGUGAUUCAUAAUAACUCUAUCGAAUCGCACCAUGGUCCCCUCGUGGGAUCGGCGAUGCUUCAUUCAAAUUUCUGCCCUAUCAACUUUCGAUGGUAGUCGCCGUGCCUACCAUGGUCGUAACGGGUAACGGAGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAAUGGCUACCACUUCUAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCCGACACGGGGAGGUAGUGACAAUAAAUAACAAUACAGGUCUUGCAAAAAGACUUGUAAUUGGAAUGAGUACAAUUUAAAUCCCUUAACGAGUAACAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUCUCGGAGUGUUUGGCAGGGCUGGUCCGCCGAAAUAGGUGAGCACCGUCCUGCCCGCUCCUCUUGUCCGGGUUCUCAUCCCUGCUAUUCACUUAGUGGGGAACCAAAGGUUCUGUUCCCGCCCUCGGGUGGGGCAGGACUGGAGGCCCGGACCAUUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGACAAGUCAAAACUGUCAUUGAAUAUAUUAGCAUGGGAUAAUGGAAUAAGCCUCUCUGCUUAUUUUGUUGGUUUCUAAGUAGGGAGAAAUGAUUGAUAGGGACAGUUGGGGGCAUUAAUAUUUAAUUGUCAGAGGUGAAAUUCUUGGAUUUAUGAAAGAUUAACUUCUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGAUGAUUAGAUACCGUCGUAGUCUUAACCAUAAACGAUGCCGACCAGCGAUUGGGAGACGUUACACAUGCUGCCCAAAAGGCAGCAUGGAGGACUCCCCCAGCAGCUUGUGAGAAAUCAUAAGUCUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCGGACAUAGUAAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAACCUGCUAAAUAGUCAUGCCAAUCCUGCUAUUCAAAACCAGGGGGUGAGCGCGGUGCGGUCGGCUCCAAUCUUCGGGUUGGGGUCGGUUCGUGCCCCUUGCCUUCUGGCGGUUGGAUUGGUAGAAGUACUUCUUAGAGGGACAAUCGGUGAUUAGCCGAGGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAUUAAUUCAACGAGUGCCACACCUUGGCCGAAAGGUCUGGGUAAUCUUGUGAAAUUUAAUCGUGAUGGGGAUAGAUUAUUGUAAUUGUUAAUCUUCAACGAGGAAUUCCUAGUAAGCGCGAGUCAUCAGCUCGCGUUGAUUACGUCCCUGCCCUUUCUACACACCGCCCGUCGCUCCUACCGAUUGAAUGGUCCGGUGAAAUCUUCGGAGCUCGACCUCUCCGCGAUCCGGGCAACUGGGUCGUGAGGUUGGGCAAAGUCGAUUAAAUCUUACCAUUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGNNNNNNNNNNNNNNNNNNNNNNN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.mediterranea.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.mediterranea.seq new file mode 100644 index 0000000..5e88cb9 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.mediterranea.seq @@ -0,0 +1,2 @@ +>d.16.e.B.mediterranea +NAACCUGGUUGAUCCUGCCAGUAGUCAUACGCUCGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAACGCUUUAUACUGUGAACCUGCGGAUGGAUCAUUAUAUCAGUUAUAGUUUAUUUGAUAAUCUCUUACUACUUGGAUAACCGUAGUAAUUCUAGAGCUAAUACAUGCGUAAACACCCAACCUCUGGACGGGUGGUAUUUAUUAGAUUGAAACCAAUAUGCUUCGGCAUUUUUGUGGUGAUUCAUAAUAACUUUGCGGAUCGCAUGGCCUUGAGCCGGCGACAGAUCAUUCAAGUUUCUGCCCUAUCAGCUUUGGAUGGUAGGGUAUUGGCCUACCAUGGCUUUAACGGGUAACGGAGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGACACAGGGAGGUAGUGACAAUAAAUAACAAUGCCGGGCCUUUUUAGGUCUGGCAAUUGGAAUGAGAACAAUUUAAAUCCCUUAUCGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCUGGUGACACGGCGUGGUCGUCUCAAUGAGUCUGUACCGUCGCAUGUGUCGCCAUCCUUGGUUAAAACUUGUCUGGCAUUAGGUUGUCGGGCUUGGGGAUAGCCAUCGUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCAGGCUUAUGCCGUUGAAUACAUUAGCAUGGAAUAAUAAGAUAAGACCCAGGUUCUAUUUUGUUGGUUUGCGUACCUAGGUAAUGAUUAAUAGGGACAGUUGGGGGUAUUUGUAUUCCGUUGUCAGAGGUGAAAUUCUUGGAUUUACGGAAGACAAACUACUGCGAAAGCAUUUACCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGAUGAUUAGAUACCAUCGUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUUGGCGGUCGUUUUUCCGACUCCGUCAGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGAAAUUGACGGAAGGGCACCACCAGGAGUGGGCGUGCGGCUUAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUAAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCCCCGCCUGCUAAAUAGUUGGCGUAAUGAAUUUCAUUGCGUACAUCUUCUUAGAGGGACUUUGCGUGACUAACGCAAGGAAGUUGGGGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCCGCACGCGCGCUACACUGAUGCAUUCAACGAGUUUAUAACCUUGACCGAGAGGCUGGGUAAUCUUUUAAACGUGCAUCGUGAUAGGGAUAGAUUAUUGCAAUUAUUAAUCUUGAACGAGGAAUUCCUAGUAAACGCAGUUCAUCAGACUGCAUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCACCUACCGAUUGAAUGGUCCGGUGAAAUUUCGGGACUGACUUUAGGUUGAUUUAUUUCGACUUAAGGUUGGGAACUUACUUAAACCUUAUCAUUUAGAGGAAGGUGAAGUCGUAACAAGGUUUCCGUAGUGAACCNNNNNNNNNNNNNNNNN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.microti.1.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.microti.1.seq new file mode 100644 index 0000000..341c71c --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.microti.1.seq @@ -0,0 +1,2 @@ +>d.16.e.B.microti.1 +NNNNNNNNAACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUUAAAGAUUAAGCCAUGCAUGUCUUAGUAUAAGCUUUUAUACAGCGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUGUUCGUUUUACAUGGAUAACCGUGGUAAUUCUAGGGCUAAUACAUGCUCGAGGCGCGUAUUUUACGCGUGGCGUUUAUUAGACUUUAACCAACCCCUUUGGGUAAUCGGUGAUUCAUAAUAAAUUAGCGAAUCGCAUGGCUUUGCCGGCGAUGUAUCAUUCAAGUUUCUGACCUAUCAGCUUUGGACGGUAGGGUAUUGGCCUACCGGGGCGACGACGGGUGACGGGGAAUUGGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACAGGGAGGUAGUGACAAGAAAUAACAAUACAGGGCUUAAAGUCUUGUAAUUGGAAUGAUGGGAAUCUAAACCCUUCCCAGAGUAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAGAAGCUCGUAGUUGAAUUUCUGCCUUGUCAUUAAAUUCGCUUCCGAGCGUUUUUUUAUUGACUUGGCAUCUUCUGGAUUUGGUUCCCUUCGGGGUUCUAUUUUCCGGGAUUUACUUUGAGAAAACUAGAGUGUUUCAAACAGGCAUUUGCCUUGAAUACUACAGCAUGGAAUAAUGAAGUAGGACUUUGGUUCUAUUUUGUUGGUUAUUGAGCCAGAGUAAUGGUUAAUAGGAGCAGUUGGGGGCAUUCGUAUUUAACUGUCAGAGGUGAAAUUCUUAGAUUUGUUAAAGACGAACUACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCCUAACCAUAAACUAUGCCGACUAGAGAUUGGAGGUCGUCAGUUUAAACGACUCCUUCAGCACCUUGAGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGUCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGCGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAACCUCACCAGGUCCAGACAUAGAGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAACCUGCUAAAUUAGGAUCUGGUACAAGCUUUGCUGUUCCAGUAUCGCUUCUUAGAGGGACUUUGCGUUCAUAAAACGCAAGGAAGUGUAAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCUGCACGCGCGCUACACUGAUGCAUUCAACGAGUUUUCCUUGGCCGUCGGGUCCGGGUAAUCUUACAGUAUGCAUCGUGAUGGGGAUAGAUUAUUGCAAUUAUUAAUCUUGAACGAGGAAUGCCUAGUAGGCGCGAGUCAUCAGCUCGUGCCGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUCGAGUGAUCCGGUGAAUUAUUCGGACCAAGAAACGUGGAUUCGUCCUUCGUUUUUUGGAAAGUUUUGUGAACCUUAUCACUUAAAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUNNNNN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.microti.2.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.microti.2.seq new file mode 100644 index 0000000..e6f2747 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.microti.2.seq @@ -0,0 +1,2 @@ +>d.16.e.B.microti.2 +NNNNNNNNAACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUUAAAGAUUAAGCCAUGCAUGUCUUAGUAUAAGCUUUUAUACAGCGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUGUUCGUUUUACAUGGAUAACCGUGGUAAUUCUAGGGCUAAUACAUGCUCGAGGCGCGUUUUUCGCGUGGCGUUUAUUAGACUUUAACCAACCCCUUUGGGAAUCGGUGAUUCAUAAUAAAUUAGCGAAUCGCAUGGCUUUGCCGGCGAUGUAUCAUUCAAGUUUCUGACCUAUCAGCUUUGGACGGUAGGGUAUUGGCCUACCGGGGCGACGACGGGUGACGGGGAAUUGGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACAGGGAGGUAGUGACAAGAAAUAACAAUACAGGGCUUAAAGUCUUGUAAUUGGAAUGAUGGGAAUCUAAACCCUUCCCAGAGUAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAGAAGCUCGUAGUUGAAUUUCUGCCUUGUCAUUAAUCUCGCUUCCGAGCGUUUUUUUAUUGGCUUGGCAUCAUCUGGAUUUGGUGCCUUCGGGUACUGUUUCCAGGGUUUACUUUGAGAAAACUAGAGUGUUUCAAACAGGCAUUUGCCUUGAAUACUACAGCAUGGAAUAAUGAAGUAGGACUUUGGUUCUAUUUUGUUGGUUAUUGAACCAGAGUAAUGGUUAAUAGGAGCAGUUGGGGGCAUUCGUAUUUAACUGUCAGAGGUGAAAUUCUUAGAUUUGUUAAAGACGAACUACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCCUAACCAUAAACUAUGCCGACUAGAGAUUGGAGGUCGUCAGUUUAAACGACUCCUUCAGCACCUUGAGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGUCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGCGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAACCUCACCAGGUCCAGACAUAGAGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAACCUGCUAAAUUAGGAUCUGGGACAAGCUUUUGCUGUUCCAGUAUCGCUUCUUAGAGGGACUUUGCGUUCAUAAAGCGCAAGGAAGUGUAAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCUGCACGCGCGCUACACUGAUGCAUUCAACGAGUUUUUCCUUGGCCGUCGGGUCCGGGUAAUCUUACAGUAUGCAUCGUGAUGGGGAUAGAUUAUUGCAAUUAUUAAUCUUGAACGAGGAAUGCCUAGUAGGCGCGAGUCAUCAGCUCGUGCCGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUCGAGUGAUCCGGUGAAUUAUUCGGACCGAGAAACGUGGAUUCGUCCUUCGUUUUUUGGAAAGUUUUGUGAACCUUAUCACUUAAAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUNNNNN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.microti.3.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.microti.3.seq new file mode 100644 index 0000000..21c1754 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.microti.3.seq @@ -0,0 +1,2 @@ +>d.16.e.B.microti.3 +NNNNNNNNAACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUUAAAGAUUAAGCCAUGCAUGUCUUAGUAUAAGCUUUUAUACAGCGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUGUUCGUUUUACAUGGAUAACCGUGGUAAUUCUAGGGCUAAUACAUGCUCGAGGCGCGUUUUACGCGUGGCGUUUAUUAGACUUUAACCAGCCCCUUUGGGUAAUCGGUGAUUCAUAAUAAAUUAGCGAAUCGCAUGGCUUUGCCGGCGAUGUAUCAUUCAAGUUUCUGACCUAUCAGCUUUGGACGGUAGGGUAUUGGCCUACCGGGGCGACGACGGGUGACGGGGAAUUGGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACAGGGAGGUAGUGACAAGAAAUAACAAUACAGGGCUUAAAGUCUUGUAAUUGGAAUGAUGGGAAUCUAAACCCUUCCCAGAGUAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAGAAGCUCGUAGUUGAAUUUCUGCCUUGUCAUUAAUCUCGCUUUCGAGCGUUAUUUUAUUGACUUGGCAUCUUCUGGAUUUGGUAUCCUUAAUUGGUUACUAUCUUCCAGUAUUUACUUUGAGAAAACUAGAGUGUUUCAAACAGGCCAUUUGCCUUGAAUACUACAGCAUGGAAUAAUGAAGUAGGACUUUGGUUCUAUUUUGUUGGUUAUUGAGCCAGAGUAAUGGUUAAUAGGAGCAGUUGGGGGCAUUCGUAUUUAACUGUCAGAGGUGAAAUUCUUAGAUUUGUUAAAGACGAACUACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCCUAACCAUAAACUAUGCCGACUAGAGAUUGGAGGUCGUCAGUUUAAACGACUCCUUCAGCACCUUGAGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGUCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGCGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAACCUCACCAGGUCCAGACAUAGAGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAACCUGCUAAAUUAGGAUCUGGGACAAGCUAUGCUGUUCCAGUAUCGCUUCUUAGAGGGACUUUGCGUUCAUAAAACGCAAGGAAGUGUAAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCUGCACGCGCGCUACACUGAUGCAUUCAACGAGUUUUUCCUUGGCCGUAGGGUCCGGGUAAUCUUACAGUAUGCAUCGUGAUGGGGAUAGAUUAUUGCAAUUAUUAAUCUUGAACGAGGAAUGCCUAGUAGGCGCGAGUCAUCAGCUCGUGCCGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUCGAGUGAUCCGGUGAAUUAUUCGGACUGAGAAACGUGGAUUCGUCCUUCGUUUUUCGGAAAGUUUUGUGAACCUUAUCACUUAAAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUNNNNN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.microti.4.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.microti.4.seq new file mode 100644 index 0000000..e92416b --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.microti.4.seq @@ -0,0 +1,2 @@ +>d.16.e.B.microti.4 +NNNNNNNNAACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUUAAAGAUUAAGCCAUGCAUGUCUUAGUAUAAGCUUUUAUACAGCGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUGUUCGUUUUACAUGGAUAACCGUGGUAAUUCUAGGGCUAAUACAUGCUCGAGGCGCGUUUUCGCGUGGCGUUUAUUAGACUUUAACCAACCCUUUGGGUAAUCGGUGAUUCAUAAUAAAUUAGCGAAUCGCAUGGCUUUGCCGGCGAUGUAUCAUUCAAGUUUCUGACCUAUCAGCUUUGGACGGUAGGGUAUUGGCCUACCGGGGCGACGACGGGUGACGGGGAAUUGGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACAGGGAGGUAGUGACAAGAAAUAACAAUACAGGGCUUAAAGUCUUGUAAUUGGAAUGAUGGGAAUCUAAACCCUUCCCAGAGUAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAGAAGCUCGUAGUUGAAUUUCUGCCUUGUCAUUAAUCUCGCUUCCGAGCGUUUUUUUAUUGGCUUGGCAUCUUCUGGAUUUGGUGCCUUCGGGUACUAUUUUCCAGGAUUUACUUUGAGAAAACUAGAGUGUUUCAAACAGGCAUUCGCCUUGAAUACUACAGCAUGGAAUAAUGAAGUAGGACUUUGGUUCUAUUUUGUUGGUUAUUGAGCCAGAGUAAUGGUUAAUAGGAGCAGUUGGGGGCAUUCGUAUUUAACUGUCAGAGGUGAAAUUCUUAGAUUUGUUAAAGACGAACUACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCCUAACCAUAAACUAUGCCGACUAGAGAUUGGAGGUCGUCAGUUUAAACGACUCCUUCAGCACCUUGAGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGUCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGCGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAACCUCACCAGGUCCAGACAUAGAGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAACCUGCUAAAUUAGGAUCUGGGACAAGCUUUGCUGUUCCAGUAUCGCUUCUUAGAGGGACUUUGCGUUCAUAAAACGCAAGGAAGUGUAAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCUGCACGCGCGCUACACUGAUGCAUUCAACGAGUUUUUCCUUGGCCGUCGGGUCCGGGUAAUCUUACAGUAUGCAUCGUGAUGGGGAUAGAUUAUUGCAAUUAUUAAUCUUGAACGAGGAAUGCCUAGUAGGCGCGAGUCAUCAGCUCGUGCCGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUCGAGUGAUCCGGUGAAUUAUUCGGACCAAGAAACGUGGAUUCGUCCUUCGUUUUUUGGAAAGUUUUGUGAACCUUAUCACUUAAAGGAAGGAGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.microti.5.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.microti.5.seq new file mode 100644 index 0000000..ac524f3 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.microti.5.seq @@ -0,0 +1,2 @@ +>d.16.e.B.microti.5 +NNNNNNNNNNNNNNNNNNNNNCUGCCAGUAGUCAUAUGCUUGUCUUAAAGAUUAAGCCAUGCAUGUCUUAGUAUAAGCUUUUAUACAGCGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUGUUCGUUUUACAUGGAUAACCGUGGUAAUUCUAGGGCUAAUACAUGCUCGAGGCGCGUUUUCGCGUGGCGUUUAUUAGACUUUAACCAACCCUUCGGGUAAUCGGUGAUUCAUAAUAAAUUAGCGAAUCGCAUGGCUUUGCCGGCGAUGUAUCAUUCAAGUUUCUGACCUAUCAGCUUUGGACGGUAGGGUAUUGGCCUACCGGGGCGACGACGGGUGACGGGGAAUUGGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACAGGGAGGUAGUGACAAGAAAUAACAAUACAGGGCUUAAAGUCUUGUAAUUGGAAUGAUGGGAAUCUAAACCCUUCCCAGAGUAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAGAAGCUCGUAGUUGAAUUUCUGCCUUGUCAUUAAUCUCGCUUCCGAGCGUUUUUUUAUUGACUUGGCAUCUUCUGGAUUUGGUGCCUUCGGGUACUAUUUUCCAGGAUUUACUUUGAGAAAACUAGAGUGUUUCAAACAGGCAUUCGCCUUGAAUACUACAGCAUGGAAUAAUGAAGUAGGACUUUGGUUCUAUUUUGUUGGUUAUUGAGCCAGAGUAAUGGUUAAUAGGAGCAGUUGGGGGCAUUCGUAUUUAACUGUCAGAGGUGAAAUUCUUAGAUUUGUUAAAGACGAACUACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCCUAACCAUAAACUAUGCCGACUAGAGAUUGGAGGUCGUCAGUUUAAACGACUCCUUCAGCACCUUGAGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGUCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGCGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAACCUCACCAGGUCCAGACAUAGAGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAACCUGCUAAAUUAGGAUCUGGGACAAGCUUUGCUGUUCCAGUAUCGCUUCUUAGAGGGACUUUGCGUUCAUAAAACGCAAGGAAGUGUAAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCUGCACGCGCGCUACACUGAUGCAUUCAACGAGUUUUUCCUUGGCCGUCGGGUCCGGGUAAUCUUACAGUAUGCAUCGUGAUGGGGAUAGAUUAUUGCAAUUAUUAAUCUUGAACGAGGAAUGCCUAGUAGGCGCGAGUCAUCAGCUCGUGCCGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUCGAGUGAUCCGGUGAAUUAUUCGGACCAAGAAACGUGGAUUCGUCCUUCGUUUUUUGGAAAGUUUUGUGAACCUUAUCACUUAAAGGAAGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.moritziana.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.moritziana.seq new file mode 100644 index 0000000..f694c36 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.moritziana.seq @@ -0,0 +1,2 @@ +>d.16.e.B.moritziana +CACCUGGUUGAUCCUGCCAGUGGUAUAUGCUUGUCUCAAAGACUAAGCCCUGCAAGUGCCUGUAUGAGUGUUUAUAUAACGAAACUGCGAAUGGCUCGGUAAAACAGUAAAAAUUUUUUCGGAGAAAAUACUACUCGGAUAACCGUAGUAAAGCUAGAGCUAAUACGUGCUACAAAAUGAGGCGAGCAAUCGUUCUCGUGGUACAAAAUAGAGAUACAACCCAGUUUUUACUGGUGAUUCAUACUUUUUUCUGAUCACACUUUUAUGUGUGUGACGCUCCGAUCAAAUUUCUGACCUAUCAACUAUGAUGGUAAGGUAGUGGCUUACCAUAGUUGUGACGGGUAACGGACCGUGGGUGCGGGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCGAACUUCGGGAGGUAGUGACAAGAAAUAGCAAUAGGGGGACCAAUGGUCUCUCUAAUUGGAAUGAAAACAAUGUAAACUCCUUAUUGAGGAGCCAGCAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUGUAAGCGUAUACCAAAGUUGUUGCAGUUAAAACGCUCGUAGUCGAACUUUGGCGAUGGUUGCUGAAACUCCGUAAGGAGAUUGAUGUAGCCUCGUCCUUGUGGAUUUUUGGGGGUGUGGUGGUACUUUAUUGUAUUGCUGCAUUUCCGCCACUGUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCAAGCGAUUGCCCUGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACCUGGUUCUGUUUUAUUGGUUUGUCUGUAUCAGGUAAUGAUUAACAGGGACGGUCGGGGGCAUUUGUAUUCCAGCGUUAGAGGUGAAAUUCUUGGAUCGUUGGAAGACAAACAGCUGCCGAAAGCGUCUGCCAAGGACGUUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACUGUAAACUAUGAGGCCUGGGGAUCGGGCGUGGCCUAUUGGUACGUUCGGCACCCUCCGGGAAACCAAAGCUUUUGCUUUCUGGGGGGAGUAUGGUCGCAAGUCUGAAACUUAAAGGAAUUGACGGAAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGCAAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUCUGUCUGGUUAAUUCCGUUAACGAGCGAGACCUGGGCGUGCUAAAUAGAAAAUGCUAUUAAACUGCGGUAGCAUCGAAAAUUUAAUCUUCUUAGACGGACUGUAGGCGUAUAGUCUAUGGAAGCUCCAGGCAAUAACAGGUCUGAGAUGCCCUUAGAUGUUCUGGGCCGCACGCGUGCUACACUGAAUGGCUCAACGGGUGAGGUAGUGCGAAAGCAUGACCCAAUCUCUAAAUCCAUUCGUGCUGGGGAUAGAAGCUUGCAAUUAUCCUUCUUGAACGAGGAAUACCUUGUAAGCGCGAGUCAUCAUCUCGUGCUGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGGUCCGGUGAGGCCUUGGGAGAGCUGGGCGAAUUAGUGUUUAUUCACGAAUUUCCUGGUUUAAACUUGGUCAAACCUUACUACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAAGCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.ostreae.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.ostreae.seq new file mode 100644 index 0000000..e9dcbc1 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.ostreae.seq @@ -0,0 +1,2 @@ +>d.16.e.B.ostreae +NNNNNGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCCAAGUAUAAACACGUUUGUACUGUGAAACUGCAGAUGGCUCAUUAUAACAGUUAUAGUUUAUUUGACAUUGAACUGUUACACGGAUAACCGUAGUAACCUAGGGCUAAUACGUGACAAACCCUGCCUCGGCGGGAGUGCAUAUUAGCUGAAAACCAACUUUGGUUGAAUAAUAAUAUUUGUCGGAUCGCGUUGGCUUCGCCAGCGACAUGUCAUUCAAGUUUCUGACCUAUCAGCUUGACGGUAGGGUAUUGGCCUACCGUGGCUUUGACGGGUAACGGGGAAUGCGGGUUCGAUUCCGGAGAGGCAGCCUGAGAAACGGCUACCACAUCCACGGGAGGCAGCAGGUGCGCAAAUUACCCAAUUCUGACUCAGAGAGGUAGUGACAAGAAAUAACGAUAUGCGGCCAACUGGUUGCUUAUCCGGAAUGAGAACAAUGUAAAAACCUUAUCGAAUUCCAGCGGAGGGCAAGCCUGGUGCCAGCAGCCGCGGUAAUACCAGCUCCGCUAGCGUAUACUAAAGUUGUUGCUGUUAAAACGCUCGUAGUUGGAUAUCUGCCCCCGGGCCGGCCCGGUCGUCCGCGACCGCACACACGUGCAGAGCGGCCGCCCGGGGGCAUAAUUCAGGAACGCCGGUCUGGCCAUUUAAUUGGUCGGGCCGCUGGUCCUGAUCCUUUACUUUGAGAAAAUUAAAGUGCUCAAAGCAGGCUCGCGCCUGAAUGCAUUAGCAUGGAAUAAUAAGACACGACUUCGGCGCCGCCUCGGCGGUUGUUUUGUCGGUUUUGAGCUGGAGUAAUGAUUGAUAGAAACAAUUGGGGGUGCUAGUAUCGCCGGGCCAGAGGUAAAAUUCUUUAAUUCCGGUGAGACUAACUUAUGCGAAAGCAUUCACCAAGCGUGUUUUCUUUAAUCAAGAACUAAAGUUGGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCCCAACCAUAAACGAUGUCAACUAAGCAUUGGGCUAUCAAACUUCCUCAGCACUUUUCGAGAAAUCAAAGUUUUCGGACUCAGGGGGAAGUAUGCUCGCAAGAGUGAAACUUAAAGGAAUUGACGGAAGGGCACCACAAGUUGUGGAGCCUGCGGCUUAAUUUGAUUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUAAGGAUUGACAGACUAAAGUUCUUUCUUGAUUCUAUGCAUGGUGGUGCAUGGCCGUUCUUAGUCCCUAGGGUGACCCCUCUGGUUAAUUCCGAUAACGGACGAGACCCCACCCAUCUAACUAGCCGGCGCUAACCCGGCGCUCGGCGCCAGUUAGCGGGGUGCAGCAUUGCGCGCCCGGCUUCUUAGAGGGACUAUCUGUGUCUCCAGCAGAUGGAAGAUUGGGGCAAUAACAGGUCAGGAUGCCCUUAGAUGCUCUGGGCUGCACGCGCGCUACAAUGGUGCGUUCAACGAGUUUGACCCGGCUUGACAAGGCCGGGUAAUCUUCAACGCGCACCCAAGUUGGGAUAGAUGAUUGCAAUUGUUCAUCUUGAACAAGGAAUAUCUAGUAAACGCAAGUCAUCAACUUGCAUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUUCUACCGAUUGAAUAAUGAGGUGAAUUAGGUGGAUAAGAGCGCUCCGCGUUCUUAGAAGCUUCGUGAACCUUGUUAUUUAGAGGAAGGAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUNN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.pacifica.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.pacifica.seq new file mode 100644 index 0000000..86d81a3 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.pacifica.seq @@ -0,0 +1,2 @@ +>d.16.e.B.pacifica +NAACCUGGUUGAUCCUGCCAGUAGUCAUACGCUCGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAACGCUUUAUACUGUGAAACUGCGAAUGGCUCAUUAUAUCAGUUAUAGUUUAUUUGAUAAUCUCUUACUACAUGGAUAACCGUAGUAAUUCUAGAGCUAAUACAUGCGUAAACACCCAACUGUUCGCGGACGGGUGGUAUUUAUUAGAUUGAAACCAAUAAGCUUCGGCUUUUUUGUGGUGAUUCAUAAUAACUUUGCGGAUCGCAUGGCCUCGAGCCGGCGACAGAUCAUUCAAGUUUCUGCCCUAUCAGCUUUGGAUGGUAGGGUAUUGGCCUACCAUGGCUUUAACGGGUAACGGAGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGACACAGGGAGGUAGUGACAAUAAAUAACAAUGCCGGGCCUUUUUAGGUCUGGCAAUUGGAAUGAGAACAAUUUAAAUCCCUUAUCGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCUGGUGAGUUCGUUUGGCCGGCCGUAAAGGUCUGUGCCGAAAUGUUAUUCGCCAUCCUUGGUGUAAUCUUGUCCGCCAUUAAGUUGUGUGGGCUUGAGGAUGCCAUCGUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCAGGCUUAUGCCGUUGAAUACAUUAGCAUGGAAUAAUAAGAUAGGACCCUGGUACUAUUUUGUUGGUUUGCGUACCUAGGUAAUGAUUAAUAGGGACAGUUGGGGGUAUUUGUAUUCCGUUGUCAGAGGUGAAAUUCUUGGAUUUACGGAAGACAAACUACUGCGAAAGCAUUUACCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGAUGAUUAGAUACCAUCGUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUUGGCGGUCGUUUUUCUGACUCCGCCAGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGAAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUAAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCCCCGCCUGCUAAAUAGUUGGCGCGAAUGAAUUUCAUUCCGUACAUCUUCUUAGAGGGACUUUGCGUGACUAACGCAAGGAAGUUGGGGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAUGCAUUCAACGAGUUUAUAACCUUGCUCGAGAGGGCUGGGUAAUCUUUUAAACGUGCAUCGUGAUAGGGAUAGAUUAUUGCAAUUAUUAAUCUUGAACGAGGAAUUCCUAGUAAACGCAGUUCAUCAGACUGCAUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCACCUACCGAUUGAAUGGUCCGGUGAAAUUUCGGGACUGAUCGUUUGGUGGUUCAUUCUGCCUUACGAUCGGGAACUUACUUAAACCUUAUCAUUUAGAGGAAGGUGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAANNN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.plumatellae.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.plumatellae.seq new file mode 100644 index 0000000..8e89a0b --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.plumatellae.seq @@ -0,0 +1,2 @@ +>d.16.e.B.plumatellae +CACCAGGUUGAUUCUGCCUGACGUAUGCGCUUGUCUUGAAGAUUUAGCCAUGCAAGCCAGUGACCGUAAGGAACGGCAGACAGCUCAGUAAUACAGUUAUAAUUUACUCGUAGGAUAUGGAUAACCAUGGAAAACUAUGGCUAAAACAUAGGGAAAAUACCGUCACAGGGAAUUUUGAGGUACUUGAUACGAUUAAGUUUCUGACCUAUUAGCUAGAUGGUAAGGUAAAGGCUUACCAUGGCUGUGAUGGGUAACGGGGGAUUAACGUUCGAUUCCGGAGAGGGAGCCUGAGAAAUAGCUCCCACGUCUAAGGAUGGCAGCAGGCGCGAAACUUACCCAAUUCCUUAUCGGGAGAGGUAGUGAAGAGACGUGGAAUAUAAUUUAGCGAGGGCAUAUUAAAUGGCAGCCUGUAAACUGGAGGGCAAGCCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAGUAGCGCAUAUAACUAUUGUUGCUGUUAAAACGUCCGUAGUAGAUUAUGCUGUUACUAUGACAAAAAUGUAUAUCUCAAAUGAAAUAUAUAGCAUAGUACAAAGUAAAGAUAGGAACAGAUGAUGGCAGCAGUAUUUAAUAGUUAGAGGUGAAAAUCGAAGACCUAUUAAGGACUAUCAGAAGCGAAAGCGGCUGUCAAGGAUGUCUCCGUUUAUCAAGGACUCAAGCUGGAGUAUCGAAGAUGAUUAGAUACCGUCGUAGUUCCAGCUGUAAACCAUGCCAACUAGGUGAGGCCAUUAGGCUACGCCUUAGGAGAAAUCAAAGUUUUUGGGCUCAGGGGAUAGUACGAAAGCAAUUUUGAAACUUAAAGAGAUUGACGGAAGGAUACCACAAGGAUUGGAUUGUGCGGCUUAAUUUGACUCGACGCGGGACAACUUACCAGGGCCGAAUGUCUAUGAGAUUGGCGAUUUGAGAGAAUUCCCGAGAUUAGACAAAGGGUGGUGCAUGGCCGUUUUCAACACGUGGGGUGACCUGUCAGGUUAAUUCCGAUAACGCGUGAGGCCCUAAAUGCAACAGUGUUGUAUGACGGACAGUGCAAACUGUAGGAAGGAGGGCGAUAACAGGUCAGUGAUGCCCCCAGAUGUUCUGGGCUGCACGCGCAAUACAAUAUAUGAAAUAGAAUAGAGUGUGAAAACACAUCAUUAAAUUCAUAUGUACCAGGGAUAAGCGCUUGUAAAUGCGUUUUGAACAUGGAAUUCCUAGUAAUCGCAGGUCAUUAUGCUGCGAUGAAUGUGUCCCUGUUCUUCGUACACACCGCCCGUCACUAUCUUAGAUGAAUGUAUAGGUGAAAUGGCUGGACGAAAGAAAGGCAGUUGAACCUGUGCAAUUAGAUAAGAUAUAAGUCGUAACAAGGCUGCUAUAGGAGAACCUGUGGCAGGAUCAAUAA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.rodhaini.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.rodhaini.seq new file mode 100644 index 0000000..0f910b0 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.rodhaini.seq @@ -0,0 +1,2 @@ +>d.16.e.B.rodhaini +NNNNNNNNAACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUUAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAGCUUUUAUACAGCGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUGUUUUUAUUACAUGGAUAACCGUGGUAAUUCUAGGGCUAAUACAUGCAUGUGCGUUUACGCAGCGUUUAUUAGACUAAACCAUCCCCUUUGGGUACCGGUGAUUCAUAAUAAAUUAGCGAAUCGCAUGGCUUUGCCGGCGAUGUAUCAUUCAAGUUUCUGACCUAUCAGCUUUGGACGGUAGGGUAUUGGCCUACCGGGGCGACGACGGGUAACGGGGAAUUGGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACAGGGAGGUAGUGACAAGAAAUAACAAUACAGGGCUCAAAGCUUUGUAAUUGGAAUGAUGGGAAUCUAAACCCUUCCCAGAGUAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAGAAGCUCGUAGUUGAAUUUCUGCCUCGUCGUUUAUGCUCGCUUCCAAGCGUUUGUAAUUGACUUGGCAUCUUUGUGGAUUAGUGCGCAAGCAUUUUUCCACUAUUUACUUUGAGAAAACUAGAGUGUUUCAAACAGGCAAUUGCCUUGAAUACUACAGCAUGGAAUAAUAAAGUAGGACUUUGGUUCUAUUUUGUUGGUUUUUGAGCCAUAGUAAUGGUUAAUAGGAGCAGUAGGGGGCAUUCGUAUUUAACUGUCAGAGGUGAAAUUCUUAGAUUUGUUAAAGACGAACUACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCCUAACCAUAAACUAUGCCGACUAGAGAUUGGAGGUCGUCAGUUUAAACGACUCCUUCAGCACCUUGAGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGUCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGCGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAACCUCACCAGGUCCAGACAUAGAAAUGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAACCUGCUAAAUUAGGAUAUGGGACUACAUUUCAGUCUCAUUAUCGCUUCUUAGAGGGACUUUGCGUUCAUAAAACGCAAGGAAGUGUAAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCUGCACGCGCGCUACACUGAUGCAUUCAACGAGUUUUCCUUGGCCGGAAGGUCCGGGUAAUCUUACAGUAUGCAUCGUGAUGGGGAUAGAUUAUUGCAAUUAUUAAUCUUGAACGAGGAAUGCCUAGUAGGCGCGAGUCAUCAGCUCGUGCCGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUCGAGUGAUCCGGUGAAUUAUUCGGACUGAAGAACUUAGAUUCGUCUAAAGUUUUUUGGGAAGUUUUGUGAACCUUAUCACUUAAAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCNNNN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.albicans.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.albicans.seq new file mode 100644 index 0000000..32b6e40 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.albicans.seq @@ -0,0 +1,2 @@ +>d.16.e.C.albicans +UAUCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAGCAAUUUAUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUCGUUUAUUUGAUAGUACCUUACUACUUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCUUAAAAUCCCGACUGUUUGGAAGGGAUGUAUUUAUUAGAUAAAAAAUCAAUGCCUUCGGGCUCUUUGAUGAUUCAUAAUAACUUUUCGAAUCGCAUGGCCUUGUGCUGGCGAUGGUUCAUUCAAAUUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGUGGCCUACCAUGGUUUCAACGGGUAACGGGGAAUAAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCCGACACGGGGAGGUAGUGACAAUAAAUAACGAUACAGGGCCCUUUUGGGUCUUGUAAUUGGAAUGAGUACAAUGUAAAUACCUUAACGAGGAACAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAAAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGAACCUUGGGCUUGGCUGGCCGGUCCAUCUUUUUGAUGCGUACUGGACCCAGCCGAGCCUUUCCUUCUGGGUAGCCAUUUAUGGCGAACCAGGACUUUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCCUUUGCUCGAAUAUAUUAGCAUGGAAUAAUAGAAUAGGACGUUAUGGUUCUAUUUUGUUGGUUUCUAGGACCAUCGUAAUGAUUAAUAGGGACGGUCGGGGGUAUCAGUAUUCAGUUGUCAGAGGUGAAAUUCUUGGAUUUACUGAAGACUAACUACUGCGAAAGCAUUUACCAAGGACGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGAUGAUCAGAUACCGUCGUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUCGGUUGUUGUUCUUUUAUUGACGCAAUCGGCACCUUACGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUCACCAGGUCCAGACACAAUAAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUUUGUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGCUUAAUUGCGAUAACGAACGAGACCUUAACCUACUAAAUAGUGCUGCUAGCAUUUGCUGGUAUAGUCACUUCUUAGAGGGACUAUCGACUUCAAGUCGAUGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGACGUUCUGGGCCGCACGCGCGCUACACUGACGGAGCCAGCGAGUAUAAGCCUUGGCCGAGAGGUCUGGGAAAUCUUGUGAAACUCCGUCGUGCUGGGGAUAGAGCAUUGUAAUUGUUGCUCUUCAACGAGGAAUUCCUAGUAAGCGCAAGUCAUCAGCUUGCGUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGAAUGGCUUAGUGAGGCCUCCGGAUUGGUUUAGGAAAGGGGGCAACCUCAUUCUGGAACCGAGAAGCUGGUCAAACUUGGUCAUUUAGAGGAAGUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.citrina.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.citrina.seq new file mode 100644 index 0000000..69158d5 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.citrina.seq @@ -0,0 +1,2 @@ +>d.16.e.C.citrina +AACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGACUAAGCCAUGCAUGUCUAAGUAUAAAUGUUAUACAGUGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUAAUCAAAAUUACAUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCUGGUUAGCCUGACUUUUGAGGAAGGGCUGUAUUUAUUAGAUAACAAAUCAAUAUUCCCCGUGUCUAUUGUGAUGACUCAUAAUAACUGAUCGAAUCGCAUGGGCUUUGCCCGCGAUACAUCAUUCAAGUUUCUGCCCCAUCAGCUUUCGAUGGUAGUGUAUUGGACUACCAUGGCUUUCACGGGUAACGGAGGAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGACUCAGGGAGGUAGUGACAAGAAAUAACGGACCGAAGCCUAUGUUUCGGGAUUGCAAUGAGUAGAAUUUAAACCCCUUUACGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCUGGGAGGGCGUCGAAGUGAGCUCGUUGCUUGUACUGAGAUGCCCUUCCAUCCUACUGUUAACGUUUCUGAUAUUCAUUUAUUGGUCUCGGGCUCAGUUAUUUUACCUUGAGAAAAUUAGAGUGUUCCAGGCAGGCUUGCGCCGGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUUUAGUCUCCUUUGUUGGUUUGAGGGACUGAAGUAAUGAUUAAUAGGGAUAGUUGGGGGCAUUAGUAUUUAAUUGUCAGAGGUGAAAUUCUCGGAUUUGUUAAAGACUAACUUAUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCAAAGACGAUCAGAUACCGUCCUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUCGGAGGCGCGCCUUAUCCGCCUUCGGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCUUGCGGCUCAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAGCCUACUAACUAGUCGACCCGUUGCUUAGCGGGCACGACUUCUUAGAGGGACUUUGUGACUAAACACAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCCGCACGCGUGCUACACUGACGCAUACAGCGAGUACGUCCCAGCUCCGUGAGGCAGCUGGUAAUCAGCAAUAUGCGUCGUGAUGGGGAUAGAUCUUUGGAAUUAUAGAUCUUGAACGAGGAAUUCCUAGUAAGCGCAAGUCAUUACCUUGCGCUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUUCGAGUGAUCCGGUGAACCUUUUGGACUGCGUGGCCUUUAGGCUGUGCGGAAAAUCAAGUAAACCAUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAUGA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.crispus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.crispus.seq new file mode 100644 index 0000000..b680862 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.crispus.seq @@ -0,0 +1,2 @@ +>d.16.e.C.crispus +CAACCUGGUUGAUCCUGCCAGUGGUAUAUGCUUGUCUCAAGGACUAAGCCAUGCAAGUGUAAGUAUGAGUGAAUUGUACAACGAAACUGCGAAUGGCUCGGUAAAACAGCUAUAGUUUCUUCGAUGGUAACUACUACUUGGAUACCCGUAGUAAUUCUAGAGCUAAUACAAGCCUUAAAGCGACAUUUAUGUCGUGGUAUAAAUUGGAGAUACAAACCAAUGUUUGGUGAUUCACAAUUUCUUUUCUGAUCGCACGUUAGUGCGACGCAUCGUUCAAAUUUCUGACCUAUCAACUUUGGAUGGUAAGGUAUUGUCUUACCAUGGUUGUGACGAGUGACGGAUCGUGGGUGCGAGACUCCGGAGAGGGAGCCUGAGAGACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCGGAUACCGGGAGGUAGUGACAAGAAAUAGCAAUAGAGGGCCCAACGGGUUUUCUAAUUGGAAUGAGAACAAGGUAAACAGCUUAUCGAGGAGCCAGCAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUGUAAGCGUAUACCAAAGUUGUUGCAGUUAAAACGCUCGUAGUCGGAGGUUGGCGGGCAGUCCAGGGCGUCCUCGCGGACGGAUCUGGAGUUGGCCGCCUUUGUGGAUGGGGGCCUAGUGGAGCUUCACUGCUUCAUUGUGGUCGCUGCCACCGUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCAGGCGUUUGCCAUGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACCUGUUUCCUGUUUUGUUGGUUUGUGAGGAUCGGGUAAUGAUUAAGAGGGACGGUUGGGGGCAUUUGUAUUCCGGCGUCAGAGGUGAAAUUCUUGGAUUGGCGGAAGACAAACGGCUGCGAAAGCGUCUGCCAAGGACGUUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACUAUAAACGAUGAGGACUGGGGAUCGGGGAGGACUGUAUUUUGGCCUACCCGGCACCCUUCGGGAAACCAAAGUGUUUGCUUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCGGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUCUGUCUGGUUAAUUCCGUUAACGAGCGAGACCUGGGCGUGCUAGCUAGGCGCCAGUACCGUUUUUUGGUACUGAGGCUUGCCUUCCUAGACGGACUGUGGGCGUCUAGUCCACGGAAGCUCCAGGCAAUAACAGGUCUGAGAUGCCCUUAGAUGUUCUGGGCCGCACGCGUGCUACACUGAGCGGGUCAACGGGUGAGGAUGUGCGAGAGCGCUUCCUAAUCUCUAAAUCCGCUCGUGCUGGGGAUCGAGGCUUGCAACUUUCCCUCUUGAACGAGGAACACCUUGUAAGCGUGGGUCAUCAUCCCGCGCUGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGGUCCGGUGAGGCCUUGGGAGGGAUGGAUGGAUUGUGUUUCACAAACUAUCUGGCCCAAACUUGGUCAAACCUUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGACAGAAUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.lunata.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.lunata.seq new file mode 100644 index 0000000..275fcb0 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.lunata.seq @@ -0,0 +1,2 @@ +>d.16.e.C.lunata +CACCAGGUUGAUUCUGCCUGACGUGGACACUUGCCUUGAAGAGUAAGCCAUGCAAGCUUGUGAAUAAAUCCUGAAACAGUGAACGGCUCAGUAGAACACAUUUCAUCUACCCAAGUUAAAAAUAACCAUGGGAAACUAUGGCUAAAUAUAAUUUGGAUGAGAGUGUGACCUAUCAGCUAGUAGGUACGGUAAGAGCGUACCUAGGCUAUGACGGGUAACGGGGAAUCAGAGUUCGAUUCCGGAGAGGGAGCCUGAGAGAUGGCUACUACGUCCAAGGAUGGCAGCAGGCGCGAAACUUACCCAAUGAACAUUGAGGUAGUUACGAGGCGUACCUAUGUAAUAUAAUUAUAUAGGGAUGAGGUAUGAUUUCAAAUCAUGCACGACAUACUGGAGGGCAAGGCUGGUGCCAGCAGCUGCGGUAAUUCCAGCUCCAGUAGUGUCUAUGUAAAUUGUUGCGGUUAAAACGUGCGUAGUCUGAUUUGCGAGAUCUAAAGUAAAGAUGCUUUUAUCUAAAAGUAGAAUAUUUUAGAGAUCAAAAAUCUUGAGACAGAGGAGAGGUAACGAAAUUCGAUGGCGAGAGGUGAAAAUUGAUGACCCAUCGAGGAGAAACAGAGGCGAAAGCGGUUACCAGAAGCUGUUCUGACGAUCAAGCACGUGAGCAGGAGUAUCGAAGGCGAUUAGACACCGUCGUAGUUCCUUGCAGUAAACGAUGCCCACACUGAUGUGCUUAACGCAUGUCAGACGCAAAAGUUAAAGUGAGGCUCCGGGGAUAGUACGGUCGCAAGAUUGAAACUUGAAGAAAUUGACGGAAGGACACCACCAGGAGUGGAGUGUGCGGGUUAAUUUGACUCAACGCGGGAAAACUUACCAGUACAGAUUACUAUCGUAUGAAGGAAUACCUGAUGAUGUAAUACGUGGUGCAUGGCCGUUCUUAACACGUGAAGUGAUUCCUCGUGUCAAAUCAGCUAACGCGUGAGAGGCGAGUCUUAUUUUAUAAAUAAGAGACGGCAUAGGCAACUAUGAGGAAGCAACGCCCAAUAACAGGUCCGUGAUGCCCGUAGAUGUUCUGGGCUCCACGCGCACUACAAUUAUAAAUACUAUUUUGUAAUUUAUAAUCAGUAGGGAUUGUUUGUUGUAAAACUUACAUGAACGUGGAAUUCCUAGUAUAUAGAUGUAAGCAACGUCUAUUGAAUAUUGUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCUAAGAUGGUUAUUAGGGGGAAGCUGAUAUAUUAUAUCAGAAGACUUCUGGUAACUAGAUUGGAUGUAAGUCGUAACAUGGUUGCAGUAGGUGAACCUGCCGCAGAUCAGUAG diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.neoformans.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.neoformans.seq new file mode 100644 index 0000000..0bf8af5 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.neoformans.seq @@ -0,0 +1,2 @@ +>d.16.e.C.neoformans +UACCUGGUUGAUUCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAACGAAUUCAUACUGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUAGUUUAUUUGAUGGUAUCUUGCUACAUGGAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCUGAAAAGCCCCGACUUCUGGAAGGGGUGUAUUUAUUAGAUAAAAAACCAAUGGGUUUCGGCCCUCUAUGGUGAAUCAUAAUAACUUCUCGAAUCGCAUGGCCUUGUGCCGGCGAUGCUUCAUUCAAAUAUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGAGGCCUACCAUGGUAUCAACGGGUAACGGGGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCCGACACGGGGAGGUAGUGACAAUAAAUAACAAUACAGGGCUCUUUUGGGCCUUGUAAUUGGAAUGAGUACAAUUUAAAUCCCUUAACGAGGAACAACUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAGUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUCGAACUUCAGGUCUGGCGAGGCGGUCCUCCUCACGGAGUGCACUGUCUUGCUGGACCUUACCUCCUGGUGGUCCUGUAUGCUCUUUACUGGGUGUGCAGGGGAACCAGGAAUUUUACCUUGAAAAAAUUAGAGUGUUCAAAGCAGGCAAUCGCCCGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACGUGCGGUUCUAUUUUGUUGGUUUCUAGGAUCGCCGUAAUGAUUAAUAGGGACGGUCGGGGGCAUUGGUAUUCCGUUGCUAGAGGUGAAAUUCUUAGAUUGACGGAAGACCAACAACUGCGAAAGCAUUUGCCAAGGACGUUUUCAUUGAUCAAGAACGAAGGUUAGGGGAUCAAAAACGAUUAGAUACCGUUGUAGUCUUAACAGUAAACGAUGCCGACUAGGGAUCGGCCCACGUCAAUCUCUGACUGGGUCGGCACCUUACGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUCACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGAUAACGAACGAGACCUUAACCUGCUAAAUAGUCAGGCCGGCUUUGGCUGGUCGUUUGACUUCUUAGAGGGACUGUCGGCGUCUAGUCGACGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGACUGAGCCAGCGAGUCUUACCGCCUUGGCCGAGAGGCCUGGGUAAUCUUGUGAAACUCAGUCGUGCUGGGGAUAGAGCAUUGCAAUUAUUGCUCUUCAACGAGGAAUACCUAGUAAGCGUGAGUCACCAGCUCGCGUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGAAUGGCUUAGUGAGAUCUCCGGAUUGGCGUUGGGGAGCCGGCAACGGCACCCCUUGGCUGAGAAGCUGAUCAAACUUGGUCAUUUAGAGGAAGUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAGUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.officinalis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.officinalis.seq new file mode 100644 index 0000000..6c217f5 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.officinalis.seq @@ -0,0 +1,2 @@ +>d.16.e.C.officinalis +CAACCUGGUUGAUCCUGCCAGUGGUAUAUGCUUGUCUCAAAGACUAAGCCAUGCAAGUCUAAGUAUGAGGAAUAAUUAAGACGAAACUGCGAAUGGCUCGGUAAAACAGCAAUAAUUUCUUCGGUGAUUUUUACUACUCGGAUAAUCGUAGUAAUUCUAGAGCUAAUACGUGCCACAAUGCUUGGGUUUACUCAGGCAGUGCCGUUUAGAUAACAACACCAACAUAUGGUGAUUCAUAAUCGUCUUUCGGAUCGCUGGCGAAAGCCGGCGACGCACCGUUCAAAUUUCUGACCUAUCAACUUUCGAUGGUAAGGUAGUGUCUUACCAUGGUGGCAACGGGUAACGGACCGUGGGUGCGGGACUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCAGACUCUGGGAGGUAGUGACAAGAAAUAUCAAUAGGGGACCCAUAAAGUCUUCUAAUUGGAAUGAGAACAAGCUAAACAGCUUAUCGAGAAUCCAGCAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUGUAAGCGUAUACCAAAGUUGUUGCAGUUAAAACGCUCGUAGUCGGACUUUGGCAAUUCCGGAUGUGUGCGCGUCGUGCGCGCACUUUGCAGGGGUUGCUUUUGUGGGCAUGCGUGGGAUGAUGCGACUUUAUUGUCGAACGUCCCUACGCAACCACCUUUUACUGUGAGAAAAUUAGAGUGUUCAAAGCAGGCAAUUGCCGUGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUCGGUCUUAUUUUGUUGGUUUGUUAGGGCUGAGUAAUGAUUAAGAGGGACAGUUGGGGGCAUUUGUAUUCAGGCGCUAGAGGUGAAAUUCUUAGAUUGCUGGAAGACAAACUGCUGCGAAAGCGUCUGCCAAGGAUGUUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACUAUAAACGAUGAGGACUGGGGAUCGGGCGAGGAAUAUCGAUGACCCGCCCGGCACCCUCCGGGAAACCAAAGUGUUUGCUUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUUACCAGGUCAGGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAGCGAGACCUGGGCGUGCUAAAUAGGGGCUACUACCAUUUUGGUAGUACGUUUUCCCCUUCUUAGACGGACUGUGGGCGUCUAGUCCACGGAAGCUCCAGGCAAUAACAGGUCUGAGAUGCCCUUAGAUGUUCUGGGCCGCACGCGUGCUACACUGAGUGGAUCAGCGGGUCAGGUUGCACGAAAGUGUUUCCUAAUCUUUAAAUCCGCUCGUGAUGGGGAUUGACGGUUGCAAUUUUCCGUCAUGAACGAGGAAUACCUUGUAAGCGCGGGUCAUCAUCCCGCGCUGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGGUCCGGUGAGGCUUUGGGAUUGCGAUGGAAAGAGCGUCUCGCUCGUUCUGUCGUGAGAACUCAGUCGAACCUUAUCAUUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAAGC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.paradoxa.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.paradoxa.seq new file mode 100644 index 0000000..bb1658f --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.paradoxa.seq @@ -0,0 +1,2 @@ +>d.16.e.C.paradoxa +AACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAACUAUUUUAUACUGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUAGUUUAUUUGAUGGUACCUUACUACUUGGAUAACCGUAGUAAUUCUAGAGCUAAUACAUGCAACAAAUCCCGACUUCUGGAAGGGAUGUAUUUAUUAGAUAAAAAACCAACACCGGGCAACCGGAUCCCUUGGUGAUUCAUAAUAACUUCUCGAAUCGCAUGGCUUUACGCCGGCGAUGCUUCAUUCAAAUUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGAGGCCUACCAUGGUAGUAACGGGUAACGGAGAAUUAGGGUUCGAUUCCGGAGAGGGCGCCUGAGAGAUGGCGACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCGCAACUCGCGGAGGUAGUGACAAUAAAUAACAAUACGGGGCUUUUCAAGUCUCGUAAUUGGAAUGAGAACAAUUUAAAUCCCUUAUCGAGGAUCCAUUGGAGGGAAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUCGGAUUUCGGGGCGGGGCAGUCGGUCUGCCUAAUAGGUGUGUACUGGCUGUACCCGUCCUUCCUUCCGGGGAUGGGUGCUGCUCUUAACUGAGUGGCAUUCAGACACGGAUCUUUUACUUUGAGUAAAUUGGAGUGUUUAAAGCAGGCCUACGCUCUGAACAUUAUUAGCAUGGAAUAAUAAAAUAGGACCCUGGUUCUAUUUUGUUGGUUUCUAGGAUUGGGGUAAUGAUUAAUAGGGAUAGUUGGGGGCAUUCAUAUUCCGUUGUCAGAGGUGAAAUUCUUGGAUUUACGGAAGAUGAACUACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUGAUCAAGAACGAAAGUUAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUAACCAUAAACGAUGCCGACUUACGAUCAGCAGGUGUUAAUUUAACGACCCUGUUGGCAGUAUAUGAGAAAUCAAAGUUUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCGGACAUAGUAAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAACCUACUAAAUAGUUACACGAACUUCUAGUUCGUGGUCAACUUCUUAGAGGGACUAUUUGUGUCUAAUGAAUGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGACGAAUUCAACGAGUUUUUCCUUGACCGAUAGGUCUGGGUAAUCUUUGAAACUUCGUCGUGAUGGGGAUAGAUCAUUGCAAUUAUUGAUCUUCAACGAGGAAUUCCUAGUAAGCGUGAGUCAUCAGCUCGCGUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAAUCGGUCCGGUGAAAUCUUCGGAUCGUGGCCAUGUACCUGGUCUCCAGGAACAAGGUCGCGAGAAGUUGAUUAAACCUUAUCAUUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAAGC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.rubrum.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.rubrum.seq new file mode 100644 index 0000000..2b1cbde --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.rubrum.seq @@ -0,0 +1,2 @@ +>d.16.e.C.rubrum +CACCCUGGUUGAUCCUGCCAGUGGUAUAUGCUUGUCUCAAGGACUAAGCCAUGCAAGUCUAAGUAUGAGUGAAUUGUACAACGAAACUGCGAAUGGCUCGGUAAAACAGCUAUAGUUUCUUCGAUGGUAAACUACUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAAUACGUGCCAUACGGCGAGGUUUUACCUCGUGGUACUAAUUGGAGAUACAAACCAAUGUUUGGUGAUUCACACUUAUUUUUCUGAUUGCACAUUUUUUGUGCGACGCAUCGUUCAAAUUUCUGACCUAUCAACUUUGGAUGGUAAGGUAUUGUCUUACCAUGGUUUUGACGGGUAACGGACCGUGGGUGCGGGACUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCGGACACCGGGAGGUAGUGACAAGAAAUAGCAAUAGAGGGCCCAAUGGGUUUUCUAAUUGGAAUGAGAACACGGUAAACAUCUUAUCGAGGAGCCAGCAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUGUAAGCGUAUACCAAAGUUGUUGCAGUUAAAACGCUCGUAGUCGGACGUUGGCGGGCGCCUCGAGUCGGCCUCACGGUCGAUCUUGUUGGCGGCCGCCUUUGUGGAGGGGGGCUUAGGUCGGUGCUUUAUUGUCACUCCUUUGUCGCUGCCACCGUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCGGGCGUUUGCCAUGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACCUGGUCCUGUUUUGUUGGUUUGUGAGUAUCAGGUAAUGAUUAAGAGGGACGGUUGGGGGCAUUUGUAUUCCGGCGUCAGAGGUGAAAUUCUUGGAUUGCCGGAAGACAAACAGCUGCGAAAGCGUCUGCCAAGGACGUUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACCAUAAACUAUGAGGACUGGGGAUCGGGCGUGGCUAUUUGGUACGCUCGGCACCCUUCGGGAAACCAAAGUAUUUGCUUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCAGGACAUAGUAAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUCUGUCUGGUUAAUUCCGUUAACGAGCGAGACUUGGGCGUGCUAGCUAGGCGCUGUUACCAUUUCCGGUAGCGAGGCGGCCUUCCUAGACGGACUGCGGGCGUCUAGUCCGCGGAAGCUCCAGGCAAUAACAGGUCUGAGAUGCCCUUAGAUGUUCUGGGCCGCACGCGUGCUACACUGAGCGGGUCAACGGGUGAGGAUGUGCGAAAGCAUUUCCCAAUCUCUAAAUCCGCUCGUGAUGGGGAUAGAGGCUUGCAACUUUCCCUCUUGAACGAGGAAUACCUUGUAAGCGCGGGUCAUCAUCCCGCGCUGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGGUCCGGUGAGGCCUUGGGAGGUCUGCAUGUCCUGUGUUUCACUUGUGUGCAGGUUGAACUUGGUCAAACCUUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAGAA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.D.melanogaster.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.D.melanogaster.seq new file mode 100644 index 0000000..658da2a --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.D.melanogaster.seq @@ -0,0 +1,2 @@ +>d.16.e.D.melanogaster +AUUCUGGUUGAUCCUGCCAGUAGUUAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUACACACGAAUUAAAAGUGAAACCGCAAAAGGCUCAUUAUAUCAGUUAUGGUUCCUUAGAUCGUUAACAGUUACUUGGAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCAAUUAAAACAUGAACCUUAUGGGACGUGUGCUUUUAUUAGGCUAAAACCAAGCGAUCGCAAGAUCGUUAUAUUGGUUGAACUCUAGAUAACAUGCAGAUCGUAUGGUCUUGUACCGACGACAGAUCUUUCAAAUGUCUGCCCUAUCAACUUUUGAUGGUAGUAUCUAGGACUACCAUGGUUGCAACGGGUAACGGGGAAUCAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCACUCCCAGCUCGGGGAGGUAGUGACGAAAAAUAACAAUACAGGACUCAUAUCCGAGGCCCUGUAAUUGGAAUGAGUACACUUUAAAUCCUUUAACAAGGACCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCGGUUAAAACGUUCGUAGUUGAACUUGUGCUUCAUACGGGUAGUACAACUUACAAUUGUGGUUAGUACUAUACCUUUAUGUAUGUAAGCGUAUUACCGGUGGAGUUCUUAUAUGUGAUUAAAUACUUGUAUUUUUUCAUAUGUUCCUCCUAUUUAAAAACCUGCAUUAGUGCUCUUAAACGAGUGUUAUUGUGGGCCGGUACUAUUACUUUGAACAAAUUAGAGUGCUUAAAGCAGGCUUCAAAUGCCUGAAUAUUCUGUGCAUGGGAUAAUGAAAUAAGACCUCUGUUCUGCUUUCAUUGGUUUUCAGAUCAAGAGGUAAUGAUUAAUAGAAGCAGUUUGGGGGCAUUAGUAUUACGACGCGAGAGGUGAAAUUCUUGGACCGUCGUAAGACUAACUUAAGCGAAAGCAUUUGCCAAAGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGAGGUUCGAAGGCGAUCAGAUACCGCCCUAGUUCUAACCAUAAACGAUGCCAGCUAGCAAUUGGGUGUAGCUACUUUUAUGGCUCUCUCAGUCGCUUCCGGGAAACCAAAGCUUUUUGGGCUCCGGGGGAAGUAUGGUUGCAAAGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUUACCAGGUCGAACAUAAGUGUGUAAGACAGAUUGAUAGCUCUUUCUCGAAUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUCGUGGAGUGAUUUGUCUGGUUAAUUCCGAUAACGAACGAGACUCAAAUAUAUUAAAUAGAUAUCUUCAGGAUUAUGGUGCUGAAGCUUAUGUAGCCUUCAUUCAUGUUGGCAGUAAAAUGCUUAUUGUGUUUGAAUGUGUUUAUGUAAGUGGAGCCGUACCUGUUGGUUUGUCCCAUUAUAAGGACACUAGCUUCUUAAAUGGACAAAUUGCGUCUAGCAAUAAUGAGAUUGAGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCUGCACGCGCGCUACAAUGAAAGUAUCAACGUGUAUUUCCUAGACCGAGAGGUCCGGGUAAACCGCUGAACCACUUUCAUGCUUGGGAUUGUGAACUGAAACUGUUCACGAUGAACUUGGAAUUCCCAGUAAGUGUGAGUCAUUAACUCGCAUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGAAUUAUUUAGUGAGGUCUCCGGACGUGAUCACUGUGACGCCUUGCGUGUUACGGUUGUUUCGCAAAAGUUGACCGAACUUGAUUAUUUAGAGGAAGUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.aediculatus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.aediculatus.seq new file mode 100644 index 0000000..dcf55c6 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.aediculatus.seq @@ -0,0 +1,2 @@ +>d.16.e.E.aediculatus +AAUCUGGUUGAUCCUGCCAGUAGUCAUACGCUUGUCUCAAGGAUUAAGCCAUGCAUGUCUAAGUAUAAAGGAUUUAUAAUGAAACUGCAAAUGGCUCAUUCAAACAGUUAUAGUUUAUUUGAUAUUCAAGCUAAUAUUCUUAUUAGUUAAAUGGAUAACCGUAGUAAUUCUAGAGCUAAUACAUGCGUUACGGGGAACUUUACGGGACCCCAGCGUUUAUUAGAUUUAAACCAAUAUUCCGCAAGGUCUACUGAGAUGAUUCAUGAUAACUGAUCGAAUUGCUGGAACUCUAGCAAUAAAUCAUGUAGGUUUCUGCUUCCCAUCAGCUUGAUGGUAGUGUAUUGGACAACCAUGGCAUUCACGGGCUAUCGGGGGAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAUAAACGGCUACCACUUCUACGGAAGGCAGCAGGCGCGAAAAUUAUCCAAUCCUGAUUCAGGGAGGUAGUGAAAGAAAUAAUGAACUAGGAUUUAUCCUGGGAUCACAAUGGGCUUGAUUUGCAAACACUUAGCGAGGAACAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGAGUAUAUAAACGUUCCUGCAGUUAUUCGAUGCUCGUAGUUGGAUUUCUGAGGUUGAGACGGGAGGGUGGCUAUGGCCAUCGCCCGACUCUUUCCUCAUCCACCUGUUUGCGAAGUCCGGGAUUGAUUUCUCGGCUUCGGGCGCAGUAUCUUACCAUUUCAAUAUUCGUAGUCUUCAUCGAUUAUGUUGUUUCUUUGAGCAAAUUAUAGUGUUUCAGGCAGGCGUGCGCCGGAAUACAUUAGCAUGGUAUAAACGAAUUGGACCGUGUGCCCGUAACUGGGCUUCUCCUUAUUGUUGGUUUGAAGGACACGGAGAUGGUUAAUAGGGACAGCGUUUAUUUCACAAGGAGGCAUUAGUAUUUAAUUUCCAGAGGUGAAAUUCUUUGAAAUAUUAAAGACUAACUUAUGCGAAAGCAUCGUUUGCCAAUGAUGUUUUCAUUAAUCAUUGAACGAAAGUUAGGGGAUCAAAGACGAUCAGAUACCGUCCUAGUCUUAACCAUAAACGUUGCCGACUAGGGAUCGGAGGGCGUGCACAAUCCGCCUUCGGCACCUUACGAGAAAUCAAAGUCUUUUGGGUUCUGUGGGUAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCUUGCGGCUCAAUUUGACUCAACACGGGAAAUCUUACCAGGUCCAGACAUAGCGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUAUUUUGGUGGUGCAUGGCCGUUCUUAGUUCGUGGAGUGAUUCGUCUGGUUAAUUCCGUUAAACGAACGAGACCUCAGCCUGCUAAAUAGUUGCUCGCCUUUUCUAUAAGACUUGACAACUUCUUAGAGGGACUUUGUGUGCAACCACAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCCGCACGCGUGCUACACUGAUACGUACAACGAGGUAUAUGUACUUGUACAUCAAUGCUGCUCCGAAAUAGACGAGCUUAAUCUUAUAAAUACGUAUCGUGCUGCGGAUAGAUCGUUGAAAUUAUGAAUCUUGAAGGUGGAAUUCCUAGUAAGCGCACGUCACUAACGUGCGUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCAAUUUCGAGUGAUCUGGUGAACCUCUUUGGACUGUCGAGCAAUCGCGAAAUUAGAGUGAACCUGACUACUUAGCAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAAUCUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.bieneusi.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.bieneusi.seq new file mode 100644 index 0000000..2b84de0 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.bieneusi.seq @@ -0,0 +1,2 @@ +>d.16.e.E.bieneusi +CACCAGGUUGAUUCUGCCUGACGUAGAUGCUAGUCUCUGAGAUUAAGCCAUGCAUGUCAGUGAAGCCUUACGGUGGAACGGCGAACGGCUCAGUAAUGUUGCGGUAAUUUGGUCUCUGUGUGUAAACUAACCACGGUAACCUGUGGCUAAAAGCGGAGAAUAAGGCGCAACCCUAUCAGCUUGUUGGUAGUGUAAAGGACUACCAAGGCCAUGACGGGUAACGGGAAAUCAGGGUUUGAUUCCGGAGAGGGAGCCUGAGAGAUGGCUCCCACGUCCAAGGACGGCAGCAGGCGCGAAACUUGUCCACUCCUUACGGGGGAGACAGUCAUGAGACGUGAGUAUAAGACCUGAGUGUAAAGACCUUAGGGUGAAGCAAUUGGAGGGCAAGCUUUGGUGCCAGCAGCCGCGGUAACUCCAACUCCAAGAGUGUCUAUGGUGGAUGCUGCAGUUAAAGGGUCCGUAGUCGUGAAUGCAAUUAAAUGUCGUUGUUCAAUAGCGAUGAGUUUGCUAAUGUUUGCGGAACGGAUAGGGAGUGUAGUAUAGACUGGCGAAGAAUGAAAUCUCAAGACCCAGUUUGGACUAACGGAGGCGAAGGCGACACUCUUAGACGUAUCUUAGGAUCAAGGACGAAGGCAGGAGUAUCGAAAGUGAUUAGACACCGCUGUAGUUCCUGCAGUAAACUAUGCCGACAGCCUGUGUGUGAGAAUACGUGGGCGGGAGAAAUCUUAGUGUUCGGGCUCUGGGGAUAGUACGCUCGCAAGGGUGAAACUUAAAGCGAAAUUGACGGAAGGACACUACCAGGAGUGGAUUGUGCUGCUUAAUUUAACUCAACGCGGGAAAACUUACCAGGGUCAAGUCAUUCGUUGAUSGAAUACGUGAGAAUGGCAGGAGUGGUGCAUGGCCGUUGGAAAUUGAUGGGGCGACCUUUAGCUUAAAUGCUUAAACCAGUGAGACCUCCUUGACAGGUGUUCUGUAACACAGGAGGGUGGAGGCUAUAACAGGUCCGUGAUGCCCUUAGAUAUCCUGGGCAGCAAGCGCAAUACAAUAUCUCUUCAGUAGACAAAGUGAUUUGAGAUGAGUAGGAUCUACGUUUGUAAAUACGUAGUGAAUAAGGAAUUCCUAGUAACGGUGCCUCAUCAAGGCAUGGUGAAUGUGUCCCUGUUCUUUGUACACACCGCCCGUCACUAUUUCAGAUGGUCAUAGGGAUGAAGAGCUUCGGCUCUGAAUAUCUAUGGCUAGAUAAAGUACAAGUCGUAACAAGGUUUCAGUUGGAGAACCAGCUGAAGGAUCAUUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.cuniculi.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.cuniculi.seq new file mode 100644 index 0000000..74a3bfa --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.cuniculi.seq @@ -0,0 +1,2 @@ +>d.16.e.E.cuniculi +CACCAGGUUGAUUCUGCCUGACGGAUGCUAUUCUCUGGGGCUAAGCCAUGCAUGCUUGUGAACUCUUUGUGGGGGAUUAGCGGACGGCUCAGUGAUAGCACGAUGAUUUGUUUGCGGGAUGAGCAGUAGCUGCGGGAAACUGCAGAUAGUGGUCUGCCCCUGUGGGGUUGGCAAGUAAGUUGUGGGCCUAUCAGCUGGUAGUUAGGGUAAUGGCCUAACUAGGCGCAGACGGGAUACGGGGGAUCAGGGUUUGGUUCCGGAGAGGGAGCCUGAGAGAUGGCUACUACGUCCAAGGAUGGCAGCAGGCGCGAAACUUGCCUAAUCCUUUGGGGAGGCGGUUAUGAGAAGUGAUGUGUGUGCGAGUGCAAAGGGGUCGCAUGUGAUUGGAGGGCAAGUCGGGUGCCAGCAGCCGCGGUAAUACCUGCUCCAAUAGUGUCUAUGGUGGAUGCUGCAGUUAAAAUGUCCGUAGUCUGUUGUGUAUGUCUUUGUGUGUGAUGUUUGUGGUUGUGUGUGGAUGUAGUGAUGUGUGUGGCAGAGGACGAGGGGCACUGGAUAGUUGGGCGAGAGGUGAAAUGCGAAGACCCUGACUGGACGAGCGGAAGCGAAGGCUGUGCUCUUGGACUAAUGUUGCGAUGAAGGACGAAGGCUAGAGGAUCGAAAUCGAUUAGAUACCGUUUUAGUUCUAGCAGUAAACGAUGCCGACUGGACGGGACAGUGUGUGUUGUCCAUGAGAAAUCUUGAGUAUGCGGGUUCUGGGGAUAGUAUGCUCGCAAGAGUGAAACUUGAAGAGAUUGACGGAAGGACACCACAAGGAGUGGAGUGUGCGGCUUAAUUUGACUCAACGCGGGGCAACUUACCGGCUCUGAAGGAUGCCUGUGAGUGCAUGGCAUGAGGCAUGCGGCGGUGGUGCAUGGCCGUUUUAAAUGGAUGGCGUGAGCUUUGUCUUAAGUUGCGUAAGAUGUGAGACCCUUUGACGGUGUUCUACGGAGCAAGGAGGGGAUGGAAAAGAACAGGUCCGUUAUGCCCUGAGAUGAGGCGGGCUGCACGCGCAUACGAUAGAUGGCGCUUCUGCCUGCUGUGAGGGAUGAAGCUGUGUAAGGGGCUUCUGAACGUGGAAUUCCUAGUAAUAGCGGCUGACGAAGCUGCUUUGAAUGUGUCCCUGUCCUUUGUACACACCGCCCGUCGCUAUCUAAGAUGACGCACUGGACGAAGAUCGGAAGGUCUGAGUCCUGAGUGUUAGAUAAGAUAUAAGUCGUAACAUGGCUGCUGUUGGAGAACCAUUAGCAGGAUCAUAA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.hellem.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.hellem.seq new file mode 100644 index 0000000..f6afe21 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.hellem.seq @@ -0,0 +1,2 @@ +>d.16.e.E.hellem +CACCAGGUUGAUUCUGCCUGACGUGGAUGCUAUUCUCUGGGGCUAAGCCAUGCAUGUUUAUGAAGCCUUUAUGGGGGAUUGACGGACGGCUCAGUGAUAGUACGAUGAUUUGAUUGGGUGCCUGGAUGUAACUGUGGGAAACUGCAGGUAAGUUCUGGGUGUGGUAGUUUUUAGCUACUGCGUACCGAGUAAGUUGUAGGCCUAUCAGCUGGUAGUUAGGGUAAUGGCCUAACUAGGCGGAGACGGGAGACGGGGGAUCAGGGUUUGAUUCCGGAGAGGGAGCCUGAGAGAUGGCUACUACGUCCAAGGAUGGCAGCAGGCGCGAAACUUGCCUAAUCCUUAUUGGGGAGGCGGUUAUGAGAAGUAAGAUGUUUAGCAAGUAUAAAUUUGUUGUGAUUUACUGGAGGGCAAGUCGGGUGCCAGCAGCCGCGGUAAUACCUGCUCCAGUAGUGUCUAUGGUGAAUGCUGCAGUUAAAAUGUCCGUAGUUGUUUGUAUGUCUUUUGUGUGAUGUUUAUAGUUUUUAGUGGAUGUAGUUUGGUUGUAGCAGAGGACGAGGGGCACUGGAUAGUUGGGCGAGGGGUGAAAUACGAAGACCCUGACUGGACGAAGAGAAGCGAAGGCUGUGUUCUUGGACUUUUGUGGUGAUGAAGGACGAAGGCUAGAGGAUCGAAAUCGAUUAGAUACCGUUUUAGUUCUAGCAGUAAACGAUGCCGACUGGACGGGACUGUUUUAGUGUUGUCCGAGAGAAAUCUUAAGUAUGUGGGUUCUGGGGAUAGUAUGCUCGCAAGAGUGAAACUUGAAGAGAUUGACGGAAGGACACCACAAGGAGUGGAGUGUGCGGCUUAAUUUGACUCAACGCGGGGCAACUUACCGGUUCUGAAGUGAGUGUGAGAGUGUUUUUACAUGAUGCUUACGGCGGUGGUGCAUGGCCGUUUUAAAUGGAUGGCGUGGGCUUUGGAUUAAGUUACGUAAGAUGUGAGACCCUUUUUGACUGUGCUCUAUGGGGCAAGGAAGGAAUGGAACAGAACAGGUCCGUUAUGCCCUGAGAUGAAGCGGGCGGCACGCGCACUACGAUAGAUGCCUAUGUGGGCUACUGUGAGGGAUGAAGCUGUGUAAUGGGCUUCUGAACGUGGAAUUCCUAGUAAGAAUGAUUGAACAAGUUAUUUUGAAUGUGUCCCUGUCCUUUGUACACACCGCCCGUCGCUAUCUAAGAUGACGCAGUGGACGAAGAUUGAGAGGUCUGAGUCUUUCGUGUUAGAUAAGAUAUAAGUCGUAACAUGGCUGCUGUUGGAGAACCAUUAGCAGGAUCAUAA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.histolytica.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.histolytica.seq new file mode 100644 index 0000000..ad17f45 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.histolytica.seq @@ -0,0 +1,2 @@ +>d.16.e.E.histolytica +UAUCUGGUUGAUCCUGCCAGUAUUAUAUGCUGAUGUUAAAGAUUAAGCCAUGCAUGUGUAAGUAUAAAGACCAAGUAGGAUGAAACUGCGGACGGCUCAUUAUAACAGUAAUAGUUUCUUUGGUUAGUAAAAUACAAGGAUAGCUUUGUGAAUGAUAAAGAUAAUACUUGAGACGAUCCAGUUUGUAUUAGUACAAAAUGGCCAAUUCAUUCAAUGAAUUGAGAAAUGACAUUCUAAGUGAGUUAGGAUGCCACGACAAUUGUAGAACACACAGUGUUUAACAAGUAACCAAUGAGAAUUUCUGAUCUAUCAAUCAGUUGGUAGUAUCGAGGACUACCAAGAUUAUAACGGAUAACGAGGAAUUGGGGUUCGACAUCGGAGAGGGAGCUUUACAGAUGGCUACCACUUCUAAGGAAGGCAGCAGGCSCGUAAAUUACCCACUUUCGAAUUGAAGAGGUAGUGACGACACAUAACUCUAGAGUUGAGUAAAAUCAAUUCUUGAAGGAAUGAGUAGGAGGUAAAUUCUCCUACGAAAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGUGUAUAUUAAAGUUGCUGUGAUUAAAACGCUCGUAGUUGAAUUAAAAUGUGGUUUUAUACAUUUUGAAGACUUUAUGUAAGUAAAGUUUCUAGAAAUGUUAAAUUAAAAUCAAAGAAGGAAACAAUUCAAGUAAUUGAGUUGUUAUUACUUUGAAUAAAAUAAGGUGUUUAAAGCAAAACAUUAUGUUAAUGAAUAUUCAAGCAUGGGACAAUGCUGAGGGGAUGUCAAUAAGACAUUUCGAGAGAAGGAUUAAAAGGAACAAUUGGGGUGAUUCAGAAAAUAACGGGAGAGGUGAAAAUCCAUGAUCGCUAUAAGAUGCACGAGAGCGAAAGCAUUUCACUCAACUGUGUCCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCCUAACUAUAAACGAUGUCAACCAAGGAUUGGAUGAAAUUCAGAUGUACAAAGAUAGAGAAGCAUUGUUUCUAGAUCUGAGUAUAUCAAUAUUACCUUGUUCAGAACUUAAAGAGAAAUCUUGAGUUUAUGGACUUCAGGGGGAGUAUGGUCACAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACACCAGGAGUGGAGCCUGCGCUUAAUUUGACUCAACACGGGAAAACUUACCAAGACCGAACAGUAGAAGGAAUGACAGAUUAAGAGUUCUUUCAUGAUUUAUUGGGUAGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCAGGUUAAUUCCGGUAACGAACGAGACUGAAACCUAUUAAUUAGUUUUCUGCCUAUAAGACAGAAAUGUUCGCAAGAACAGGUGCGUAAGUACCACUUCUUAAAGGGACACAUUUCAAUUGUCCUAUUUUAAUUGUAGUUAUCUAAUUUCGGUUAGACCUCUUUUAACGUGGGAAAAAGAAAAAGGAAGCAUUCAGCAAUAACAGGUCUGUGAUGCCCUUAGACAUCUUGGGCCGCACSCSCGCUACAAUGGAGUUACUAGAGAGUAUUUUAUCAUUUACACCUUAUUUAUUAGGCUUUGUCUAAUAAUUAAGGAUAGUAAGUGGUGUACCGAGAUUGAAAUAGUUAAGGAAAACUCAAAAGAACGUACAUGACAGGGAUAAAUGAUUGGAAUUAUUUGUUUUGAACGAGGAAUUCCUUGUAAUAUCGAGUCAUUAACUCGAGAUGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAAUAAAGAGGUGAAAUUCUAGGAUUCUGUCUUAUAGAUAGAAAAAUGGAUUUAAAUCUCCUUAUUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.mobilis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.mobilis.seq new file mode 100644 index 0000000..ca7e6aa --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.mobilis.seq @@ -0,0 +1,2 @@ +>d.16.e.E.mobilis +AACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGACUAAGCCAUGCAUGUCUAAGUAUAAAUGUUAUACAGUGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUAAUCGAAUUUACAUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCUGGUUAGCCUGACUUUUAGGAAGGGCUGUAUUUAUUAGAUAACAAACCAAUAUUCCUCGUGUCUAUUGUGACGACUCAUAAUAACUGAUCGAAUCGCAUGGACUUUGUCCGCGAUACAUCAUUCAAGUUUCUGCCCCAUCAGCUUUCGAUGGUAGUGUAUUGGACUACCAUGGCUUUAACGGGUAACGGAGGAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGACUCAGGGAGGUAGUGACAAGAAAUAACGGACCGAAGCCUAUGUUUCGGGAUUGCAAUGAGUAGAAUUUAAACCCCUUUGCGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCUGAGAGGGCUCCAAUGUCCGCUGAUGCGUGUGCAGCGGAGCCCUCUCAUCCUUCUGUUAACGUUUCUUGGUAUUCAGUUACUGGUUUCGGGCUCAGAUAUUUUACCUUGAGAAAAUUAGAGUGUUUCAGGCAGGCUUGCGCCGGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUUUAGUCUCCUUUGUUGGUUUGAGGGACUGAAGUAAUGAUUAAUAGGGAUAGUUGGGGGCAUUAGUAUUUAAUUGUCAGAGGUGAAAUUCUCGGAUUUGUUAAAGACUAACUUAUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCAAAGACGAUCAGAUACCGUCCUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUCGGAGGCGCGUAUUGUCCGCCUUCGGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCUUGCGGCUCAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAGCCUACUAACUAGUCGAGCCAAUCCCGAUUGGCCCCGACUUCUUAGAGGGACUUUGUGAUUAAACACAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCCGCACGCGUGCUACACUGACGCAUACAGCGAGUACGUCCCAGCUCCGCGAGGCAGCUGGUAAUCAGCAAUAUGCGUCGUGAUGGGGAUAGAUCUUUGGAAUUAUAGAUCUUGAACGAGGAAUUCCUAGUAAGCGCAAGUCAUUACCUUGCGCUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUUCGAGUGAUCCGGUGAACCUUUUGGACUGCGGACAUCCUCGUGGUGUUUGCGGAAAAUCAAGUAAACCAUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAUGA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.schubergi.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.schubergi.seq new file mode 100644 index 0000000..69b8094 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.schubergi.seq @@ -0,0 +1,2 @@ +>d.16.e.E.schubergi +CACCAGGUUGAUUCUGCCUGACGUAGACGCUAGUCUCUGAGAUUAAGCCAUGCAUGUCUAUGGAACAAGGACGAACAGCUCAGUAAAACUGCGAUGAUUCAGUCUGUCUGUCAAGAUAACCACGCGAAAGUGUGGCUAAGAGGGGACAGAACAAGACGCAGGACUAUCAGUUAGUUGGUAGUGUAAUGGACUACCAAGACGGUGACGGUUGACGGGGAAUGAGGGUUCUAUACCGGAGAGGGAGCCUGAGAGAUAGCUCCCACGUCCAAGGACGGCAGCAGGCGCGAAAAUUGCCCACUGUUUGGAGGAGGCAGUUAUGAGACGUGAGAAAGAGUGCUUGUAAAGAGAAGCAGGAGAAUUGGAGGGCAAGUUUGGUGCCAGCAGCCGCGGUAAUACCGACUCCAAGAGUGUGUAUGAGAGAUGCUGCAGUUAAAAAGUCCGUAGUCGUGGAGACGGAAAGAGAGGCGGAGCCUCUUUGAGAUGCUCUGGAGAAGCCAACAGGGGGCACAGUAUACCAGGGCGAGAGAUGAAAUGCCAAGACCCCUGGUGGACUGAGCGAGGCGAAAGCGGUGCUCUUGUGGGUGUUCGGUGAUCAAGGACGAAGGCUGGAGGAUCGAAAGUGAUUAGAUACCGCUGUAGUUCCAGCAGUAAAAGAUGCCGACAUGCUCGGUGGCAACACGGGGCAGGGAGAAAUCUUAGAGUUCGGGCUCUGGGGAUAGUAUGCUCGCAAGGGUGAAAAUUAAAGAAAUUGACGGAGCUACACCACAAGGAGUGGAUUGUGCGGCUUAAUUUGACUCAACGCGAGGAAGCUUACCAGGGCCAAGUGCUGUGGAGAAAGGAGCAGUACAGAAGUGGUGCAUGGUCGUUGGAAAUUGAUGGGAUGACUUUGGCCUUAAAUGGCUGAAUGAGUGAGAUCUUUGGACAUGUUCCCACGGAACAGGAAGGGGAGGCUAUAACAGAUCAGAGAUGCCCUUAGAUGCCCUGGGCUGCACGCGCAAUACAAUAGCACGUAGACGUAGAGAACAACACGUGCUGAGGUGGACUGUGCUCUGCAAGGGGCACACGAAAGAGGAAUUCCUAGUAAGCGCCCAUCACCAGUGGGCGUUGAAUCAGUCCCUGUAGCUUGUACACACCGUCCGUCACUAUCUCAGAUGUUUUUCGGGAUGAAGAGUCCAGGCUCUGAAUAACGGAAAGUAGAUAAGAUGUAAGUCGUAGCAAGGUUGCGGUCGGUGAACCAUUAGCAGGAUCAUAA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.Encephalitozoon.sp.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.Encephalitozoon.sp.seq new file mode 100644 index 0000000..a4c4989 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.Encephalitozoon.sp.seq @@ -0,0 +1,2 @@ +>d.16.e.Encephalitozoon.sp +CACCAGGUUGAUUCUGCCUGACGUGGAUGCUGUUCUCUGGGACUAAGCCAUGCAUGUUGAUGAACCUUGUGGGGGAUUGACGGACGGCUCAGUGAUAGUACGAUGAUUUGGUUGGCGGGAGAGCUGUAACUGCGGGAAACUGCAGGUAGGGGGCUAGGAGUGUUUUUGACACGAGCCAAGUAAGCUGUAGGCCUAUCAGCUGGUAGUUAGGGUAAUGGCCUAACUAGGCGGAGACGGGAGACGGGGGAUCGGGGUUUGAUUCCGGAGAGGGAGCCUGAGAGAUGGCUACUACGUCCAAGGAUGGCAGCAGGCGCGAAACUUGCCUAAUCCUUUGGGGAGGCGGUUAUGAGAAGUGAGUUUUUUUCGAGUGUAAAGGAGUCGAGAUUGAUUGGAGGGCAAGUCGCGUGCCAGCAGCCGCGGUAAUACCUGCUCCAAUAGUGUCUAUGGUGAAUGCUGCAGUUAAAAAGUCCGUAGUCUUUUGUAUGUCUUUGUUUGGGGGAUUAUGUCCUGAUGUGGAUGUAAGAGGUUUGGCAGAGGACGAGGGGCACCGGAUAGUUGGGCGAGGGGUGAAAUACGAAGACCCUGACUGGACGGACAGAAGCGAAGGCUGUGCUCUUGGACUUAUGUGACGAUGAAGGACGAAGGCUAGAGGAUCGAAAUCGAUUAGAUACCGUUUUAGUUCUAGCAGUAAACGAUGCCGACUGGACGGGACUAUAUAGUGUUGUGCAUGAGAAAUCUUGAGUAUGUGGGUUCUGGGGAUAGUAUGCUCGCAAGAGUGAAACUUGAAGAGAUUGACGGAAGGACACCACAAGGAGUGGAGUGUGCGGCUUAAUUUGACUCAACGCGGGGCAACUUACCGGUUCUGAAGCGGGCAGGAGAACGAGGACGGGAUGCGUGCGGCGGUGGUGCAUGGCCGUUUGAAAUGGAUGGCGUGAGCUUUGGAUUAAGUUGCGUAAGAUGUGAGACCCUUUGACAGUGCUCUUUGGGGCAAGGGAGGAAUGGAACAGAACAGGUCCGUUAUGCCCUGAGAUGAAGCGGGCGGCACGCGCACUACGAUAGAUGGCGAGGGAGCCUGCUGUGAGGGAUGAAGCUGUGUAAUGGGCUUCUGAACGUGGAAUUCCUAGUAAUAACGAUUGAACAAGUUGUUUUGAAUGGGUCCCUGUCCUUUGUACACACCGCCCGUCGCUAUCCAAGAUGACGCAGUGGACGAAGAUUGGAAGGUCUGAGUCCUUCGUGUUAGAUAAGAUAUAAGUCGUAACAUGGCUGCUGUUGGAGAACCAUUAGCAGGAUCAUAA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.F.x.ananassa.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.F.x.ananassa.seq new file mode 100644 index 0000000..1b84530 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.F.x.ananassa.seq @@ -0,0 +1,2 @@ +>d.16.e.F.x.ananassa +UACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUGUAAGUAUGAACUAAUUCAGACUGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUAGUUUGUUUGAUGGUAUCUACUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCAACAAAUCCCGACUUCUGAGAAGGGAUGCAUUUAUUAGAUAAAAGGUCAACGCGGGCUCUGCUCGCAUUGAUGAUUCAUGAUAACUCGACGGAUCGCACAGCCUUUGUGCUGGCGACGCAUCAUUCAAAUAUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGUGGCCUACCAUGGUGGUGACGGGUGACGGAGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACGGGGAGGUAGUGACAAUAAAUAACAAUACCGGGCUCUUUGAGUCUGGUAAUUGGAAUGAGUACAAUCUAAAUCCCUUAACGAGGAUCCAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUUAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGACCUUGGGUUGGGUCGACCGGUCCGCCUUAUGGUGUGCACCGGUCGGCUCGUCCCUUCUACCGGCGAUACGCUCCUGGCCUUAACUGGCCGGGUCGUGCCUCCGGUGCUGUUACUUUGAAGAAAUUAGAGUGCUCAAAGCAAGCCUACGCUCUGGAUACAUUAGCAUGGGAUAACAUCAUAGGAUUUCGGUCCUAUUCUGUUGGCCUUCGGGAUCGGAGUAAUGAUUAACAGGGACAGUCGGGGGCAUUCGUAUUUCAUAGUCAGAGGUGAAAUUCUUGGAUUUAUGAAAGACGAACAACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUGGGGGCUCGAAGACGAUCAGAUACCGUCCUAGUCUCAACCAUAAACGAUGCCGACCAGGGAUCGGCGGAUGUUACUUUUAGGACUCCGCCGGCACCUUAUGAGAAAUCAAAGUUUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCAGACAUAGUAAGGAUUGACAGACUGAGAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUCAGCCUGCUAACUAGCUAUCGGGAGGUCUCCUCGGGCCAGCUUCUUAGAGGGACUAUGGCCGCUUAGCGAACCAAGUUUGAGGCAAUAACAGGUCUGUCAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAUGUAUUCAACGAGUCUAUAGCCUUGGCCGACCACGGGGUAAUCUUUGAAAUUUCAUCGUGAUGGGGAUAGAUCAUUGCAAUUGUUGGUCUUCAACGAGGAAUUCCUAGUAAGCGCGAGUCAUCAGCUCGCGUUGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAAUGGUCCGGUGAAGUUGUUCGGAUCGCGGCGACGGGGGGCCGGUUCGCUGCCCGCGACGUCGCGAGAAGUUCCACUGAACCUUAUCAUUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUG diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.G.intestinalis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.G.intestinalis.seq new file mode 100644 index 0000000..4d70b84 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.G.intestinalis.seq @@ -0,0 +1,2 @@ +>d.16.e.G.intestinalis +CAUCCGGUCGAUCCUGCCGGAGCGCGACGCUCUCCCCAAGGACGAAGCCAUGCAUGCCCGCUCACCCGGGACGCGGCGGACGGCUCAGGACAACGGUUGCACCCCCCGCGGCGGUCCCUGCUAGCCGGACACCGCUGGCAACCCGGCGCCAAGACGUGCGCGCAAGGGCGGGCGCCCGCGGGCGAGCAGCGUGACGCAGCGACGGCCCGCCCGGGCUUCCGGGGCAUCACCCGGUCGGCGCGGUCGCGGCGCGCCGAGGGCCCGACGCCUGGCGGAGAAUCAGGGUUCGACUCCGGAGAGCGGGCCUGCGAGACGGCCCGCACAUCCAAGGACGGCAGCAGGCGCGGAACUUGCCCAAUGCGCGGCGCGCGAGGCAGCGACGGGGAGCGCGCGAGCGAGGCGGGCCCACAGCCCCCGCCGCGGAGCCGAGGGCAAGGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCGGCGAGCGUCGCGCGGCGCUGCUGCAGUUGAAACGCCCGUAGUUGGCCCCCCGCCGCCACGAGGAAACGGGAGCGCUCCAGGCAGGCCCGUUGGACCCGCCGCGUGGGACCGCGCAGCGGGCCGGCGCGCCGCGGCAGCCCCGAGGAGAGCGGGCGGGGGCACCGGUACCGGCCGGGGACGGGUGAAACAGGAUGAUCCCGCCGAGACCGCCGGCCGCGCAGGCGCCUGCCAAGACCGCCUCUGUCAAUCAAGGGCGAAGGCCGGGGGCUAGAAGGCGAUCAGACACCACCGUAUUCCCGGCCGUAAACGGUGCCGCCCCGCGGCCGGCGCGCGCGUCCCGCCGGCCGCCCAGGGAAACCGGGAGGCUCCGGGCUCUGGGGGGAGUAUGGCCGCAAGGCUGAAACUUGAAGGCAUUGACGGAGGGGUACCACCAGACGUGGAGUCUGCGGCUCAAUCUGACUCAACGCGCGCACCUCACCAGGCCCGGACGCGCGGAGGACCGACAGCCGGGCGCGCUUUCGCGAUCGCGCGGGCGGUGGUGCAUGGCCGCUCCCAGCCCGUGGCGCGAGCCGUCUGCUCCAUUGCGACAACGAGCGAGACCCCGGCCGCGGGCGCCGCGGGACGGCCCGCGCGAGCGGGAGGACGGCGGGGCGAUAGCAGGUCUGUGAUGCCCUCAGACGCCCUGGGCCGCACGCGCGCUACACUGGCGGGGCCAGCCGGCGCGCGCGAGGACGCGCGGAGCCCCCGCCGUGGCCGGGACCGCGGGCUGGAACGCCCCCGCGCACCAGGAAUGUCUUGUAGGCGCCCGCCCCCACCGCGCGCCGGACGCGUCCCUGCCCCUUGUACACACCGCCCGUCGCUCCUACCGACUGGGCGCGGCGGCGAGCGCCCCGGACGCGCGAAGGGCCGCGAGCCCCCGCGCCUGGAGGAAGGAGAAGUCGUAACAAGGUAUUCCGUAGGUGAACCUGCGGAUGGAUCCCUC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.G.max.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.G.max.seq new file mode 100644 index 0000000..6e4347c --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.G.max.seq @@ -0,0 +1,2 @@ +>d.16.e.G.max +UACUUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUGUAAGUAUGAACUAAUUCAGACUGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUAGUUUGUUUGAUGGUAUCUACUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCAACAAACCCCGACUUCUGGAAGGGAUGCAUUUAUUAGAUAAAAGGUCAACACAGGCUCUGCCUGUUGCUUUGAUGAUUCAUGAUAACUCGUCGGAUCGCACGGCCUUUGUGCCGGCGACGCAUCAUUCAAAUUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGUGGCCUACCAUGGUGGUGACGGGUGACGGAGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACGGGGAGGUAGUGACAAUAAAUAACAAUACCGGGCUCAUUGAGUCUGGUAAUUGGAAUGAGUACAAUCUAAAUCCCUUAACGAUGGAUCCAUUGAAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUUAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGACCUUGGGUUGGGUCGAUCGGUCCGCCUCCGGUGUGCACCGGUCGGCUCGUCCCUUCUGCCGGCGAUGCGCUCCUGUCCUUAACUGGCCGGGUCGUGCCUCCGGUGCUGUUACUUUGAAGAAAUUAGAGUGCUCAAAGCAAGCCUACGCUCUGUAUACAUUAGCAUGGGAUAACACCACAGGAUUCUGAUCCUAUUGUGUUGGCCUUCGGGAUCGGAGUAAUGAUUAACAGGGACAGUCGGGGGCAUUCGUAUUUCAUAGUCAGAGGUGAAAUUCUUGGAUUUAUGAAAGACGAACAACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUGGGGGCUCGAAGACGAUCAGAUACCGUCCUAGUCUCAACCAUAAACGAUGCCGACCAGGGAUCAGCGGAUGUUGCUUUUAGGACUCCGCUGGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCAGACAUAGUAAGGUUGACAGACUGAGAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUCAGCCUGCUAAAUAGCUAUGUGGAGGUAACCCUCCACGGCCAGCUUCUUAGAGGGACUAUGGCCGCUUAGGCCACGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAUGUAUUCAACGAGUCUAUAGCCUUGGCCGACAGGUCCGGGUAAUCUUUGAAAUUUCAUCGUGAUGGGGAUAGAUCAUUGCAAUUGUUGGUCUUCAACGAGGAAUUCCUAGUAAGCGCGAGUCAUCAGCUCGCGUUGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAAUGGUCCGGUGAAGUGUUCGGAUUGCGGCGACGUGAGCGGUUCGCUGCCCGCGACGUUGUGAGAAGUCCACUGAACCUUAUCAUUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUG diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.G.steinii.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.G.steinii.seq new file mode 100644 index 0000000..2188860 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.G.steinii.seq @@ -0,0 +1,2 @@ +>d.16.e.G.steinii +AACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGACUAAGCCAUGCAUGUCUAAGUAUAAAUGUUAUACAGUGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUAAUCAAAUUUACAUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCUGUUAAGCCUGACUUUUAGGAAGGGCUGUAUUUAUUAGAUAACAAAUCAAUAUUCCUCGUGUCUAUUGUGAUGACUCAUAAUAACUGAUCGAAUCGCAUGGGCUUUGCCCGCGAUACAUCAUUCAAGUUUCUGCCCCAUCAGCUUUCGAUGGUAGUGUAUUGGACUACCAUGGCUUUCACGGGUAACGGAGGAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGACUCAGGGAGGUAGUGACAAGAAAUAACGGACCGAAGCCUAUGUUUCGGGAUUGCAAUGAGUAGAAUUUAAACCCCUUUACGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCUGGGAGGGUGCCGAUGUCGUCUUGUUGAUUGUGCAGAGGCGCCCUUCCAUCCUUCUGUUAACGUUUCUGAUAUUCAUUUAUUGGUCUCGGGCUCAGAUAUUUUACCUUGAGAAAAUUAGAGUGUUCCAGGCAGGCUCGCGCCGGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUUUAGUCUCCUUUGUUGGUUUGAGGGAUUGAAGUAAUGAUUAAUAGGGAUAGUUGGGGGCAUUAGUAUUUAAUUGUCAGAGGUGAAAUUCUCGGAUUUGUUAAAGACUAACUUAUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCAAAGACGAUCAGAUACCGUCCUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUCAGAGGCGCGCUUUAUCCGCCUUUGGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCUUGCGGCUCAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAGCCUACUAACUAGUCGAUCCGUUGCUUAGCGGACACGACUUCUUAGAGGGACUUUGUGACUAAACACAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCCGCACGCGUGCUACACUGACGCAUACAGCGAGUACUUCCCAGCUCCGUGAGGCAGCUGGUAAUCAGCAAUAUGCGUCGUGAUGGGGAUAGAUCUUUGGAAUUAUAGAUCUUGAACGAGGAAUUCCUAGUAAGCGCAAGUCAUUAGCUUGCGCUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUUCGAGUGAUCCGGUGAACCAUUUGGACCGCGGAGUUCUCGUAAUUCUGUGGAAAAUCUAGUAAACCAUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAUGA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.G.vagum.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.G.vagum.seq new file mode 100644 index 0000000..7343a20 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.G.vagum.seq @@ -0,0 +1,2 @@ +>d.16.e.G.vagum +CAACCUGGUUGAUCCUGCCAGUGGUAUAUGCUUGUCUCAAGGACUAAGCCAUGCAAGUGUAAGUAUGAGUGAAUUGUACAACGAAACUGCGAAUGGCUCGGUAAAACAGCUAUAGUUUCUUCGAUGGUAACUCUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCCACAAGGCAACUUUUGUCGUGGUAUAAAUUGGAGAUACAAACCAAUAUUUGGUGAUUCACGAUUUCUUUUCUGAUCGCACUAUGUGCGACGCAUCGUUCAAAUUUCUGACCUAUCAACUUUGGAUGGUAAGGUAUUGUCUUACCAUGGUUGUGACGGGUAACGGACCGUGGGUGCGGGACUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCGGACACCGGGAGGUAGUGACAAGAAAUAGCAAUAGAGGGCCCGAUGGGUUUUCUAAUUGGAAUGAGAACAAGGUAAACAGCUUAUCGAGGAGCCAGCAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUGUAAGCGUAUACCAAAGUUGUUGCAGUUAAAACGCUCGUAGUCGGAACUUGGCGGGCGACGCAGGGCGUCUUUGCGGACGGUUCUGUAUCGGCCGCCUUUGUGGAGGGGGGCUUAGCGGUGCUUUAUUGCCUUGCUAAGUCGCUGCCACCGUUUACUGUGAAAAAAUUGGAGUGUUCAAAGCAGGCGUUUGCCUUGUACACAUUAGCAUGGAAUAAUAGAAUAGGACCUGGUUCUGUUUUGUUGGUUUGUGAGAAUUAGGUAAUGAUUAAGAGGGACGGUUGGGGGCAUUUGUAUUCUGCCGUCAGAGGUGAAAUUCUUAGAUUGGCGGAAGACAAACAGCUGCGAAAGCGUCUGCCAAGGACGUUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACUAUAAACGAUGAGGACUGGGGAUCGGGCGGCGCUGCUUUAUGGCCCGCCCGGCACCCUUCGGGAAACCAAAGUGUUUGCUUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCGGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUCUGUCUGGUUAAUUCCGUUAACGAGCGAGACCUGGGCGUGCUAGCUAGGCGCCGUUACCUCUUUCGGUAGCGAGGCUUGCCUUCCUAGACGGACUGCGGGCGUCUAGUCCGCGGAAGCUCCAGGCAAUAACAGGUCUGAGAUGCCCUUAGAUGUUCUGGGCCGCACGCGUGCUACACUGAGCGGGUCAACGGGUGAGGAUAGGCGAGAGCCUUUCCUAAUCUCUAAAUCCGCUCGUGCUGGGGAUCGAGGCUUGCAAUUUUCCCUCUUGAACGAGGAAUACCUUGUAAGCGCGGGUCAUCAUCCCGUGCUGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGGUCCGGUGAGGCCUUGGGAGGGCUAGUCGGACUGUGUUUUACAGACCAUCUGGCCCAAACUUGGUCAAACCUUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGACCCUGCAGAAGGAUCAAGC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.G.vavrai.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.G.vavrai.seq new file mode 100644 index 0000000..acaa018 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.G.vavrai.seq @@ -0,0 +1,2 @@ +>d.16.e.G.vavrai +CACCAGGUUGAUUCUGCCUGACGUGGACGCUUGCCUUAAAGAUUAAGCCAUGCAAGCCAGCGAAGGUAACGGAGCGGCGAACGGCUCAGUAGGACAGGGUUAUCUGACCACCGAACAGGAUAACCGCGGUAAUCUGUGGCUAAUACGUGUGUGGGUGAGACUCUGCCCUAUCAGCUUGGGGGUACGGUAAGUGCGUACCCUUGCGACGACGGGUAACGGGAAAUCGGGGUUUGAUUCCGGAGAGGGAGCCUGAGAGAUGGCUACCACGUCCAAGGAUGGCAGCAGGCGCGGAAAUUACCCACUUGGAGGACCAGAGGUAGUGACGAGGCGUUUUUAAUGAGAAUAGUGUAAAAAGCUGUUCGAAAGCAACUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAGGAGCGUCUGCGUGUGUUGCUGCGGUUAAAGAGUGCGUAGUCGGGUUAUUUGCCAGCAAUAAAGGUGCAGUCUCUAACUGUAUAUUGUGCUGGUACUUUGAUCUAGGAACUGGAUAAAGGUUAUGGUAUUCGACAGCGAGGGGUGAAAAUUAAUGACCUGUUGAGGAGCGACUGAUGCGAAAGCGGUAAUCUAUGACGGGUUUGACGAUAAAGCGCGUAGGCAGGAGUAUCGAAGGCGAUUAGAGACCGUCGUAGUUCUUUGCAGUAAACGAUGCCAACAGGAAUGCAAGUGCUGUGUUCCUAGGGAAACUGAGUGUAUGGGCUCUGGGGAUAGUACAGGCGCAAGCUAGAAACUUGAGGAAAUUGACGGAAGGACACCACAAGGAGUGGAGUGUGCGGGUUAAUUUGACUCAACGCGGGACAACUUACCAGGGUAUGUGACAUUGAGCGAAGAGCAUGGAUGCGAUCUGUGUUCUGAUGAUGUUACGUGUGGUGCAUGGCCGUUCUUAACACGUGGGGUGACCUGUCUGGUUAAAUCCGAUAACGCGUGAGACCCUGGAUAAUGACGAUACUUGACAAGAGUAGGGAAGCUCGGGUCGAUAACAGGUCUGUGAUGCCCAUAGAUAUUUUGGGCGCCACGCGCACUACAUUGGGGAUGGUUACGUGAAACGGAACAUCCUUUCGGUUGGGAUUGACGUUUGUAAAUACGUCAUGAACUCGGAAUUCCUAGUAAUUUGUUGUCAUUAACGACAUAUGAAUAUGUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCUAAGAUGAAUGUGCGGAUGAAGUUGGUUAGGUCAAAAGAAUCCGUGCGAUUAGAUUGGAUACAAGUCGUAACAAGGUUACUGUAGGAGAACCUGCAGUAGGAUCAAUAA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.Gracilariopsis.sp.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.Gracilariopsis.sp.seq new file mode 100644 index 0000000..78438aa --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.Gracilariopsis.sp.seq @@ -0,0 +1,2 @@ +>d.16.e.Gracilariopsis.sp +CAACCUGGUUGAUCCUGCCAGUGGUAUAUGCUUGUCUAUAGGACUAAGCCAUGCAAGUGCAAGUAUGAGUGUAUUAUACAACGAAACUGCGAAUGGCUCUGUAAAACAGCUAUAAUUUCUUCGGUGCUAAAUACUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCCUACACAGCGACGCAAGUCGUGGUACAAAUUAGAUACACAAGCCAGCUUUUUUGGUGAUUCUAGAUUUUUUUUCUGAUCGCACAUUGUUGCGACGCACCGUUCAAAUUUCUGACCUAUCAACUUUGGAUGGUAAGGUAAUGGCUUACCAUGGUUGUGACGGGUAACGGACCGUGGGUGCGGGACUCCGGAGAGGGAGCCUGAGAGACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAACUUACCCAAUCCGGACACCGGGAGGUAGUGACAAGAAAUAGCAAUAGAGGGCCCGAUGGGUUUUCUAAUUGGAAUGAGAACAAGAUAAACAGCUUAUCGAGGAGCCAGCAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUGUAAGCGUAUACCAAAGUUGUUGCAGUUAAAACGCUCGUAGUCGAAUUUUGGCGUGUGAUUUGGGUCGUUCUCGCGGACGCGCUCAGGUUGUGCGCCUUUGUGGAGAGGGGGUGUGGUGGUGCUUGAGUGCGCUGCCAUGCUGCCGCCACCGUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCAGGCGAUUGCCCUGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACCCGGUUCUAUUUUGUUGGUUUGUUUGAAUCAGGUAAUGAUUAACAGGGACGGUUGGGGGCAUUCGUAUUCCGGCGCUAGAGGUGAAAUUCUUGGAUUGUCGGAAGACGAACAGCUGCGAAAGCGUCUGCCAAGGACGUUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACUAUAAACGAUGAGGACUGGAGAUCGGACAAGACUGAUUUAUGGCUUGUUCGGCAUCCUUCGAGAAAUCAAAGUGUUUGCUUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUUACCAGGUCAGGACAUAGUAAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUCUGUCUGGUUAAUUCCGUUAACGAGCGAGACCUGGGCGUGCUAGCUAGGCGCCGUUACCAAUUGAGUUUGGUAGCGAGGCGGUGCCUUCCUAGACGGACUGUGGGCGUCUAGCCCACGGAAGCUCCAGGCAAUAACAGGUCUGAGAUGCCCUUAGAUGUCCUGGGCCGCACGCGUGCUACACUGAACGGCCCAACGAGUGGAGGAUGUGCGAGAGCAUUUCCGAAUCUCCAAAUCCGUUCGUGAUGGGGAUCGACGGUUGCAAUUUUCCGUCGUCAACGAGGAAUACCUUGUAAGCGCGGGUCAUCAUCCCGCGCUGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGGUCCGGUGAGGCCUUGGGAGGGCUGGAUGCGCUGUUUUUAUGCAGACAUUUUGGCCUGAACCUGGUCAAACCUUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAGAA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.H.anguillarum.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.H.anguillarum.seq new file mode 100644 index 0000000..9c2f96f --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.H.anguillarum.seq @@ -0,0 +1,2 @@ +>d.16.e.H.anguillarum +CACCAGGUUGAUUCUGCCUGACGUGGACGCUAGUCUCAUAGGUUAAGCCAUGCAUGUGUAGGCGAAGCAUUUUGUGGAGCGGCGGAAGGCUCAGUAACGGGCGUCUAUUUGAUCUUCUGAGACGGACAACCUCUGUAACCGGAGGCCAAUACGUCAGAGGCACGGUUACCCUGUGUGGUGGUGUGCCGAAAGCAUUGCGCGGAAGAGUAAGGAGCCAUCCCAUCAGUUAGUAAGUAGGGUAAGGGCCUACUUAGACGAAGACGGGUACGGGGAAUUGUGGUUUGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCAGGUCCAAGGACAGCAGCAGGCGCGAAAAUUACCGAAGCCUCCGGUGAGGGCGGUAGUAAGGAGACGUGGAAACGAUGAGGAGGUAAAGAAUGCUCUGGUAACAGGAGGUCAAGACUGGUGCCAGCAUCCGCGGUAAUACCAGCUCCUGGAGUGUCUAUGAUGAUUGCUGCAGUUAAAGAGUUCGUAGUCGGGCUGCGUGACUGGCGUGAAAGGCCUUCUUUCAAGGGGGGCACAGCGCGGGGAAAGCAGAGGAUAAGGAGCGUUUUGGGGCCAGGUUAUUAAGCGACGAGAGGUGAAAUUUGAUGACUCGCUUAGGAGGAACAGAGGCGAAAGCGCUGGCCAGGGGCGAAUCCGAUGAUAAAGGACGUAGGCUAGAGGAUCGAAGACGAUUAGAGACCGUUGUAGUUCUAGCAGUAAACGAUGCCGAUGCCGUGGUGCGUGCGCGCGACGCGGAGGAGAAAUUGAGUAGGGCCCUGGGGAGAGUACACGCGCAAGCGAGAAAUUUAAAGGAAAUUGACGGAAGAACACCACAAGGAGUGGAGUGUGCGGCUUAAUUUGACUCAACGCGGGACAGCUUACCAGGCCCGACGACCGCACGAGUGUUGUACACGAUAGGUCGAAGAGUGGUGCAUGGCCGUUAACGACAAGUGGGGUGACCUUUGGGUUAAGUCCGGGAAGUAGUGAGACCCCUGCUGUCCGGCAGACAGGACAGGUGCUCAAAGCACAGGAAGGAAGGGUCAAGAACAGGUCAGUGAUGCCCUUAGAUGGCGUGGGCUGCACGCGCACUACAGUGGUCACAGAAAGAAUCGCGGAGAGACAAUGGUGAUCGAGAGGGAAUGAGCUUUGCAAGAGGCUCAGGAACGAGGAAUUGCUAGUAAUCGCGGGCUCAUUAAGACGCGAUGAAUACGUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCGAAGAUGGAGUCAGGCGCGAACAAGCGAGAGCGAGUGAGUGCAGGGUUCUAGAUGUGAUACAAGUCGUAACAAGGUAGCUGUAGGAGAACCUGUAGCUGGAUCAGCG diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.H.plana.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.H.plana.seq new file mode 100644 index 0000000..4d623b3 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.H.plana.seq @@ -0,0 +1,2 @@ +>d.16.e.H.plana +CACCUGGUUGAUCCUGCCAGUGGUAUAUGCUUGUCUCAAGGACUAAGCCAUGCAAGUGUAAGUAUGAGUGAAUUGUACAACGAAACUGCGAAUGGCUCGGUAAAACAGCUAUAGUUUCUUCGAUGGUAAACUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCCCUAAGACGACGCAAGUCGUGGUAUAAAUUGGAGAUACAAACCAAUGUUUGGUGAUUCACGAUUUCUUUUCUGAUUGCACUUUUGUGCGACGCAUCGUUCAAAUUUCUGACCUAUCAACUUUGGAUGGUAAGGUAGUGUCUUACCAUGGUUGUGACGGGUAACGGACCGUGGGUGCGGGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCGGACACCGGGAGGUAGUGACAAGAAAUAGCAAUAGAGGGCCCGAUGGGUUUUCUAAUUGGAAUGAGAACAAGGUAAACAGCUUAUCGAGGAGCCAGCAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUGUAAGCGUAUACCAAAGUUGUUGCAGUUAAAACGCUCGUAGUCGAAAUUUGGCGGGCGACUUAAGUCGUCUUUACCGACGAUCUUAGGUUGGCCGCCUUUGUGGAGGGGGGCCUAGUGGUGCUUAACCGCUUCGCUAGGUCGCUGCCACCGUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCAGGCGUUUGCCCUGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACCUGUUUUCUAUUUUGUUGGUUUGUUAGGAUCGGGUAAUGAUUAAGAGGGAUGGUUGGGGGCAUUUGUAUUCCAGCGUCAGAGGUGAAAUUCUUGGAUUGUUGGAAGACAAACAGCUGCGAAAGCGUCUGCCAAGGACAUUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACUAUAAACGAUGAGGACUGGAGAUCGGGCGGGGCUGUUUUUGGCCCGCCCGGCAUCCUUCGGGAAACCAAAGUGUUUGCUUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGGAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCGGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUCUGUCUGGUUAAUUCCGUUAACGAGCGAGACCUGGGCGUGUUAGCUAGGCGCCAUUACCCCUUUUGGUAGUGAGGCUAGCCUUCCUAAACGGACUGCGGGCGUCUAGCCCGCGGAAGCUCCAGGCAAUAACAGGUCUGAGAUGCCCUUAGAUGUUCUGGGCCGCACGCGUGCUACACUGAGCGGGUCAACGGGUGAGGAUGUGCGAGAGCGCUUCCCAAUCUCUAAAUCCGCUCGUGCUGGGGAUCGAGGCUUGCAAUUUUCCCUCUUGAACGAGGAAUACCUUGUAAGCGCGGGUCAUCAUCCCGUGCUGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGGUCCGGUGAGGCCUUGGGAGGGCUAGAUAGUCGGUGUUUUCACAGAUCAUCUGGCCCAAACUUGGUCAAACCUUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAAGCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.H.rubra.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.H.rubra.seq new file mode 100644 index 0000000..734e464 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.H.rubra.seq @@ -0,0 +1,2 @@ +>d.16.e.H.rubra +CAACCUGGUUGAUCCUGCCAGUGGUAUAGUCUUGUCUCAAGGACUAAGCCAUGCAAGUGCCAGUAUGAGUGAAUUGUACAACGAAACUGCGAAUGGCUCGGUAAAACAGCUAUAGUUUCUUCGGGGGUAAUACUACCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCCCGAAAGCGAGUCUCUCGCGGUACAAAUUGGAGACACAAGCCAAUAUUUUGGUGAUUCACAAUUUUUUUUCUGAUUGCACUUUUUAGUGCGACACCCCGUUCAAAUUUCUGACCUAUCAACUUUGGAUGGUAAGGUAUUGUCUUACCAUGGUUGUGACGGGUAACGGACCGUGGGUGCGGGAYUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUACUAAUUCAGUGAGGUAGUGACAAAGAGUAUCAAUAGGGGGGCCAUCGGCUCUUCUAGUUGGAAUGAGUACAGAGUAAACAAUUUAACGAGGACCAAUAGGAGGGCAAGCCAAGUGCCAGCAGCCGCGGUAAUACUUACUCCUAGGGUGUUUGUUCACAGUGCUGCAGUUAAAAAGUUCGUAGUCGGACCUAUGAGCUGGGCGGUGGUGUGGGCGCAAGCCUGUGGUGCCGCCCGGCUCUUUUGGGGAAAUGGCCGGAGUAGGGUUUUAAGCGGCUUUGCUCCGGGCGUCCCCCGUUUACUGUGAAAAAAUGAGAGUGUUCAAAGCAGGCGAUGAGCCGUGAAUACCAUAGCAUGGAAUAAUAGAAUAGGGCCGCUGAUGCCUAUUUUGUUGGUUUCGAGGUGUCGGGCAAUGAUUAAGAGGGACGGUUGGGGUCAUUUGUAUUAAGUCGUCAGAGGUGAAAUUCUUAGAUUGACGUAAGACAAACAGCUGCGAAAGCGUCUGACAAGGACGUUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACUAUAAACGAUAAGAACUGGGGAUCGGAAGAGUAUUUAAAUAGGGCUCAUCCGGCACCCUCCGGGAAACCAAAGUGUUUGCUUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGAAAUUGACGGAAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAGUUGACUCAACACGGGAAAACUUACCAGGUCCGGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAGCGAGACCUGAGCGUGGUAGCUAGGGGACUUGUGCAUUUAUGCACGGGCUUUUUCUCCUUCCUACACGGACUGCUGGCGAAUAGUCAGCGGAAGCCUCAGGCAAUAACAGGUCUGUGAUGCCCUUUGAUGUUCUGGGCCGCACGCGCGCUGCACUGAGCGGACCAGCGGGCGAGGAUAGCCGAAAGGUUUUCCGGACCCUUAAAUUCGCUCGUGCUGGGGAUGGAGGCUUGCAAUUGUCCCUCUUGAACGAGGAAUACCUUGUAGGCGUGAGUCAUCAGCUCGCGCCGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGGGUGAGGAGGUGAGAAGUUGGGAGGUGUUGGUUCGGGCCCGCAAGGUGUCUGGGCUAGCGCUAAACUCGUUCAAACCUUAUCAUUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAGAA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.H.sapiens.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.H.sapiens.seq new file mode 100644 index 0000000..c04feb9 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.H.sapiens.seq @@ -0,0 +1,2 @@ +>d.16.e.H.sapiens +UACCUGGUUGAUCCUGCCAGUAGCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUACGCACGGCCGGUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUGGUUCCUUUGGUCGCUCGCUCCUCUCCUACUUGGAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCCGACGGGCGCUGACCCCCUUCGCGGGGGGGAUGCGUGCAUUUAUCAGAUCAAAACCAACCCGGUCAGCCCCUCUCCGGCCCCGGCCGGGGGGCGGGCGCCGGCGGCUUUGGUGACUCUAGAUAACCUCGGGCCGAUCGCACGCCCCCCGUGGCGGCGACGACCCAUUCGAACGUCUGCCCUAUCAACUUUCGAUGGUAGUCGCCGUGCCUACCAUGGUGACCACGGGUGACGGGGAAUCAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCACUCCCGACCCGGGGAGGUAGUGACGAAAAAUAACAAUACAGGACUCUUUCGAGGCCCUGUAAUUGGAAUGAGUCCACUUUAAAUCCUUUAACGAGGAUCCAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGCUGCAGUUAAAAAGCUCGUAGUUGGAUCUUGGGAGCGGGCGGGCGGUCCGCCGCGAGGCGAGCCACCGCCCGUCCCCGCCCCUUGCCUCUCGGCGCCCCCUCGAUGCUCUUAGCUGAGUGUCCCGCGGGGCCCGAAGCGUUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCCCGAGCCGCCUGGAUACCGCAGCUAGGAAUAAUGGAAUAGGACCGCGGUUCUAUUUUGUUGGUUUUCGGAACUGAGGCCAUGAUUAAGAGGGACGGCCGGGGGCAUUCGUAUUGCGCCGCUAGAGGUGAAAUUCCUUGGACCGGCGCAAGACGGACCAGAGCGAAAGCAUUUGCCAAGAAUGUUUUCAUUAAUCAAGAACGAAAGUCGGAGGUUCGAAGACGAUCAGAUACCGUCGUAGUUCCGACCAUAAACGAUGCCGACCGGCGAUGCGGCGGCGUUAUUCCCAUGACCCGCCGGGCAGCUUCCGGGAAACCAAAGUCUUUGGGUUCCGGGGGGAGUAUGGUUGCAAAGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAACCUCACCCGGCCCGGACACGGACAGGAUUGACAGAUUGAUAGCUCUUUCUCGAUUCCGUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGAUAACGAACGAGACUCUGGCAUGCUAACUAGUUACGCGACCCCCGAGCGGUCGGCGUCCCCCAACUUCUUAGAGGGACAAGUGGCGUUCAGCCACCCGAGAUUGAGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCGGGGCUGCACGCGCGCUACACUGACUGGCUCAGCGUGUGCCUACCCUACGCCGGCAGGCGCGGGUAACCCGUUGAACCCCAUUCGUGAUGGGGAUCGGGGAUUGCAAUUAUUCCCCAUGAACGAGGAAUUCCCAGUAAGUGCGGGUCAUAAGCUUGCGUUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGGAUGGUUUAGUGAGGCCCUCGGAUCGGCCCCGCCGGGGUCGGCCCACGGCCCUGGCGGAGCGCUGAGAAGACGGUCGAACUUGACUAUCUAGAGGAAGUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.I.hoferi.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.I.hoferi.seq new file mode 100644 index 0000000..f212fda --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.I.hoferi.seq @@ -0,0 +1,2 @@ +>d.16.e.I.hoferi +CAACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAACAACUUUAUACUGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUAGUUUAUUUGAUAAUACCUACUACUUGGAUAACCGUAGUAAUUCUAGAGCUAAUACAUGCGAAAAAACCCGACUUCUGGAAGGGUUGUAUUUAUUAGAUACAGAACCACUGCAGGGCAACCUGGUUACUUGGUGAUUCAUAAUAACUUCGCGAAUCGAAUGGCUUGUGCCGUCGAUGAUUCAUUCAAAUCUCUGCCCUAUCAACUUUCGGUGGUAAGGUAUUGGCUUACCAUGGUUCCAACGGGUAACGGAGAAUUAGGGUUCGAUUCCCGAGAGGGAGCCUGAGAAACGGCUACCACUUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACAGGGAGGUAGUGACAAAAAAUAACAAUACAGGAUCUUUAAAGGUCUUGUAAUUGGAAUGAGUACAAUUUAAACCCCUUAACGAGGAACAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUUGGAAAUUGCUUACUGGUCGGCCGCAAGGUCUGUACUGGUACGGCAGUUUCUUCUUCUCGAAGGCAGUGGGUGCUCUUAAUUGAGUGUCUACUGAGUUCGGGACUUUUACUGUGAGAAAAUUAGAGUGUUCAAAGCAGGCUUAUGCUUGAAUAUUGCAGCAUGGAAUAAUGGAAUAGGAUCCCGAUCUUAUUUUGUUGGUUUCUAAGAUCGAGAUAAUGAUUAAUAGGGACGGUUGGGGGCAUUAAUAUUUAAUUGUCAGAGGUGGAAUUCUUGGAUUUAUGAAAGAUUAACUUCUGCGAAAGCAUUUGCCAAGGAUGUUUUCGUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGAUGAUCAGAUACCAUCGUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUUAGUGGACGUUUAAUAAUGACACCAUUAGCACCUUAUGAGAAAUCAAAGUUUUUGGGUUCCGGGGGGAGUAUGGUCCCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUCACCAGGUCCGGACAUAGGAAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGCCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAACCUACUAAAUAGUUACAUGAUUUUCGAAUCAUGGGCAACUUCUUAGGGGGACUAUUGGUGUAUAAUCAAUGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAUGAGGUCAACGAGUAUCAUCCUUCACCGGAAGGUGCGGGUAAUCUUUUGAAACCUUAUCGUGAUGGGGAUAGAUCAUUGCAAUUAUUGAUCUUCAACGAGGAAUUCCUAGUAAGCGUGAGUCAUCAGCUCGCGUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGAAUGGUUUAGUGAGGUCCUCGGACUGGUACAGCGCGUGGCAACACAUACUGCGCCGGGAAGUUGAACAAACUUGAUCAUUUAGAGGAAGUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCUAGU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.Ichthyosporidium.sp.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.Ichthyosporidium.sp.seq new file mode 100644 index 0000000..aea2f0f --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.Ichthyosporidium.sp.seq @@ -0,0 +1,2 @@ +>d.16.e.Ichthyosporidium.sp +CACCAGGUUGAUUCUGCCUGACGUGGAUGCUAGUCUCUAAAGUUAAGCCAUGGAUGUCUAAGCAAAGCGUAAGUCGAGCGGCACAGGCUCAGUAACGGGCGAAUAUUUAAUCUCCUCGAGUGGAUAUCCUCUGUAACCGGAGGGCAAAACACAGGACGUGCAGUUGUAUAAGGAUUGUUCGUUUAACAUUAGUGGGGGAGAGUAAGACGCCAGUCCAUCAGUUAGUAAGUAGGGUAAGGGCCUACUUAGACGAAUACGGAUACGGGGAAUUAUCGUUUGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCGGGUCCAAGGACAACAGCAGGCGCGAAAAUUACCGCAGCCUGCAUUCAGGUCGGUAGUAAGGAGACGUGUAAACGAUGUGCAGGUAAAGAAUGCACUGUAUACAGGAGGACAAGACUGGUGCCAGCACCCGCUGUAAUACCAGCUCCUGGAGUGUCUAUGAUGAUUGCUGCAGUUAAAGCGUUCGUAGUCGAACCGGGUUGAAUUGCGUGACAGUCAGACUCUCAAGGUGUGAUGAGCGCUGUGAUUCUGGGGAAUAAGGAGUGUUUAGGGGCCAGGGUAUUAAACGGCAAGCGGUGAAAUGUGUUGACCCGUUUAUGGAGCGACAGAGGCGAAAGGCUGGCCAGGGGCAAAUCCGAUGAUAAAGGACGUAGGCUAGAGGAUCGAAGACGAUUAGAGACCGUUGUAGUUCUAGCAGUAAACAAUGCCGAUGUUGUGGUGCCGUAACGGACGCAAAAGAGAAAUCUAGUAGGGCCCUGGGGAGAGUACACGCGCAACAGGAAAUUUAAAGGAAAUUGACGGAAGAACACCACAAGGAGUGGAGUGUGCGGCUUAAUUUGACUCAACGCGGGACACCUUACCGGGCCCACGGCCACACGAGUGUGACACACGAUAGCCGAGGAGUGGUGCAUGGCCCGUUAACGACAAGUGAGUGAUCUUUGGGUUAAGUCCGUAAAUUAGUGAGACCCCAGCAAAGGACAGGUGCGCAAAGCACAGGAAGGAUGGGUCAAGGACAGGUCAGUGAUGCCCUUAGAUGGUCCGGGCUGCACGCGCACUACAGUGGUCGCCGAAAUUUAGAUAUAGAGCUAAAGGCGAUCGAGAGGGAAUGAGCUUUGGAAGAGGCUCAGGAACGUGGAAUUGCUAGUAAUCGCGGACUCAUUAAGACGCGAUGAAUACGUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCGAAUACGGUGCUCGGCGCGAGCAAGGUGAAAUCACUGAGCGAGCGCAAGGUACCGGAUCUGAUACAAGUCGUAACAAGGUAGCUGUAGGAGAACCAUUAGCAGGAUCAUAA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.J.debaisieuxi.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.J.debaisieuxi.seq new file mode 100644 index 0000000..0970601 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.J.debaisieuxi.seq @@ -0,0 +1,2 @@ +>d.16.e.J.debaisieuxi +CACCAGGUUGAUUCUGCCUGACGUAUGUGCUUGUCUUAAAGAUUUAGCCAUGCAAGUUAGUGAAACUUUUUAAGUGAAACGACAGACAGCUCAGUAAUACAGUAAUGAUUAACUUGCCUAAUAUAGGAUAACCUUGGUAACCUAAGGCUAACACUUUUUUCAAAUUAAAAUGUAGGUGAAACUAUUUUUAAUUUUUUUUUGGGGCAAUUAAGUUUCUGACCUAUCAGCUAGAUGUUAGGGUAAAGGCUUAACAUGGCUACAACGGGUAACGGAGAAUCAGGGUUUGAUUCCGGAGAGGGAGCCUGAGAAUUAGCUACCACGUCUAAGGAUGGCAGCAGGCGCGAAAAUUACCCAAUUCCUUAAUGGGAGAGGUAGUGAAAAGACAUGAUUUUCAUUUCGAUUGAGUCGGUACAUUAAAUAAGUACUGAAGCAACUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAGUAGCGCAUAUAAUAGUUGCUGCAGUUAAAAUGUCCGUAGUUGAUUUAAUUAAACUGUGAGUAAAUUAUAGAGCUCAAAACUAUAAGUAAGCAUGGUAUUAUAAGAUAAUAGGAACAGAUGAUGGCAAUAGUAUUCAAUAGUUAGAGGUGAAAAUUUAAGACCUAUUGAGGACUACCAGAAGCGAAAGCGAUUGUCAAGGAUGUCUCCAUUAAUAAGGGACUUAAGCUAGAGUAUCGAAGAUGAUUAGAUACCGUCGUAGUUCUAGCUGUAAACGAUGCCUACUAGGUGAUGUUUAAAUGGCUAUGCCUUAGGAGAAAUCAAAGUCUACGGGCUCUGGGGAUAGUAUACUGGCAACGGUGAAACUUAAAUGAAAUUGACGGAAGAAUACCACGAGGAGUGGAUUAUGCGGCUUAAUUUGACUCAACGCGGGACAACUUACCAGAGCCGAACCUGUAUGAGAAUUUAUAAUGUAAAUGAUAAUAGGGAAGGUGGUGCAUGGCCGUUUUCAACACGUGGGGUGACUUGUCAGGUUAAUUCCGAUAACGCGUGAGGUUUAUUAAAUAAUUGUUUAUUUGACGGAUGAUAAGAAAUCAUAGGAAGUUAAGCUAUAACAGGUCGGUGAUGCCCCUAGAUGUUCUGGGCUGCACGCGUACUACAAUGAUAUAUUUAAUAUUAAUAUUGAGAAAUAUAACUCUAAUAUAUAUCGAAGCUGGGAUAAGCUAUUGUAAAUUAGUUUUGAACUUGGAAUUCCUAGUAAUCAUAAGUCAUUAUGUUAUGAUGAAUGCGUCCCUGUUCUUUGUACACACCGCCCGUCACUAUCUAAGAUGGAUGUAUAGGUGAAAUGGCUAGACGUAAAUGGAAAGCAGUUAACCUGUGCAACUAAUAGGAUAUAAGUCGUAACAAGGCUGCUAUAGGUGAACCAGCAGCAGGAUCAUAA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.L.acerinae.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.L.acerinae.seq new file mode 100644 index 0000000..b74a2ea --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.L.acerinae.seq @@ -0,0 +1,2 @@ +>d.16.e.L.acerinae +CACCAGGUUGAUUCUGCCUGGUGUGGAUGCUAGUCUCAUAGGUUAAGCCAUGCAUGUGUAAGCAAAGCUAGAAGUGGAGCGGCGCAAGGCUCAGUAACGGGCGGACAUUUGAUCUUCUCGUGUGGACAUCCUCUGUAAGCGGAGGGAAAAACACAGGACGCGCGGACGCAGCCCGUGGGUGUAACGGCGGUGGAGAAGAGUAAGACGCCAUCCCAUCAGUUAGUAAGUAGGGUAAGGGCCUACUUAGACGAAGACGGGUACGGGGAAUGAGUGUUUGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCAGGUCCAAGGACAGCAGCAGGCGCGAAAAUUACCGCAGCCUGCCUCAGGGCGGUAGUAAGGAGACGUGAAUGCGAAGUGCUAGCAAAGAAAGCACUGACAACAGGAGGACAAGACUGGUGCCAGCACCCGCGGUAAUACCAGCUCCUGGAGUGUCUAUGAUGAUUGCUGCAGUUAAAGGGUUCGUAGUCUGAGCGGAACGAGGGGUGUGACGGGUCCCAGCUCAAGGGGGACAUAGCACCGCGAUGCCGCGGAACAAGGAGCGUCUAGGGGCCAGGGUAUUAAGCGACGAGGGGUGAAAUCUGGUGACUCGCUUAGGAGCAACAGAGGCGAAAGCGCUGGCCAGGGGCGAGUCCGAUGAUAAAGGACGUAGGCUAGAGGAUCGAAGACGAUUAGAGACCGUUGUAGUUCUAGCAGUAAACGAUGCCGAUGCCGUGGUGCCGCAAGGCGACGCGGAAGAGAAAUUGAGUAGGGCCCUGGGGAGAGUACACGCGCAAGCGAGAAAUUUAAAGGAAAUUGACGGAAGAACACCACAAGGAGUGGAGUGUGCGGCUUAAUUUGACUCAACGCGGGACAGCUUACCAGUCCCGACGAUCGGAGGAGUGUGUUACACGAUAGGUCGGAGAGUGGUGCAUGGCCGUUAACGACGAGUGGGGUGACCUUUGGGUUAAGUCCGUGAAGUAGUGAGACCCCUGCCGCAAGGGACAGGUGCCGAACGCACAGGAAGGAAGGGUCAAGAACAGGUCAGUGAUGCCCUCAGAUGGGCUGGGCUGCACGCGCACUACAGUGGUCGCAGAAAAGGAAGGAAAGAGAUAAAGGCGAUCGAGAGGGAACGAGCUUUGGAAGAGGCUCGGGAACGAGGAAUUGCUAGUAAUCGCGGGCUCAUUAGGACGCGAUGAAUACGUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCGAAGAUGGAGUCAGGCGCGAACAAGCGAGAGCGAGUGAGUGCAGGAUUCUAGAUGUGAUACAAGUCGUAACAAGGUAGCUGUAGGAGAACCAGCAGCAGGAUCAUAA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.M.musculus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.M.musculus.seq new file mode 100644 index 0000000..1e52f3a --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.M.musculus.seq @@ -0,0 +1,2 @@ +>d.16.e.M.musculus +UACCUGGUUGAUCCUGCCAGUAGCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUACGCACGGCCGGUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUGGUUCCUUUGGUCGCUCGCUCCUCUCCUACUUGGAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCCGACGGGCGCUGACCCCCCUUCCCGGGGGGGGAUGCGUGCAUUUAUCAGAUCAAAACCAACCCGGUGAGCUCCCUCCCGGCUCCGGCCGGGGGUCGGGCGCCGGCGGCUUGGUGACUCUAGAUAACCUCGGGCCGAUCGCACGCCCCCCGUGGCGGCGACGACCCAUUCGAACGUCUGCCCUAUCAACUUUCGAUGGUAGUCGCCGUGCCUACCAUGGUGACCACGGGUGACGGGGAAUCAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCACUCCCGACCCGGGGAGGUAGUGACGAAAAAUAACAAUACAGGACUCUUUCGAGGCCCUGUAAUUGGAAUGAGUCCACUUUAAAUCCUUUAACGAGGAUCCAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGCUGCAGUUAAAAAGCUCGUAGUUGGAUCUUGGGAGCGGGCGGGCGGUCCGCCGCGAGGCGAGUCACCGCCCGUCCCCGCCCCUUGCCUCUCGGCGCCCCCUCGAUGCUCUUAGCUGAGUGUCCCGCGGGGCCCGAAGCGUUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCCCGAGCCGCCUGGAUACCGCAGCUAGGAAUAAUGGAAUAGGACCGCGGUUCUAUUUUGUUGGUUUUCGGAACUGAGGCCAUGAUUAAGAGGGACGGCCGGGGGCAUUCGUAUUGCGCCGCUAGAGGUGAAAUUCUUGGACCGGCGCAAGACGGACCAGAGCGAAAGCAUUUGCCAAGAAUGUUUUCAUUAAUCAAGAACGAAAGUCGGAGGUUCGAAGACGAUCAGAUACCGUCGUAGUUCCGACCAUAAACGAUGCCGACUGGCGAUGCGGCGGCGUUAUUCCCAUGACCCGCCGGGCAGCUUCCGGGAAACCAAAGUCUUUGGGUUCCGGGGGGAGUAUGGUUGCAAAGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGGCCUGCGGCUUAAUUUGACUCAACACGGGAAACCUCACCCGGCCCGGACACGGACAGGAUUGACAGAUUGAUAGCUCUUUCUCGAUUCCGUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGAUAACGAACGAGACUCUGGCAUGCUAACUAGUUACGCGACCCCCGAGCGGUCGGCGUCCCCCAACUUCUUAGAGGGACAAGUGGCGUUCAGCCACCCGAGAUUGAGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCGGGGCUGCACGCGCGCUACACUGACUGGCUCAGCGUGUGCCUACCCUGCGCCGGCAGGCGCGGGUAACCCGUUGAACCCCAUUCGUGAUGGGGAUCGGGGAUUGCAAUUAUUCCCCAUGAACGAGGAAUUCCCAGUAAGUGCGGGUCAUAAGCUUGCGUUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGGAUGGUUUAGUGAGGCCCUCGGAUCGGCCCCGCCGGGGUCGGCCCACGGCCCUGGCGGAGCGCUGAGAAGACGGUCGAACUUGACUAUCUAGAGGAAGUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.M.racemosus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.M.racemosus.seq new file mode 100644 index 0000000..93e0dc2 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.M.racemosus.seq @@ -0,0 +1,2 @@ +>d.16.e.M.racemosus +UACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAAUAAAUUUAUAUUGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUGAUCUACGUGACAUAUUCUUUACUACUUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCAAAAAAACCCAAACUUACGAAUGGGUGCACUUAUUAGAUAAAGCCAACGCUGGGUAAAACCAGUUUCCCUUGGUGAUUCAUAAUAAUUUAGCGGAUCGCAUGGCCUUGUGCUAGCGACAGUCCACUCGAUUUUCUGCCCUAUCAUGGUUGAGAUUGUAAGAUAGAGGCUUACAAUGCCUACAACGGGUAACGGGGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCCGACACGGGGAGGUAGUGACAAUAAAUAACAAUGCAGGGCCUUUAAGGUCUUGCAAUUGGAAUGAGUACAAUUUAAAUCCCUUAACGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAACGUCCGUAGUCAAAUUUUAGCCUUUAGAUGAGGUGGCCUGGUCUUCAUUGAUCAAGCUCGCUUUUAUCGAGGCUUUUUUUCUGGUUAUGCUAUGAAUAGCUUCGGUUGUUUAUAGUCUCUAGCCAGAUGAUUACCAUGAGCAAAUCAGAGUGUUUAAAGCAGGCUUUCAAGCUUGAAUGUGUUAGCAUGGAAUAAUGAAAUAUGACUUUAGUCCCUAUUUCGUUGGUUCAGGAACUUAAGUAAUGAUGAAUAGAAACGGUUGGGGACAUUUGUAUUUGGUCGCUAGAGGUGAAAUUCUUGGAUUGACCGAAGACAAACUACUGCGAAAGCAUUUGAUCCAGGACGUUUUCAUUGAUCAAGGUCUAAAGUUAAGGGAUCGAAGACGAUUAGAUACCGUCGUAGUCUUAACCACAAACUAUGCCGACUAGAGAUUGGGCUUGUUUAUUAUGACUAGCUCAGCAUCUUAGCGAAAGUAAAGUUUUUGGGUUCUGGGGGGAGUAUGGGACGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUCACCAGGUCCAGACAUAGUAAGGAUUGACAGAUUGAAAGCUCUUUCUAGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUCGUGGAGUGAUUUGUCUGGUUAAUUCCGAUAACGAACGAGACCUUAUUCUGCUAAAUAGGCAGGUCAACUUUUUAGUUGAUUAAUAGAUUUAUCUAUCUGGCUUCUUAGAGAGACUAUCGGCUUCAAGCCGAAGGAAGUUUUAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAUGAAAUCAGCGAGUUUAUAACCUUAGCCGGAAGGUUUGGGUAAACUUUUGAAAUUUCAUCGUGCUGGGGAUAGAGCAUUGUAAUUAUUGCUCUUCAACGAGGAAUUCCUAGUAAGCGCAAGUCAUCAGCUUGCGUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGAAUGGUUAUAGUGAGCAUAUGGGAUCAGUAGAAUUAGGUUGGCAACAACCUUUCUCUGCAGAGAACUAUGGCAAACUAGGCUAUUUAGAGGAAGUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.Microsporidium.sp.DP119.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.Microsporidium.sp.DP119.seq new file mode 100644 index 0000000..100309a --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.Microsporidium.sp.DP119.seq @@ -0,0 +1,2 @@ +>d.16.e.Microsporidium.sp.DP119 +CACCAGGUUGAUUCUGCCUGGUGUAGAUGCUAGUUUCUAAGAUUUAGCCAUGCAUGUUUUGUGAAUUCUUACGAAGGAACGGCGAACGGCUCAGUAAUAUUGCGUUAAUCUGGUCUAAAUAUAAAAAUAACUACGGUAACCUGUAGCUAAUAAUUUAGAAUGAGACGCAAAUUUAUCAGUUUGUUGGUAGUGUAAUGGACUACCAAGACUAUGACGAAUAACGGGAAAUUAGGGUUUUAUUCCGGAGAGGGAGCCUGAGAGAUGGCUCCCACGUCCAAGGACGGCAGCAGGCGCGAAAAUUGUCCACUCUUUUAUGAGGAGACAGUUAUGAAACGUGAAUAUAAGUUUGAAUUUUAAAAUAAUUUAUUUUAUGCAAUUGGAGGGCAAGUUUUGGUGCCAGCAGCCGCGGUAAUACCAACUCCAAGAGUGUCUAUGAARGUUGCUGCAGUUAAAGCGUCCGUAGUUUUUUUAUUGCAAUUUAAAAACUAUGAUUAAAUUAGUUAAGUUUCCAAUACAUUGUGAAACGGAUAGGGAAAAUUGUAUAGCUAGGUGAAGAAUGAAAUCUCAAGACCCUAACUCGACAAACAGAGGCGAAGGCGAUUUUCUUAUACGUAUUCUUAAAUAAAGGACGAUAGUUAGAGGAUCGAAGGUGAUUAGAGACCGCUGUAGUUCUAACUGUAAACUUUGCCGACAUUUCAUAUUGUUUUGAUAAGAAAGGGAGAAAUCUUAGUUUUCGGGCUCUGGGGAUAGUACACUCGCAAGGGAGAAACUUAAAGCGAAAUUGACGGAAGAACACUACCAGGAGUGGAUUGUGCUGCUUAAUUUGACUCAACGCGGGAAAACUUACCAGAGUCAAAUAUAUUUAUGAUUUUUUUAAAUGAAAUAUAUAAAAGUGGUGCAUGGCCGUUGCAAAUUGAUGGGUUGACUUUUAACUUAAUUGUUGAAACCAGUGAGAUCAUUUAUGACUGGUAUUUUAAAUACAGGAAGGAAAUGGCAAUAACAGGUCCGCACGCCCUUAGACAUUCUGGGCUGCAAGCGCAAUACAAUAUCUUGUUAUUUAUAUUUAUUUAUACAAUUAUAUGUAGGAUUAAUUCUUGUAAAUGAAUUAUGAAUCAGGAAUUCCUAGUAAUAAUAUUUCAUUAAGAUAUUAUGAAUUUGUCCCUGUUCUUUGUACACACCGUCCGUCACUAUUUCAGAUGGUUAUAAAGAUGAAGAGCUAAGGUUCUGAAUAUUUAUAACUAGAUAAAGUACAAGUCGUAGCAAGGUUGCAGUCGGUGAACCAUCAGCAGGAUCAUAA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.colligata.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.colligata.seq new file mode 100644 index 0000000..6ff328d --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.colligata.seq @@ -0,0 +1,2 @@ +>d.16.e.O.colligata +CACCAGGUUGAUUCUGCCUGACGUGGAUGCUAGUGUCUGAGAUUAAGCCAUGCAUGUGAGUGAAUGUAGUAAGCAGGAACUGCGGACGGCUCAGUAAGACUACGAUGAAAUGAUCUGCGAAGAAGAAGUAACGGCGGGAAACUGAAGAAGAGAGUUUUUGAGAAUACUUGAAGGGAUGCGGAGAAGUGAUUUUUGAAGUGAUGUUGAGUAUUUGAGCGGAGUGUGUUGUAGACCUAUCAGCUGGUAGCUAGGGUAAUGGCCUAGGUAGGCGACGACGGGAGACGGGGGAUUAGGGUUUGAUUCCGGAGAGGGAGCCUGAGAGAUGGCUACUACGUCCAAGGAUGGCAGCAGGCGCGAAACUUGCCUAAUCCUGUGGGGAGGCGGUUAUGAGACGUAUGAUAUUGUUAUGAAGCGGACGAUGAAAGAGUCAGUGGAUAUUGGAGGGCAAGUCGGGUGCCAGCAGCCGCGGUAAUACCUGCUCCGAUGGUGUCUAUGGUGAAUGCUGCGGUUAAAAAGUCUGUAGUCAAGUGAGGAUGUGUAUGAGUAUGAAGGUGAGUGAACUAGAGUUGAAUAAGCUUGUAUGUAUGAGGAGAGCAACGGAGGGGGUGCACUGGAUAGCUGGGCGAGAGGUGAAAUGUGAAGACCCUGGCUGGACGAACGGAGGCGAAGGCUGUGUGCCAUGACGAAUGUGAUGAUCAAGGACGAAGGCCAGAGGAUCGAAAUCGAUUAGAUACCGUUUUAGUUCUGGCAGUAAACGAUGCUGACGGGAUGACAUGUAUGUGUGUUAUGCAAGAGAAAUUGAGUAUGUGAGCUCUGGGGAUAGUAUGUUCGCAAGGGUGAAACUUAAAGAGAUUGACGGAAGGACACCACAAGGAGUGGAGUGUGCGGCUUAAUUUGACUCAACGCGGGGCAACUUACCAGGGCUGAAGAUGUGUGGAGAACUGAGAGGGGAGCACAUUGGCGGUGGUGCAUGGCCGUUUGAAACGGAUGGCGUGAGCUGAGGAUUAAUUUCCGGAAGGCGUGAGACCCACAAGACAGGUUGUUUGGAUGACAGGAGGGAGUGGAACAGAACAGGUCCGUUAUGCCCUGAGAUGUCCUGGGCGGCACGCGCACUACGAUACGUGUAUGAGAUGUGUGAGGGAUGAAUGUGUGGAAUGGCAUUCUGAACGUGGAAUUCCUAGUAAUGGUGGCUCAACAAGCCGACGUGAAUGUGUCCCUGUCCUUUGUACACACCGCCCGUCGCUAUCUGAGAUGGCACAUGGGACGAACACCGAGGGGUGUGAGUCUUCUGUGGUAGAUGAGAUAUAAGUCGUAACAUGGCUGCGGUUGGAGAACCAGCUGCAGGAUCAUCA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.cuniculus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.cuniculus.seq new file mode 100644 index 0000000..7ec9865 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.cuniculus.seq @@ -0,0 +1,2 @@ +>d.16.e.O.cuniculus +UACCUGGUUGAUCCUGCCAGUAGCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUACGCACGGCCGGUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUGGUUCCUUUGGUCGCUCGCUCCUCUCCUACUUGGAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCCGACGGCGCUGACUCCCUUUGUGUGGGAUGCGUGCAUUUAUCAGAUCAAAACCAACCCGGUCAGCCUCCCCGCCGGCCGGGGGGGUGGGGCGGCGGCUUUGGUGACUCUAGAUAACCUCGGGCCGAUCGCAGCCCUCCGUGGCGGCGACGACCCAUUCGAACGUCUGCCCUAUCAACUUUCGAUGGUAGUCGCCGUGCCUACCAUGGUGACCACGGGUGACGGGGAAUCAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCACUCCCGACCCGGGGAGGUAGUGACGAAAAAUAACAAUACAGGACUCUUUCGAGGCCCUGUAAUUGGAAUGAGUCCACUUUAAAUCCUUUAACGAGGAUCCAUUGGAGGGCAAGUCUGGUCGCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGCUGCAGUUAAAAAGCUCGUAGUUGGAUCUUGUGGAGGGUGCGUAGCGGGCGGUCCGCCGCGAGGCGAGCCACCGCCCGUCCCCGCCCCUUGCCUCUCGGCGCCCCCUCGAUGCUCUUAGCUGAGUGUCCCGCGGGGCCCGAAGCGUUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCCCGAGCCGCCUGGAUACCGCAGCUAGGAAUAAUGGAAUAGGACCGCGGUUCUAUUUUGUUGGUUUUCGGAACUGAGGCCAUGAUUAAGAGGGACGGCCGGGGGCAUUCGUAUUGCGCCGCUAGAGGUGAAAUUCUUGGACCGGCGCAAGACGGACCAGAGCGAAAGCAUUUGCCAAGAAUGUUUUCAUUAAUCAAGAACGAAAGUCGGAGGUUCGAAGACGAUCAGAUACCGUCGUAGUUCCGACCAUAAACGAUGCCGACUGGCGAUGCGGCGGCGUUAUUCCCAUGACCCGCCGGGCAGCUUCCGGGAAACCAAAGUCUUUGGGUUCCGGGGGGAGUAUGGUUGCAAAGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAACCUCACCCGGCCCGGACACGGACAGGAUUGACAGAUUGAUAGCUCUUUCUCGAUUCUGUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGAUAACGAACGAGACUCUGGCAUGCUAACUAGUUACGCGACCCCCGAGCGGUCGGCGUCCCCCAACUUCUUAGAGGGACAAGUGGCGUUCAGCCACCCGAGAUUGAGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCGGGGCUGCACGCGCGCUACACUGACUGGCUCAGCGUGUGCCUACCCUACGCCGGCAGGCGCGGGUAACCCGUUGAACCCCAUUCGUGAUGGGGAUCGGGGAUUGCAAUUAUUCCCCAUGAACGAGGAAUUCCCAGUAAGUGCGGGUCAUAAGCUUGCGUUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGGAUGGUUUAGUGAGGCCCUCGGAUCGGCCCGCCGGGGUCGGCCCACGGCCCUGGCGGAGCGCUGAGAAGACGGUCGAACUUGACUAUCUAGAGGAAGUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.granulifera.1.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.granulifera.1.seq new file mode 100644 index 0000000..d6a7e62 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.granulifera.1.seq @@ -0,0 +1,2 @@ +>d.16.e.O.granulifera.1 +AACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGACUAAGCCAUGCAUGUCUAAGUAUAAAUGUUAUACAGUGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUAAUCGAAUUUACAUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCUGGUUAGCCUGACUUUUGUGGAAGGGCUGUAUUUAUUAGAUAACAAACCAAUAUUCCCCGUGUCUAUUGUGACGACUCAUAAUAACUGAUCGAAUCGCAUGGACUUUGUCCGCGAUACAUCAUUCAAGUUUCUGCCCCAUCAGCUUUCGAUGGUAGUGUAUUGGACUACCAUGGCUUUAACGGGUAACGGAGGAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGACUCAGGGAGGUAGUGACAAGAAAUAACGGACCGAAGCCUAUGUUUCGGGAUUGCAAUGAGUAGAAUUUAAACCCCUUUACGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCUGGGAGGGUGCCAAUGUCCGCUCGUUUGCGUGUGCAGCGGCGCCCUUCCAUCCUUCUGUUAACGUUUCUUGGUAUUCAUUUACUGGUUUCGGGCUCAGAUACUUUACCUUGAGAAAAUUAGAGUGUUCCAGGCAGGCUUGCGCCGGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUUUAGUCUCCUUUGUUGGUUCGAGGGACUGAAGUAAUGAUUAAUAGGGAUAGUCGGGGGCAUUAGUAUUUAAUUGUCAGAGGUGAAAUUCUCGGAUUUGUUAAAGACUAACUUAUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCAAAGACGAUCAGAUACCGUCCUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUCGGAGGCGCGCUUUAUCCGCCUUCGGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCUUGCGGCUCAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAGCCUACUAACUAGUCGAACCAAUCUCCGAUUGGCUGCGACUUCUUAGAGGGACUUUGUGGGCCAAACACAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCCGCACGCGUGCUACACUGACGCAUACAGCGAGUACGUCCCAGCUCCGCGAGGCAGCUGGUAAUCAGCAAUAUGCGUCGUGAUGGGGAUAGAUCUUUGGAAUUAUAGAUCUUGAACGAGGAAUUCCUAGUAAGCGCAAGUCAUUACCUUGCGCUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUUCGAGUGGUCCGGUGAACCUUUUGGACUGCGCGAGGCCCCGAGCCUUGUGCGGAAAAUCAAGUAAACCAUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.granulifera.2.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.granulifera.2.seq new file mode 100644 index 0000000..024562d --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.granulifera.2.seq @@ -0,0 +1,2 @@ +>d.16.e.O.granulifera.2 +AACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGACUAAGCCAUGCAUGUCUAAGUAUAAAUGUUAUACAGUGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUAAUCAAACUUACAUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCUGUUUAGCCUGACUUUUAGGAAGGGCUGUAUUUAUUAGAUAACAAACCAAUAUUCCUUGUGUCUAUUGUGAUGACUCAUAAUAACUGAUCGAAUCGCAUGGACUUUGUCCGCGAUACAUCAUUCAAGUUUCUGCCCCAUCAGCUUUCGAUGGUAGUGUAUUGGACUACCAUGGCUCUUACGGGUAACGGAGGAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGAUUCAGGGAGGUAGUGACAAGAAAUAACGGACCGAAGCACAUGUUUCGGGAUUGCAAUGAGUAGAAUUUAAACCCCUUUACGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCAUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCUGGGAGGGUGCUGAUGUCCGCAUGUUUGCGUGUGCAGAGCGCCCUCCCAUCCUUCUGUUAACGUUUCUUGGUAUUCAUUUACUGGUUUCGGGCUCAGAUAUUUUACCUUGAGAAAAUUAGAGUGUUCCAGGCAGGCUUGCGCCGGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUUUAGUCUCCUUUGUUGGUUUGAGGGAUUGAAGUAAUGAUUAAUAGGGAUAGUCGGGGGCAUUAGUACUUAAUUGUCAGAGGUGAAAUUCUCGGAUUUGUUAAAGACUAACUUAUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCAAAGACGAUCAGAUACCGUCCUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUCGGAGGCGCGCAUUAUCCGCCUUCGGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCUUGCGGCUCAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAGCCUACUAACUAGUCGAACCAAUUCCGAUUGGCUCCGACUUCUUAGAGGGACUUUGUGACUAAACACAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCCGCACGCGUGCUACACUGACACAUACAACGAGUACAUCCCAGCUCCGAGAGGCAGCUGGUAAUCAGCAAUAUGUGUCGUGAUGGGGAUAGAUCUUUGGAAUUAUAGAUCUUGAACGAGGAAUUCCUAGUAAGCGCAAGUCAUUACCAUGCGCUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCUUACCGAUUUUGAGUGAUCCGGUGAACCUUUUGGACUGCGCGGAGUCUCGUGCUCUGUGUGGAAAAUCAAGUAAACCAUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAUGA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.longa.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.longa.seq new file mode 100644 index 0000000..f69e872 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.longa.seq @@ -0,0 +1,2 @@ +>d.16.e.O.longa +AACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGACUAAGCCAUGCAUGUCUAAGUAUAAAUGUUAUACAGUGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUAAUCGAAUUUACAUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCUGGUUAGCCUGACUUUUAGGAAGGGCUGUAUUUAUUAGAUAACAAAUCAAUAUUCCUCGUGUCUAUUGUGAUGACUCAUAAUAACUGAUCGAAUCGCAUGGGCUUUGCCCGCGAUAAAUCAUUCAAGUUUCUGCCCCAUCAGCUUUCGAUGGUAGUGUAUUGGACUACCAUGGCUUUCACGGGUAACGGAGGAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGACUCAGGGAGGUAGUGACAAGAAAUAACGGACCGAAGCUUUUGUUUCGGGAUUGCAAUGAGUAGAAUUUAAACCCCUUUACGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCUGAAGGGGUGCCAAUGUCCGCUGUUGCGUGUUCAGCGGCGCCCCUUCAUCCUUCUGUUAACGUCUCGGGUAUUCAUUUACUCGUUUCGGGCUCAGAUAUUUUACCUUGAGAAAAUUAGAGUGUUCUAGGCAGGCUUGCGCCGGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUUUAGUCUCCUUUGUUGGUUUGAGGGAUUGAAGUAAUGAUUAAUAGGGAUAGUUGGGGGCAUUAGUAUUUAAUUGUCAGAGGUGAAAUUCUCGGAUUUGUUAAAGACUAACUUAUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCAAAGACGAUCAGAUACCGUCCUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUCGGAGGCGCGCCUUAUCCGCCUUCGGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCUUGCGGCUCAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAGCCUACUAACUAGUCGUCCCGUUGCUAAGCGGGCACGACUUCUUAGAGGGACUUUGUGACUAAACACAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCCGCACGCGUGCUACACUGACGCAUACAGCGAGUACUUCCCAGCUCCGUGAGGCAGCUGGUAAUCAGCAAUAUGCGUCGUGAUGGGGAUAGAUCUUUGGAAUUAUAGAUCUUGAACGAGGAAUUCCUAGUAAGCGCAAGUCAUUAGCUUGCGCUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUUCGAGUGGUCCGGUGAACCUUUUGGACUGCGUGGUCCUCGUGGCCGUGCGGAAAAUCAAGUAAACCAUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAUGA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.operophterae.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.operophterae.seq new file mode 100644 index 0000000..4acb186 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.operophterae.seq @@ -0,0 +1,2 @@ +>d.16.e.O.operophterae +CACCAGGUUGAUUCUGCCUGACGUAGAUGCUAGCCUCCGAGGCUAAGCCAUGCAUGCCCGUGACGCAAGGAACGGCGAACGGCUCAGUAAUACUGCGAUGAUCUGCUCCGCGCGGACGAUAACUACGGGAAACUGUGGCUAAGAGCGCGGAUUGAGACGCAGCCCUAUCAGCAAGUUGGUAGUGUAACGGACUACCAAGGCGGCGACGGGUGACGGGAAAUCAGGGUUUGAUUCCGGAGAGGGAGCCUGAGAGAUGGCUCCCACGUCCAAGGACGGCAGCAGGCGCGAAAAUUGCCCACUCUCUUGCGAGGAGGCGGUUACGAGGCGUGACGGAAGGGCGCACUGUAAAGACGUGCGCGAACGCGAUUGGAGGGCAAGUUCGGUGCCAGCAGCCGCGGUAAUACCGACUCCAAGAGUGUCUAUGGUGGAUGCUGCAGUUAAAAAGUCCGUAGUCGGCACUGCGACGAAAGCGCGCUGCUCGAUGGCGCAGGCGUUGCAGGGGCUUGCGGAGCGGGCGGGGGGCACGGUAUAGGCAGGCGAGAGAUGAAAUGGCCAAGACCCUGCCUGGACCGACGGUGGCGAAGGCGGUGCCCUCGCACGCAUCUGUGGAUCAAGGACGAAGGCCGGAGGAUCGAAAGUGAUUAGAGACCGCUGUAGUUCCGGCAGUAAACGAUGCCGACACCGCGCGGCGGGGCUGCGCGGGGGGAGAAACCUUAGUGUUCGGGCUCUGGGGAUAGUAUGCUCGCAAGUGUGAAAAUUAAACGAAAUUGACGGAGCUACACCACAAGGAGUGGAUUGUGCGGCUUAAUUUGACUCAACGCGGGGCACCUUACCAGGGCCACGCGCGCCUGAGACCGCAUGCGCGAGGCGCGCAGGAGUGGUGCAUGGUCGUUGCAAAUUGGUGGGGCGACUUUUGGCUUAAAUGCCGGAACGAGUGAGAUCUCCGAGACGGGUGCGCGCAGCACAGGAGGGUGGAGGCGAUAACAGAUCAGUGAUGCCCUUAGAUGCCCUGGGCUGCACGCGCAAUACAAUCCCCGCGCGCUGCACAGAACGGUCGCGGGGGUGUGGGACCGGCGCCUGUAAGGGCGCCGCGAACGAGGAAUUCCUAGUAACGGCGGCUCACCAAGCCGCGGUGAAUGUGUCCCUGUAGCUUGUACACACCGCCCGUCACUAUCUCAGAUGGCCGUGUCGGUGAAGGGAGCAAUCUCUGUGCCUCCGCGGCUAGAUAAGAUGUAAGUCGUAACAAGGUUGCGGUCGGUGAACCAGCAGCAGGAUCAUAA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.quadricornutus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.quadricornutus.seq new file mode 100644 index 0000000..aae8387 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.quadricornutus.seq @@ -0,0 +1,2 @@ +>d.16.e.O.quadricornutus +AACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGACUAAGCCAUGCAUGUCUAAGUAUAAAUGCUAUACAGUGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUAAUCAAAUUUACAUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCUGUUAAGCCUGACUUUGAGGAAGGGCUGUAUUUAUUAGAUAACAAAUCAAUAUUCCUUGUGUCUAUUGUGACGAUUCAUAAUAACUGAUCGAAUCGCAUGGGCUUUGCUCGCGAUACAUCAUUCAAGUUUCUGCCCCAUCAGCUUUCGAUGGUAGUGUAUUGGACUACCAUGGCGUUCACGGGUAACGGAGGAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGACUCAGGGAGGUAGUGACAAGAAAUAACGGACCGAAGCCUAUGUUUCGGGAUUGCAAUGAGUAGAAUUUAAACCCCUUUACGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCUGGGAGAGUGCCAAUGUCGUCUUGUUGACUGUGCAGCGGCGCUCUUCCAUCCUUCUGUUAACGUUUCUGCUAUUUAUUUAGUGGUCUCGGGCUCAGAUAUUUUACCUUGAGAAAAUUAGAGUGUUCCAGGCAGGCUCGCGUCGGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUUUAGUCUCCUUUGUUGGUUUGAGGGAUUGAAGUAAUGAUUAAUAGGGAUAGUUGGGGGCAUUAGUAUUUAAUUGUCAGAGGUGAAAUUCUCGGAUUUGUUAAAGACUAACUUAUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCAAAGACGAUCAGAUACCGUCCUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUCGGAGGCGCGCUUUACCUCCGUUCGGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCUUGCGGCUCAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAGCCUACUAACUAGUUGACUCGUUGCUAAGCGAGAUUAACUUCUUAGAGGGACUUUGUGACUARACACAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCCGCACGCGUGCUACACUGACGCAUACAGCGAGUACUUCCCAGCUCCGAGAGGCAGCUGGUAAUCAGCAAUAUGCGUCGUGAUGGGGAUAGAUCUUUGGAAUUAUAGAUCUUGAACGAGGAAUUCCUAGUAAGCGCAAGUCAUUAGCUUGCGCUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUUCGAGUGAUCCGGUGAACCAUUUGGACUGCGAGGUCCUCGUGACUUUGUGGAAAAUCUAGUAAACCAUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAAGC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.sativa.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.sativa.seq new file mode 100644 index 0000000..e0d3525 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.sativa.seq @@ -0,0 +1,2 @@ +>d.16.e.O.sativa +UACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUGCAAGUAUGAACUAAUUCGAACUGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUAGUUUGUUUGAUGGUACGUGCUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCAACAAACCCCGACUUCCGGGAGGGGCGCAUUUAUUAGAUAAAAGGCUGACGCGGGCUCCGCCCGCUGAUCCGAUGAUUCAUGAUAACUCGACGGAUCGCACGGCCCUCGUGCCGGCGACGCAUCAUUCAAAUUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGGGGCCUACCAUGGUGGUGACGGGUGACGGAGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACGGGGAGGUAGUGACAAUAAAUAACAAUACCGGGCGCUUUAGUGUCUGGUAAUUGGAAUGAGUACAAUCUAAAUCCCUUAACGAGGAUCCAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUUAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGACCUUGGGCGCGGCCGGGCCGGUCCGCCUCACGGCAGGCACCGACCUGCUCGACCCUUCUGCCGGCGAUGCGCUCCUGGCCUUAACUGGCCGGGUUCGUGCCUCCGGCGCCGUUACUUUGAAGAAAUUAGAGUGCUCAAAGCAAGCCAUCGCUCUGGAUACAUUAGCAUGGGAUAACAUCAUAGGAUUCCGGUCCUAUUGUGUUGGCCUUCGGGAUCGGAGUAAUGAUUAAUAGGGACAGUCGGGGGCAUUCGUAUUUCAUAGUCAGAGGUGAAAUUCUUGGAUUUAUGAAAGACGAACAACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUGGGGGCUCGAAGACGAUCAGAUACCGUCCUAGUCUCAACCAUAAACGAUGCCGACCAGGGAUCGGCGGAUGUUGCUUAUAGGACUCCGCCGGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGCGUGGGGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCAGACAUAGCAAGGAUUGACAGACUGAGAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUCAGCCUGCUAACUAGCUAUGCGGAGCCAUCCCUCCGCAGCUAGCUUCUUAGAGGGACUAUGGCCGUUUAGGCCACGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCGCACGCGCGCUACACUGAUGUAUCCAACGAGUAUAUAGCCUGGUCCGACAGGCCCGGGUAAUCUUGGGAAAUUUCAUCGUGAUGGGGAUAGAUCAUUGCAAUUGUUGGUCUUCAACGAGGAAUGCCUAGUAAGCGCGAGUCAUCAGCUCGCGUUGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAAUGGUCCGGUGAAGUGUUCGGAUCGCGGCGACGGGGGCGGUUCGCCGCCCCCGACGUCGCGAGAAGUCCAUUGAACCUUAUCAUUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUG diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.anophelis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.anophelis.seq new file mode 100644 index 0000000..0d42d11 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.anophelis.seq @@ -0,0 +1,2 @@ +>d.16.e.P.anophelis +CACCAGGUUGAUUCUGCCUGACGUGGAUGCUCGCCUUAAAGACUAAGCCAUGCAAGUUUGCGAGCUGAGCAGCGAACGGCUCAGUAAAACAGGGCACUCUAACGCACGGAAGAGAUAACCACGGGAAACUGUGGCUGAGAAGUGCGAUGAGGCUCUGACCUAUUAGUUUGUCGGUACGGUAAGUGCGUACGGAGACGAUGAUGGGUAACGGGGGAUCAAGUCCGAUUCCGGAGAGGGAGCCUGAGAGAUGGCUGCCACGUCCAAGGACGGCAGCAGGCGCGCAACUUACCCAAUGAGGAUUGAGGUAGUGACGAGGCGUAGAUUGUGAGUUGAGAGUAAAGAACUUAACGAGAGCGACUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAGGGGCGUAUGUGUGUGUUGCUGCGGUUAAAAAGCGCGUAGUUUGUGGUGUAGCGGGUCGUUGUGGGGCGAGAUCAAUGCGUUCUGUGUGACUUAUGCUCAUUGCUAGGGAGCGCGAGACGCCGGUGGUAUUCGGUAGCGAGGGGUGAAAACUGCAGACCUACCGAGGAGCGACAGAGGCGUAAGCGGCCGGCGAGUGCGGAUCCGACGAUCAAGCGCGUGGGCAGGAGUAUCGAAGACGAUUAGAGACCGUCGUAGUUCCUGCAGUAAACGAUGCCGACAUGGUUGAAUAGAAUUGACCAAAGGGAAACUGAGUGUACGGGCUCCGGGGAGAGUACGGGCGCAAGCCAGAAACUUGAAGAAAUUGACGGAAGGACACCACCAGGCGUGGAGUGUGCGGGUUAAUUUGACUCAACGCGGGGCAACUUACCCGGGCCGCAGCCUCUUGAGAGGAAACCGAUGGGGCCUCGUGGUGCAUGGCCGUUCUCAACGCGAGGGGUGACCACUGAGUUAGUUCUGGCAAGCCGUGAGGCCCCUGUACUUUUGUAGACGGCGGACGGCAAGUCCGAGGAAGCGAGGGCGUAUAACAGGUCUGUGAUGCCCGCAGAUGUCCGGGGCUCCACGCGCACUACAAUAGCAAAUGGUAGACGAGAGUAAGUUUGUUGUGGUUGGGAUUGACGCUUGUAAAUGCGUCAUGAACGAGGAAUGCCUAGUAGUUGUCUGUCAGCAGCGGACAACGAAUAAGUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCUAAGAUGGCGGUGCGGAUGAAGCUGCUACGUGGCAAGAAUCCGUGCUGCUAGAUUGGAUACAAGUCGUAACAUGGUUGCAGUAGGUGAACCUGCCGCAGAUCAAGCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.anserina.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.anserina.seq new file mode 100644 index 0000000..bf550f0 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.anserina.seq @@ -0,0 +1,2 @@ +>d.16.e.P.anserina +UACCUGGUUGAUUCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAGCAAUUAUACAGCGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUCGUUUAUUUGAUAUUACCUUACUACAUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCAAAAAAUCCCGACUUCGGAAGGGAUGUGUUUAUUAGAUUAAAAACCAAUGCCCUCCGGGGCUCACUGGUGAUUCAUAAUAACCUCUCGAAUCGCACGGCCUUGCGCCGGCGAUGGUUCAUUCAAAUUUCUGCCCUAUCAACUUUCGACGGCUGGGUCUUGGCCAGCCAUGGUGACAACGGGUAACGGGGAGUUAGGGCUCGACUCCGGAGAAGGAGCCUGAGAAACGGCUACUACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCCGACACGGGGAGGUAGUGACAAUAAAUACUGAUACAGGGCUCUUUUGGGUCUUGUAAUUGGAAUGAGUACAAUUUAAAUCCCUUAACGAGGAACAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGAGGUUAAAAAGCUCGUAGUUGAACCUUGGGCCCGGCCCUCCGGUCCCCCUCACCGGGUGCACUGGCUCGGCCGGGCCUUUCCUUCUGGAGAACCGCAUGCCCUUCACUGGGCGUGCCGGGGAACCAGGACUUUUACUCUGAACAAAUUAGAUCGCUUAAAGAAGGCCUAUGCUCGAAUAGUCUAGCAUGGAAUAAUGGAAUAGGACGUGUGGUUCUAUUUUGUUGGUUUCUAGGACCGCCGUAAUGAUUAAUAGGGACAGUCGGGGGCAUCAGUAUUCAAUUGUCAGAGGUGAAAUUCUUGGAUUAAUUGAAGACUAACUACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAGGAACGAAAGUUAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUAACCAUAAACUAUGCCGAUUAGGGAUCGGACGGUGUUAUUUUUUGACCCGUUCGGCACCUUGCGAUAAAUCAAAAUGUUUGGGCUCCUGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGAAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUCACCAGGUCCAGACACGAUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUUCGUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGCUUAAUUGCGAUAACGAACGAGACCUUAACCUGCUAAAUAGCCCGCAUCGCUUUGGCGGUGCGCCGGCUUCUUAGAGGGACUAUCGGCUCAAGCCGAUGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGACAGAGCCAGCGAGUACUCCCUUGGCCGGAAGGCCCGGGUAAUCUUGUUAAACUCUGUCGUGCUGGGGAUAGAGCAUUGCAAUUAUUGCUCUUCAACGAGGAAUUCCUAGUAAGCGCAAGUCAUCAGCUUGCGCUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGAAUGGCUCAGUGAGGCUUCCGGACUGGCCCAGGGAGGUCGGCAACGCCAACCCAGGGCCGGAAAGCUAUCCAAACUCGGUCAUUUAGAGGAAGUAAAAGUCGUAACAAGGUCUCCGUUGGUGAACCAGCGGAGGGAUCAUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.carinii.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.carinii.seq new file mode 100644 index 0000000..054fe8f --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.carinii.seq @@ -0,0 +1,2 @@ +>d.16.e.P.carinii +UACCUGGUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAGCAAGUUAUACAGUGAAACUGCGAAUGGCUCAUUAUAUCAGUUAUAGUUUAUUUGAUAGUAUCUUACUACUUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCAAAAAAUCCCGACUUUAUGGAAGGGAUGUAUUUAUUAGAUAAAAAACCAAUGCCUUCGGGCUUUUUGGUGAUUCAUGAUAACUUCGCGGAUCGCAUGGCCUUGUGCUGGCGAUGAUUCAUUCAAAUUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGAGGCCUACCAUGGUUUCGACGGGUAACGGGGAAUAAGGGUUCUAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCCGACACGGGGAGGUAGUGACAAUAAAUAACAAUACAGGGCUCUUUUGGGUCUUGUAAUUGGAAUGAGUACAAUUUAGAUACCUUAACGAGGAACAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGCUGCAGUUAAAAAGCUCGUAGUUGAAUUUAGGGAUUGGUUGCCUGGUCCUCCGAAGUUGUGUGCACUGGCGCAACUGAUCCUUCCCUCCUGGAUUACCGGCUGCCCUUCGCUGGGUGUGCCGGAUAGCCAGGGCAUUUUACUUUGAGAAAAUUAGAGUGUUCAAAGCAGGCGUUUGCUCGAAUACAUUAGCAUGGAAUAAUAAAAUAGGACAUGUGGUUCUAUUUUGUUGGUUUCUAGGACCAUUGUAAUGAUUAAUAGGGACAGUUGGGGGCAUUAGUAUUCAAUUGUCAGAGGUGAAAUUCUUAGAUUUAUUGAAGACUAACUACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUAACCAUAAACUAUGCCGACUAGAGAUCGGGCGAUGUUUUUUUCUUGACUCGCUCGGCAUCUUAUGAGAAAUCAAAGUCUUCGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUCACCAGGUCCAGACAUAGUAAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGAAGUGAUUUGUCUGCUUAAUUGCGAUAACGAACGAGACCUUAACCUGCUAAAUAGCCAGAUUAGCUUUUGCUGAUCGCGGGCUUCUUAGAGGGACUGUUGGCAUGAAGCCAAUGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGUGCUACACUGACAGAGCCAGCAAGUUCAUUUUCCUUGGCCGAAAGGUCUGGGUAAUCUUGUGAAACUCUGUCGUGCUGGGGAUAGAGCAUUGCAAUUAUUGCUCUUCAACGAGGAAUUCCUAGUAAGCGCAAGUCAUCAGCUUGCGUUGAUUAUGUCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGAAUGGCUUAAUGAGGUCUUCGGACUGGUGAUGGGUUAUUGGCAACGAUAAGCCUAUUACUGGAAAGUUGAUCAAAUUUGGUCAUUUAGAGGAAGUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.cristatellae.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.cristatellae.seq new file mode 100644 index 0000000..3a8ce15 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.cristatellae.seq @@ -0,0 +1,2 @@ +>d.16.e.P.cristatellae +CACCAGGUUGAUUCUGCCUGACGUAUGCGCUUGUCUUGAAGAUUUAGCCAUGCAAGCUAGCGAAGCCUUAUGGUGGAGCGGCGGACAGCUCAGUAAUACAGUUAUUAUUUACUCGUAGUAUGUAUACGGAUAACCAUGGUAAGCUAUGGCUAAUACGUGAACAGGUUAUUGCAUAGAUGAAACAGCGAUAACUGAGAGAGCAAUCGACUACGACUAAGUUUCUGGCCUAUCAGCUAGAUGGUAAGGUAAUGGCUUACCAUGGCUAUAACGGGUAACGGGAAAUCAGUGUUUGAUUCCGGAGAGGGAGCCUGAGAAAUAGCUCCCACGUCCAAGGACGGCAGCAGGCGCGAAACUUACCCAAUUCCUUAGCGGGAGAGGUAGUGAAGAGACAUGAAGUUCUACUUAGAGACUGUACGGUAAAAUAGUACAGGAUCUACUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAGUAGCGCAUAUAAUAGUUGCUGCAGUUAAAACGUCCGUAGUUGAUCACAAGGUAUUCUUCUGCAUAGUAUUUGUGGAGUGUAUCUCGAUACUGUGAGAAAAAUAUGGUUCUCAAAGCGGAUUACGUGAGUAAUUUAGCAUGGGACAUGGUGAAUAUAGGAACAGAUGAUGGCAAUAGUAUUCAGCAGUUAGAGGUGAAAAUCGUUGACCUGCUGAGGACUCUCUGAAGCGAAAGCGAUUGUCAAGUAUGUCUCCGUUAAUAAAGGACUUAAGCUGGAGUAUCGAAGAUGAUUAGAUACCGUCGUAGUUCCAGCUGUAAACUAUGCCGACUAGGUGAGGCCGUCAGGCUGCGCCUUAGGAGAAAUCAAAGUUUUUGGGCUCUGGGGAUAGUAUGGAUGCAAAUCUGAAACUUAAAGAAAUUGACGGAAGGACACCACAAGGAGUGGAUUGUGCGGCUUAAUUUGACUCAACGCGGGGCAACUUACCAGGGCCGAAUGCAUAGGAGAUCGGCUGUCUGAGAGGGUACCCGAGAUUAUGCAGGAGGUGGUGCAUGGCCGUUUUCAACACGUGGGGUGGCCUGUCUGGUUAAUUCCGUAAACGCGUGAGGCCUGGGAAGCAAUUCAUUGCUUGACGGAUAGCGGCAAGCUAUAGGAAGACAGGCUAUAACAGGUCAGUGAUGCCCCUAGAUGUUCUGGGCUGCACGCGCAAUACAAUGGUAUAGUGAGACUAUGUACUGAAAAGUAUGCUUUAAGCUAUAUCGAAUCUGGGAUAAGCUCUUGUAAAUGAGUUUUGAACGAGGAAUUCCUAGUAAUCGCAGGUCAUAAUGCUGCGAUGAAUGCGUCCCUGUUCUUUGUACACACCGCCCGUCACUAUCUUAGAUGGAUGUAUCGGUGAAAUGGCUGGACGAAAGAAAGGCAGUUGAACCUAUACAAUUAGAUAAGAUAUAAGUCGUAACAAGGCUGCUAUAGGUGAACCUGUGGCAGGAUCAUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.falciparum.A.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.falciparum.A.seq new file mode 100644 index 0000000..66edb7f --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.falciparum.A.seq @@ -0,0 +1,2 @@ +>d.16.e.P.falciparum.A +AACCUGGUUGAUCUUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAAGUGAAAGUAUAUAUAUAUUUUAUAUGUAGAAACUGCGAACGGCUCAUUAAAACAGUUAUAGUCUACUUGACAUUUUUAUUAUAAGGAUAACUACGGAAAAGCUGUAGCUAAUACUUGCUUUAUUAUCCUUGAUUUUUAUCUUUGGAUAAGUAUUUGUUAGGCCUUAUAAGAAAAAAGUUAUUAACUUAAGGAAUUAUAACAAAGAAGUAACACGUAAUAAAUUUAUUUUAUUUAGUGUGUAUCAAUCGAGUUUCUGACCUAUCAGCUUUUGAUGUUAGGGUAUUGGCCUAACAUGGCUAUGACGGGUAACGGGGAAUUAGAGUUCGAUUCCGGAGAGGGAGCCUGAGAAAUAGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUUCUAAAGAAGAGAGGUAGUGACAAGAAAUAACAAUGCAAGGCCAAUUUUUGGUUUUGUAAUUGGAAUGGUGGGAAUUUAAAACCUUCCCAGAGUAACAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAAUUGUUGCAGUUAAAACGCUCGUAGUUGAAUUUCAAAGAAUCGAUAUUUUAUUGUAACUAUUCUAGGGGAACUAUUUUAGCUUUUGGCUUUAAUACGCUUCCUCUAUUAUUAUGUUCUUUAAAUAACAAAGAUUCUUUUUAAAAUCCCCACUUUUGCUUUUGCUUUUUUGGGGAUUUUGUUACUUUGAGUAAAUUAGAGUGUUCAAAGCAAACAGUUAAAGCAUUUACUGUGUUUGAAUACUAUAGCAUGGAAUAACAAAAUUGAACAAGCUAAAAUUUUUUGUUCUUUUUUCUUAUUUUGGCUUAGUUACGAUUAAUAGGAGUAGCUUGGGGACAUUCGUAUUCAGAUGUCAGAGGUGAAAUUCUUAGAUUUUCUGGAGACGAACAACUGCGAAAGCAUUUGUCUAAAAUACUUCCAUUAAUCAAGAACGAAAGUUAAGGGAGUGAAGACGAUCAGAUACCGUCGUAAUCUUAACCAUAAACUAUGCCGACUAGGUGUUGGAUGAAAGUGUUAAAAAUAAAAGUCAUCUUUCGAGGUGACUUUUAGAUUGCUUCCUUCAGUACCUUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGCGAGUAUUCGCGCAAGCGAGAAAGUUAAAAGAAUUGACGGAAGGGCACCACCAGGCGUGGAGCUUGCGGCUUAAUUUGACUCAACACGGGGAAACUCACUAGUUUAAGACAAGAGUAGGAUUGACAGAUUAAUAGCUCUUUCUUGAUUUCUUGGAUGGUGAUGCAUGGCCGUUUUUAGUUCGUGAAUAUGAUUUGUCUGGUUAAUUCCGAUAACGAACGAGAUCUUAACCUGCUAAUUAGCGGCGAGUACACUAUAUUCUUAUUUGAAAUUGAACAUAGGUAACUAUACAUUUAUUCAGUAAUCAAAUUAGGAUAUUUUUAUUAAAAUAUCCUUUUCCCUGUUCUACUAAUAAAUUGUUUUUUACUCUAUUUCUCUCUUCUUUUAAGAAUGUACUUGCUUGAUUGAAAAGCUUCUUAGAGGAACAUUGUGUGUCUAACACAAGGAAGUUUAAGGCAACAACAGGUCUGUGAUGUCCUUAGAUGAACUAGGCUGCACGCGUGCUACACUGAUAUAUAUAACGAGUUUUUAAAAAUAUGCUUAUAUUUGUAUCUUUGAUGCUUAUAUUUUGCAUACUUUUCCUCCGCCGAAAGGCGUAGGUAAUCUUUAUCAAUAUAUAUCGUGAUGGGGAUAGAUUAUUGCAAUUAUUAAUCUUGAACGAGGAAUGCCUAGUAAGCAUGAUUCAUCAGAUUGUGCUGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAAAGAUAUGAUGAAUUGUUUGGACAAGAAAAAUUGAAUUAUAUUCUUUUUUUUCUGGAAAAACCGUAAAUCCUAUCUUUUAAAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.falciparum.S.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.falciparum.S.seq new file mode 100644 index 0000000..b5b366a --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.falciparum.S.seq @@ -0,0 +1,2 @@ +>d.16.e.P.falciparum.S +AACCUGGUUGAUCUUGCCAGUAGUCAUAUGCUUGUCUCACAGAUUAAGCCAUGCAAGUGAAAGUACAUAUGUAAGUAAUAUAUUGAAACUGCGAACGGCUCAUUAAAACAGUUAUAAUCUACUUGAUGUUUUUAAUAUAAGGAUAACUACGGAAAAUCUGUAGCUAAUACUUGUGAAAAUACCUUUUGAUAUAUACAUAUGUAUGUAUCAUUAAGGUAUGUAUUUGUUAGAUAUAAGAAUAAAAUAAAUAUAAUUGAAUUAUAACAAAGAAGAAACACAUAAAAUAUGUGUAUUAUCAAUCGAGUAUCUGACCUAUCAGCUUUUGAUGUUAGGGUAUUGACCUAACAUGGCUAUGACGGGUAACGGGGAAUUAGAGUUCGAUUCCGGAGAGGGAGCCUGAGAAAUAGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUUCUAAAAAAGAGAGGUAGUGACAAGAAAUAACAAUACAAUAUCGAAAAAUGAUUUUGUAAUUGGAAUGAUAGGAAUUUACAAGGUUCCUAGAGAAACAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCAUAUAUUAAAAUUGUUGCAGUUAAAACGUUCGUAGUUGAAUAUUAAAGAAUCCGAUGUUUCAUUUAAACUGGUUUGGGAAAACCAAAUAUAUUAUAUAUUUUGCUUUGUUCAAAAUAAGGUUUUCUAAUAAAUUAUGUUUUUAUCAGAUAUGACAGAAUCUUUUUUAAAAUCUCUUCAAUAUGCUUUUAUUGCUUUUGAGAGGUUUUGUUACUUUGAGUAAAAUUAAGUGUUCAUAACAGACGGGUAGUCAUGAUUGAGUUCAUUGUGUUUGAAUACUACAGCAUGGAAUAACAAAUAUGAAUAAGCUAAUUAUUUUUUUUUUCAUUAUUUUUUUUGAUAUUCUUAUUAGCUUAGUUACGAUUAAUAGGAGUAGCUUUGGGGGCAUUCGUAUUCAGAUGUCAGAGGUGAAAUUCUAAGAUUUUCUGGAGACGGACUACUGCGAAAGCAUUUGCCUAAUCUAUUUCCAUUAAUCAAGAACGAAAGUUAAGGGAGUGAAGACGAUCAGAUACCGUCGUAAUCUUAACCAUAAACUAUACCGACUAGGUGUUGGAUGAAUAUAAAAAAUAUAUAAAUAUGUAGCAUUUCUUAGGGAAUGUUGAUUUUAUAUUAGAAUUGCUUCCUUCAGUACCUUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGCGAGUAUUCGCGCAAGCGAGAAAGUUAAAAGAAUUGACGGAAGGGCACCACCAGGCGUGGAGCUUGCGGCUUAAUUUGACUCAACACGGGAAAACUCACUAGUUUAAGACAAGAGUAGGAUUGACAGAUUAAUAGCUCUUUCUUGAUUUCUUGGAUGGUGAUGCAUGGCCGUUUUUAGUUCGUGAAUAUGAUUUGUCUGGUUAAUUCCGAUAACGAACGAGAUCUUAACCUGCUAAUUAGCGGUAAGUACACUAUAUUUUUAUUUGAAAUUGAAUAUAGGUUACUAUACGUUUAUUCAGUGUUCAAAUUAGGAUAUUUUUUUUAUUAAAAUAUUCUUUUCCCUGUUUUACUAAUAAUUUGUUUUUUUUUACUCUAUUUCUCUCUUCUUUUAAGAAUGUACUUGCUUGAUUAAAUAAAGCUUCUUAGAGGAACAGUGUGUAUCUAACACAAGGAAGUUUAAGGCAACAACAGGUCUGUGAUGUCCUUAGAUAAACUAGGCUGCACGCGUGCUACAAUGAUAUAUAUAACAAGUUGUUAAAAAUGUACUUAUAAAUAAGUGUGUACAAUUUUUCCUGUACUGAAAAGUAUAGGUAAUCUUUAUCAGUAUAUAUCGUAAUUGGGAUAGAUUAUUGCAAUUAUUAAUCUUGAACGAGGAAUGCCUAGUAAGCAUGAUUCAUUAGAUUGUGCUGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAAAGAUAUGAUAAAUUGUUUGGAUAUGAAUUAAAAUAAUGAAAUUUUAUAUUUCUGAUUUUUUCUAGAAGAACUGUAAAUCCUAUCUUUUAAAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.hippoglossoideos.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.hippoglossoideos.seq new file mode 100644 index 0000000..74cb22c --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.hippoglossoideos.seq @@ -0,0 +1,2 @@ +>d.16.e.P.hippoglossoideos +CACCAGGUUGAUUCUGCCUGACGUGGAUGCUAGUUUCAUAGGUUAAGCCAUGCAUGUGUAAGCGAAGCUUUUAGUGGAGCGGCGCAAGGCUCAGUAACGGGCGUCUGAUUUGAUCUCUCGGAGUGGACAACCUCUGUAACCGGAGGCCAAAACACGGGAGGGGCAUGCAGUGGAGAUGCCCCGAGAACAUUUAGUGAGAGAGAGUAAGGAGCCAUCCCAUCAGUUAGUAAGUAGGGUAAGGGCCUACUUAGACGAGGACGGGUACGGGGAAUUAGAGUUUGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCAGGUCCAAGGACAGCAGCAGGCGCGAAAAUUACCGAAGCCUGCAUUCAGGGCGGUAGUAAGGAAACGUGAAAACGAUGUGCAGGUAAAGAAUGCACUAGUAACAGGAGGUCAAGACUGGUGCCAGCAUCCGCGGUAAUACCAGCUCCUGGAGUGUCUAUGAUGAUUGCUGCAGUUAAAGAGUUCGUAGUCGGACUGCGUGACUGGCGUGAAAGACCCUUUUAUUCAUUCAAGGGGGGCGCAGCGCCGGAAAAGCAGGGAAUAAGGAGCGGCCGGGGCACAGGUUAUUAAGCGACGAGAGGUGAAAUUUGAUGACUCGCUUAGGAGCAACAGAGGCGAAAGCGCUGUGCAGGGGCGAUUCCGAUGAUAAAGGACGUAGGCUAGAGGAUCGAAGAUGAUUAGAGACCGUUGUAGUUCUAGCAGUAAACGAUGCCGAUGCCGUGGGGCAGUUCUUAGACUGCGCCGCGGAAGAGAAAUUGAGUAGGGCCCUGGGGAGAGUACACGCGCAAGCGAGAAAUUUAAAGGAAAUUGACGGAAGAACACCACAAGGAGUGGAGUGUGCGGCUUAAUUUGACUCAACGCGGGACAGCUUACCAGGCCCGACGACCGCACGAGUGUGGUACACGAUAGGUCGGAGAGUGGUGCAUGGCCGUUAACGACAAGUGGGGUGACCUUUGGGUUAAGUCCGGGAAGUUGUGAGACCCCUGCUGGCGAGCCAGGACAGGUGCUCAAAGCACAGGAAGGAAGGGUCAAGAACAGGUCAGUGAUGCCCUUAGAUGGUCUGGGCUGCACGCGCACUACAGUGGUCACACGAGUUUAUAGAUAGAAGAAAUGGUGAUCGAGAGGAAAUGAGCUUUGCAAGAGGCUCAGGAACGAGGAAUUGCUAGUAAUCGCGGGCUCAUUAAGACGCGAUGAAUACGUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCGAAGGUGGAGUCAGGCGCGAACAAGCGAGAGCGAGUGAGUGCAGGGUUCUAGAUGUGAUACAAGUCGUAACAAGGUAGCUGUAGGAGAACCAGCAGCAGGAUCAUAA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.lepisma.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.lepisma.seq new file mode 100644 index 0000000..0825b4a --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.lepisma.seq @@ -0,0 +1,2 @@ +>d.16.e.P.lepisma +AACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGACUAAGCCAUGCAUGUCUAAGUAUAAAGGUUAUACAAUGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUAAUCGAAAUUACAUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCUGGUUAGCCUGACUUUUAGGAAGGGCUGUAUUUAUUAGAUAACAAACCAAUAUUCCUUGUGUCUAUUGUGACGACUCAUAAUAACUGAUCGAAUCGCAUGGACUUUGUCCGCGAUAAAUCAUUCAAGUUUCUGCCCCAUCAGCUUUCGAUGGUAGUGUAUUGGACUACCAUGGCUUUCACGGGUAACGGAGGAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGACUCAGGGAGGUAGUGACAAGAAAUAACGGACCGAGGCUUUGCUUCGGGAUUGCAAUGAGUAGAAUUUAAACCCCUUUACGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCAUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCUGGGAGGGUGCCGAUGUCCGCAUGUUGCGUGUGCAGAGGCGCUCUUCCAUCCUUCUGUUAACGUUUCUGGUAUUCAGUUACUGGACUCGGGCUCAGAUACUUUACCUUGAGAAAAUUAGAGUGUUCCAGGCAGGCUUGCGCCGGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUUGAGUCUCCUUUGUUGGUUUGAGGGACUGAAGUAAUGAUUAAUAGGGAUAGUUGGGGGCAUUAGUAUUUAAUUGUCAGAGGUGAAAUUCUCGGAUUUGUUAAAGACUAACUUAUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCAAAGACGAUCAGAUACCGUCGUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUCGGAGGCGCGUUUUAUCCGCCUUCGGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCUUGCGGCUCAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAGCCUGCUAACUAGUCGACUCAAUUUCGAUUGGGAACGACUUCUUAGAGGGACUUUGUGACUAAACACAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCCGCACGCGUGCUACACUGAUGCAUACAACGAGUACUUCCCAGCUCCGAAAGGUAGCUGGUAAUCAGCAAUAUGCAUCGUGAUGGGGAUAGAUCCUUGGAAUUAUGGAUCUUGAACGAGGAAUUCCUAGUAAGCGCAAGUCAUCACCUUGCGCUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUUCGAGUGGUCCGGUGAAUCAUUUGGACUGCGUGAGGUUUCGUACCUCGUGUGGAAAAUCUAGUAAACCAUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAUGA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.mirandellae.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.mirandellae.seq new file mode 100644 index 0000000..86c7a36 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.mirandellae.seq @@ -0,0 +1,2 @@ +>d.16.e.P.mirandellae +CACCAGGUUGAUUCUGCCUGGCGUGGAUGCUAGUCUCAUAGGUUAAGCCAUGCAUGUGUAAGCGAAGCAUUUUGUGGAGCGGCAUAAGGCUCAGUAACGGGCGUCUAUUUGAUCUCCUGAUGUGGACAACCUCUGUAACCGGAGGCCAAUACACAUGAGGCACUGUUUCCGUUUGGUGGGGUGUCAAUAGCUAUUUAAUUUUUAUAGCGCGGGAGAGUAAGGAGCCAUCCCAUCAGUUAGUAAGUAGGGUAAGGGCCUACUUAGACGAAGACGGGUACGGGGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAGAUGGCUACCAGGUCCAAGGACAGCAGCAGGCGCGAAAAUUACCGAAGCCUCCGGUGAGGGCGGUAGUAAGGAGACGUGAAUACGAUGUGCAGGUAAAUAAUGCACUAGUAACAGGAGGUCAAGACUGGUGCCAGCAUCCGCGGUAAUACCAGCUCCUGGAGUGUCUAUGAUGAUUGCUGCAGUUAAAGUGUUCGUAGUCGGGCUGCAUGACUGGCGUGAAAGACCUUCCUUUCAAGGGGGUACAGCGCGGGGAAAGCAGAGAAUAAGGAGCGUUUUGGGGUCAGGUUAUUAAGCGACGAGAGGUGAAAUUUAAUGACUCGCUUAGGAGCAACAGAGGCGAAAGCGCUGGCCAGGGGCGAAUCCGAUGAUAAAGGACGUAGGCUAGAGGAUCGAAGACGAUUAGAGACCGUUGUAGUUCUAGCAGUAAACGAUGCCGAUGCCGUGGAGCGAGUUUUAUUCGCUUCGCGGAAGAGAAAUUUAGUAGGGCCCUGGGGAGAGUACACGCGCAAGCGAGAAAUUUAAAGGAAAUUGACGGAAGAACACCACAAGGAGUGGAGUGUGCGGCUUAAUUCAACUCAACGUGGGACAGCUUACCAGGCCGGACGACCGCACGAGUGUAGUACACGAUAGGUUGAAGAGUGGUGCAUGGCCGUUAACGACAAGUGGGGUGACCUUUGGGUUAAGUCCGGGAAGUAGUGAGACCCCUGCUGUUACGAGUAAUGGUGACAGGACAGGUGCUCAAAGCACAGGAAGGAAGGGUCAAGAACAGGUCAGUGAUGCCCUUAGAUGGUCUGGGCUGCACGCGCACUACAGUGGUCACAGAAAGAGAUUAUUGAGAGAUAAUGGUGAUCGAGAGGGAAUGAGCUUUGUAAGAGGCUCAGGAACGAGGAAUUGCUAGUAAUCGCGGGCUCAUUAAGACGCGAUGAAUACGUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCGAAGAUGGAGUCAGGCGCGAACAAGCGAGAGCGAGUGAGUGCAGGAUUCUAGAUGUGAUACAAGUCGUAACAAGGUAGCUGUAGGAGAACCAGCAGCAGGAUCAUAA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.palmata.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.palmata.seq new file mode 100644 index 0000000..897f945 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.palmata.seq @@ -0,0 +1,2 @@ +>d.16.e.P.palmata +UGGUUGAUCCUGCCAGUGGUAUAUGCUUGUCUCAAGGACUAAGCCAUGCAAGUGUAAGUAUAAGUAAUUUUUACGACGAAACUGCGAAUGGCUCGGUAAAACAGCUAUAGUUUCUUCGAUGGUACCUACUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCCACAACGCGGGGUAACCCGUGGUACCAAUCAGAUAUCAAACCAAUGUGUGGUGAUUCAUGAUUUUUUUUCUGAUCGCACGUUAGUGCGACGCAUCGUUCAAAUUUCUGACCUAUCAACUUUCGAUGGUAAGGUAUUGUCUUACCAUGGUUGUGACGGGUAGCGGACCGUGGGUGCGGGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACAGGGAGGUAGUGACAAGAAAUAUCAAUAGAGGGCGUUUAUACGUCUUCUAAUUGGAAUGAGAACAAGGUAAACAGCUUAUCGAGGAUCCAGCAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUGUAAGCGUAUACCAAAGUUGUUGCAGUUAAAACGCUCGUAGUCGGAUUUUGGCGUGGCCCGUGCUGUGCGCGUAAUGCGUGCGGCGCUGGGGCGCGCUUUUGUGGAGGGCGGCGCGUUGUGGCUUCACUGUCGCGGCGUGUCGGCGCCACCGUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCAGGCGUUUGCCGUGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUUGGUUUCUAUUUUGUUGGUUUGUGAGAGCCGAGUAAUGAUUAAGAGGGCCGGUUGGGGGCAUUUGUAUUCCAGCGUCAGAGGUGAAAUUCUUGGAUUGCUGGAAGACAAACCGCUGCGAAAGCGUCUGCCAAGGACGAUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACUAUAAACGAUGAGAACUGGGGAUCGGGCAGGCAUUACGAUGACCUGUCCGGAACCCUCCGGGAAACCAAAGUGUUUGCUUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUUACCAGGUCCGGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAGCGAGACCUGGGCGUGCUAACUAGGGGCCGCUACCAUUGUGUAGCUGUUCGCCCCUUCUUAGACGGACUGCGGGCGUCUAGUCCGCGGAAGCUCCAGGCAAUAACAGGUCUGAGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAGCGGACCAACGGGUGAGGAUGCGCGAAAGCGUUUCCCAAUCCCCAAAUCCGCUCGUGCUGGGGAUAGAGGCUUGCAAUUUUCCCUCUUGAACGAGGAAUACCUUGUAAGCGUGGGUCAUCAGCCCGCGCUGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGAUCCGGUGAGGCUUUGGGACUGCCGCGGUUGAGGCGUUUACGCCCUGGCCGCAGUGGGAACUUAUCCGAACCUUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGACAGAAU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.pulvinata.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.pulvinata.seq new file mode 100644 index 0000000..a076ef4 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.pulvinata.seq @@ -0,0 +1,2 @@ +>d.16.e.P.pulvinata +CACCUGGUUGAUCCUGCCAGUGGUAUAUGCUUGUCUCAAGGACUAAGCCAUGCAAGUCUAAGUAUGAGUGAUUUAUACAACGAAACUGCGAAUGGCUCGGUAAAACAGCUAUAGUUUCUUCGAUGUUACACUACCGGAUAACCGUAGUAAAUCUAGAGCUAAUACGUGCCACUAAAACGGUGAAAACCGUGGUAUAAAUUGGAGAUACAAACCAAUGUUUGGUGAUUCACAAUUUCUUUUCUGAUUGCAAUCAUGUUUUGCGACACAUCGUUCAAAUUUCUGACCUAUCAACUUUGGAUGGUAAGGUAUUGUCUUAUCAUGGUCGUGACGGGUAACGGACCGUGGGUGCGGGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCGGACACCGGGAGGUAGUGACAAGAAAUAGCAAUAGAGGGCCCGAUGGGUUUUCUAAUUGGAAUGAGAACAAGGUAAACAUCUUAUCGAGUAGCCAGCAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUGUAAGCGUAUACCAAAGUUGUUGCAGUUAAAACGCUCGUAGUCGGAAUUUGGCGGGCGAUGUGGGGCGUCUUAACCGACGAUCUCAUGUCGGCUGCCUUUGUGGAGGGGGGCCUAGUGGUGCUUCACUGCAUUGUUAGGUUUCUGCCACCGUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCGGGCGUUUGCCAUGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACCUGUUUCCUGUUUUGUUGGUUUGUGAGGAUCGGGUAAUGAUUAAGAGGGACGGUUGGGGGCAUUUGUAUUCCGGCGUCAGAGGUGAAAUUCUUGGAUUGGCGGAAGACAAACAGCUGCGAAAGCGUCUGCCAAGGACGUUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACUAUAAACGAUGAGGACUGGAGAUCGGGUGAGACUGUUUUUGGCUCACCCGGCAUCCUUCGGGAAACCAAAGUAUUUGCUUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUUACCAGGUCCGGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUCUGUCUGGUUAAUUCCGUUAACGAGCGAGACCUGGGCGUGCUAGCUAGGCGCUACUACCACUAUGGUAGUAAGGCUUGCCUUCCUAGACGGACUGCGGGCGUCUAGUCCGCGGAAGCUCCAGGCAAUAACAGGUCUGAGAUGCCCUUAGAUGUUCUGGGCCGCACGCGUGCUACACUGAGCGGAUCAACGGGUGAGGAUGUGCGAGAGCAUUUCCCAAUCUCUAAAUCCGCUCGUGCUGGGGAUAGAGGCUUGCAAUUUUCCCUCUUGAACGAGGAAUACCUUGUAAGCACGGGUCAUCAUCCCGUGCUGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGGUCCGGUGAGGCCUUGGGAGGGCUAGAUGAACUGUGCUACACAGAUUUUUUGGCCCGAACUUGGUCAAACCUUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAAGCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.vivax.A.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.vivax.A.seq new file mode 100644 index 0000000..76544cb --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.vivax.A.seq @@ -0,0 +1,2 @@ +>d.16.e.P.vivax.A +AACCUGGUUGAUCUUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAAGUGAAAGUAUAUGCAUAUUUUAUAUGUAGAAACUGCGAACGGCUCAUUAAAACAGUUAUAAUCUACUUGACAUUUUUUCUAUAAGGAUAACUACGGAAAAGCUGUAGCUAAUACUUGCCUUAGCACUCUUGAUUCAUUUCUUGAGUGUGUACUUGUUAAGCCUUUUAAGAAAAAAGUUAUUAACUUAAGGAAUUAUAACAAAGAAGCGACACGUAAUGGAUCCGUCCAUUUUUAGUGUGUAUCAAUCGAGUUUCUGACCUAUCAGCUUUUGAUGUUAGGGUAUUGGCCUAACAUGGCUAUGACGGGUAACGGGGAAUUAGAGUUCGAUUCCGGAGAGGGAGCCUGAGAAAUAGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUUCUAAAGAAGAGAGGUAGUGACAAGAAAUAACAAUACAAGGCCAAUCUGGCUUUGUAAUUGGAAUGAUGGGAAUUUAAAACCUUCCCAAAACUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAAUUGUUGCAGUUAAAACGCUCGUAGUUGAAUUUCAAAGAAUCGAUAUUUUAAGCAACGCUUCUAGCUUAAUCCACAUAACUGAUACUUCGUAUCGACUUUGUGCGCAUUUUGCUAUUAUGUGUUCUUUUAAUUAAAAUGAUUCUUUUUAAGGACUUUCUUUGCUUCGGCUUGGAAGUCCUUGUUACUUUGAGUAAAUUAGAGUGUUCAAAGCAAACAGAUAUAGCAUUGCGCGUUUGAAUACUACAGCAUGGAAUAACAAAUUGAACAAGUCAGAAUUUUUGUUCUUUUUUCUUAUUUUGGCUUAGUUACGAUUAAUAGGAGUAGCUUGGGGGCAUUUGUAUUCAGAUGUCAGAGGUGAAAUUCUUAGAUUUUCUGGAGACAAACAACUGCGAAAGCAUUUGCCUAAAAUACUUCCAUUAAUCAAGAACGAAAGUUAAGGGAGUGAAGACGAUCAGAUACCGUCGUAAUCUUAACCAUAAACUAUGCCGACUAGGCUUUGGAUGAAAGAUUUUAAAAUAAGAAUUUUCUCUUCGGAGUUUAUUCUUAGAUUGCUUCCUUCAGUGCCUUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGCGAGUAUUCGCGCAAGCGAGAAAGUUAAAAGAAUUGACGGAAGGGCACCACCAGGCGUGGAGCUUGCGGCUUAAUUUGACUCAACACGGGAAAACUCACUAGUUUAAGACAAGAGUAGGAUUGACAGAUUAAUAGCUCUUUCUUGAUUUCUUGGAUGGUGAUGCAUGGCCGUUUUUAGUUCGUGAAUAUGAUUUGUCUGGUUAAUUCCGAUAACGAACGAGAUCUUAACCUGCUAAUUAGCGGCAAAUACGACAUAUUCUUACGUGGGACUGAAUUCGGUUGAUUUGCUUACUUUGAAGAAAAUAUUGGGAUACGUAACAGUUUCCCUUUCCCUUUUCUACUUAGUUCGCUUUUCAUACUGUUUCUUUUUCGCGUAAGAAUGUAUUUGCUUGAUUGUAAAGCUUCUUAGAGGAACGAUGUGUGUCUAACACAAGGAAGUUUAAGGCAACAACAGGUCUGUGAUGUCCUUAGAUGAACUAGGCUGCACGCGUGCUACACUGAUAUGUAUAACGAGUUAUUAAAAUUACGAUUCAGCUUGCUGUUUCGUAUUUUUCCUCCACUGAAAAGUGUAGGUAAUCUUUAUCAGUACAUAUCGUGAUGGGGAUAGAUUGUUGCAAUUAUUAAUCUUGAACGAGGAAUGCCUAGUAAGCAUGAUUCAUCAGAUUGUGCUGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAAAGAUAUGAUGAAUUGUUUGGACAAGAAGAAGGGGGAUUAUAUCUCCUUUUUUCUGGAAAAACCGUAAAUCCUAUCUUUUAAAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGUGAACCUGCGGAAGGAUCAUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.vivax.S.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.vivax.S.seq new file mode 100644 index 0000000..13a90ad --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.vivax.S.seq @@ -0,0 +1,2 @@ +>d.16.e.P.vivax.S +AACCUGGUUGAUCUUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAAGUGAAAGUACAUGCAUAUUUUUAUAUGCGGAAACUGCGAACGGCUCAUUAAAACAGUUAUAAUCUACUUGACAUUUUUUUCUAUAAGGAUAACUACGGAAAAGCUGUAGCUAAUACUUGCUUUAAUGCUCUCGACGAAUGUCUUGGGCAUGUACUUGUUAAGCCUUUAUAAGAAAAAAGUUAAUAACUUAAGGAAUGAUAACAAAGAAGUGACACAUAGAAGGACCUGCGUCCAUUUAUAGUGUGUAUCAAUCGAGUUUCUGACCUAUCAGCUUUUGAUGUUAGGGUAUUGGCCUAACAUUGCUAUGACGGGUAACGGGGAAUUAGAGUUCGAUUCCGGAGAGGGAGCCUGAGAAAUAGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUUCUAAAGAAGAGAGGUAGUGACAAGAAAUAACAAUACAAGACCAAAACUGGUUUUGUAAUUGGAAUGAUGGGAAUUUAAAUCCUUCCCAUAAUACAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAAUUGUUGCAGUUAAAACGCUCGUAGUUGAAUUUCAAAGAACCAAUAUUUUAAUAACGCCGUUAGCUAGAUCCACAAGGGGUUGAGCCAAUCACGGUUUCGGCUUCUGUGCGCAUCCUACCUAUCAAGCGUUUUUUUAAUUAAAGUGUUUCUUUUUAAAAUCUUCUUUACCUUAACCAUAUGGAAGAUUUUGUUACUUUGAGUAAAUUAAAGUGUUCAUAGCAAACAGAUACAGCAUUGCGCGUUUUGAAUACUACAGCAUGGAAUAACAAAAUUGAACAAGUCAAAACUAUGUUUCUUUUUUUUUAUUUUUGGCUUAGUUACGAUUAAUAGGAGUAGUUUGGGGACAUUUGUAUUCAGAUGUCAGAGGUGAAAUUCUAAGAUUUUCUGGAGACAAACAACUGCGAAGGCAUUUGUCUAAAAUACUUCCAUUAAUCAAGAACGAAAGUUAAGGGAGUGAAGACGAUCAGAUACCGUCGUAAUCUUAACCAUAAACUAUACCGACUAGGUUUUGGAUGAAAGUUAAACAAAUAAGGAUAGUCUCUUCGGGGAUAGUCCUUAGAUUUCUUCCUUCAGUACCCUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGCGAGUAUUCGCGCAAGCGAGAAAGUUAAAAGAAUUGACGGAAGGGCACCACCAGGCGUGGAGCUUGCGGCUUAAUUUGACUCAACACGGGAAAACUCACUAGUUUAAGACAAGAGUAGGAUUGACAGAUUGAGAGCUCUUUCUCGAUUUCUUGGAUGGUGAUGCAUGGCCGUUUUUAGUUCGUGAAUAUGAUUUGUCUGGUUAAUUCCGAUAACGAACGAGAUCUUAACCUGCUAAUUAGCGGUAAGUACGACAUAUUUUUAUGUCGGAUUGGAUCUGGAUGAUUUGCUUAUAUUGAGGUGCAAUCUAAAUAGGGGAUUGCAAUUAUACUUCGUGUCGGUGUUUCUUAAUCGAAUAGCUGAUGCGUUUGGUAUAUUGCUUUCCUUUUUUUUAUUUCUGCGCUUCUUUACUUGGCUUAUCGUACCGUUUCCUUUUUGUGUAGAAAUGUAUUUGCAUUAUAUUAAAGCUUCUUAGAGGAACGAUGUGUGUCUAACACAAGGAAGUUUAAGGCAACAACAGGUCUGUGAUGUCCUUAGAUGAACUAGGCUGCACGCGUGCUACACUGAUAUGUACAACGAGUUAUUAAAAUUACGAUUCAGCUUGCUGUUACGUAUUUUUCCUCCACUGAAAAGUGUAGGUAAUCUUUAUCAGUACAUAUCGUGAUGGGGAUAGAUUAUUGCAAUUAUUAAUCUUGAACGAGGAAUGCCUAGUAAGCACGAUUCAUUAGAUUGUGCUGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUCGAAAGAUAUGAUGAAUUGUUUGGACAAGAAGAAAGGGGAUUAUAUCUUCUUUUUUCUGGAAAAACCGUAAAUCCUGUCUUUUAAAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.weissei.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.weissei.seq new file mode 100644 index 0000000..64ca28d --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.weissei.seq @@ -0,0 +1,2 @@ +>d.16.e.P.weissei +AACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGACUAAGCCAUGCAUGUCUAAGUAUAAAUGUUAUACAGUGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUAAUCAAAAUUACAUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCUGGUUAGCCUGACUUUUAGGAAGGGCUGUAUUUAUUAGAUAACAAAUCAAUAUUCCCCGUGUCUAUUGUGACGACUCAUAAUAACUGAUCGAAUCGCAUGGGCUUUGCCCGCGAUACAUCAUUCAAGUUUCUGCCCCAUCAGCUUUCGAUGGUAGUGUAUUGGACUACCAUGGCUUUCACGGGUAACGGAGGAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGACUCAGGGAGGUAGUGACAAGAAAUAACGGACCGAAGCCUAUGUUUCGGGAUUGCAAUGAGUAGAAUUUAAACCCCUUUACGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAUUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCUGAGAGGGCGCCAAUGUCCGCUGAUUGCGUGUGCAGCGGUGCCCUCUCAUCCUUCUGUUAACGUUUCUGAUAUUCAUUUAUUGGUCUCGGGCUCAGAUAUUUUACCUUGAGAAAAUUAGAGUGUUCCAGGCAGGCUAGCGCCGGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUUUAGUCUCCUUUGUUGGUUUGAGGGACUGAAGUAAUGAUUAAUAGGGACAGUUGGGGGCAUUAGUAUUUAAUUGUCAGAGGUGAAAUUCUCGGAUUUGUUAAAGACUAACUUAUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCAAAGACGAUCAGAUACCGUCCUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUCGGAGGCGCGCCUUAUCCGCCUUCGGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCUUGCGGCUCAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAGCCUACUAACUAGUCGACCCGUUGCUAAGCGGGCACGACUUCUUAGAGGGACUUUGUGACUAAACACAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCCGCACGCGUGCUACACUGACGCAUACAGCGAGUACGUCCCAGCUCCGUAAGGCAGCUGGUAAUCAGCAAUAUGCGUCGUGAUGGGGAUAGAUCUUUGGAAUUAUAGAUCUUGAACGAGGAAUUCCUAGUAAGCGCAAGUCAUUACCUUGCGCUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUUCGAGUGAUCCGGUGAACCUUUUGGACCGCGAAGUCCUCGUGGCUUUGUGGAAAAUCAAGUAAACCAUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAUGA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.Ple.lanceolata.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.Ple.lanceolata.seq new file mode 100644 index 0000000..7479150 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.Ple.lanceolata.seq @@ -0,0 +1,2 @@ +>d.16.e.Ple.lanceolata +AACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGACUAAGCCAUGCAUGUCUAAGUAUAAAUGUUAUACAGUGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUAAUCAAAUUUACAUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCUGUUAAGCCUGACUUUUAGGAAGGGCUGUAUUUAUUAGAUAACAAAUCAAUAUUCCUUGUGUCUAUUGUGAUGAUUCAUAAUAACUGAUCGAAUCGCUUCGGCUUUGCCAGCGAUACAUCAUUCAAGUUUCUGCCCCAUCAGCUUUCGAUGGUAGUGUAUUGGACUACCAUGGCUUUCACGGGUAACGGAGGAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGACUCAGGGAGGUAGUGACAAGAAAUAACGGACCGAAGCCUAUGUUUCGGGAUUGCAAUGAGUAGAAUUUAAACCCCUUUACGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCUGGGAGAGUGCCAAUGUCGUCUUGUUGACUGUGCAGCGGCGCUCUUCCAUCCUUCUGUUAACGUUUCUGAUAUUCAUUUAUUGGUCUCGGGCUCAGAUAUUUUACCUUGAGAAAAUUAGAGUGUUCCAGGCAGGCUCGCGCCGGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUUUAGUCUCCUUUGUUGGUUUGAGGGACUGAAGUAAUGAUUAAUAGGGAUAGUUGGGGGCAUUAGUAUUUAAUUGUCAGAGGUGAAAUUCUCGGAUUUGUUAAAGACUAACUUAUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCAAAGACGAUCAGAUACCGUCCUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUCGGAGGCGCGCUUUAUCCGCCUUCGGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCUUGCGGCUCAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAGCCUACUAACUAGUCAACCCGUUGCUAAGCGGGAAUGACUUCUUAGAGGGACUUUGUGACUAAACACAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCCGCACGCGUGCUACACUGACGCAUACAGCGAGUACUUCCCAGCUCCGAGAGGCAGCUGGUAAUCAGCAAUAUGCGUCGUGAUGGGGAUAGAUCUUUGGAAUUAUAGAUCUUGAACGAGGAAUUCCUAGUAAGCGCAAGUCAUUAGCUUGCGCUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUUCGAGUGAUCCGGUGAACCAUUUGGACUGCGAGGUCCUCGUGAUCUUGUGGAAAAUCUAGUAAACCAUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAUGA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.R.carriebowensis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.R.carriebowensis.seq new file mode 100644 index 0000000..093c07a --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.R.carriebowensis.seq @@ -0,0 +1,2 @@ +>d.16.e.R.carriebowensis +CACCUGGUUGAUCCUGCCAGUGGUAUAUGCUUGUCUCAAGGACUAAGCCAUGCAAGUCUAAGUAUAAGUGAUUCUGAUGACGAAACUGCGAAUGGCUCGGUAAAACAGCUAUAAUUUCUUCGAUGGUAACUUACUAUUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCCACAAAUGCGGGGUUUCGGCUCCGUGGUGCCAAUUAGAUAACAACACCAACAUUUGGUGAUUCAUAAUUUUCUUUCUGAUCGCUGCAUGCAUUGCGGCGACGCAUCGUUCAAAUUUCUGACCUAUCAACUUUCGAUGGUAAGGUAGUGUCUUACCAUGGUGGUGACGGGUAACGGACCGUGGGUGCGGGACUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCGGACUCCGGGAGGUAGUGACAAGAAAUAUCAAUAGGGGACCCGAUGGGUGCCCUAAUUGGAAUGAGAACAAGGUAAACAGCUUAUCGAGGAUCCAGCAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUGUAAGCGUAUACCAAAGUUGUUGCAGUUAAAACGCUCGUAGUCGGAAGUUGGUGGUCUUGCGGGUGCGCGCGUUGAGCGUACGCCUGUCGAGGCUGCUUUUGUGGAUUGCGCGCACGGGCGGCUUUAGUGUCGAACGUGUUGGGUUUCGCUGCUUUGGCGUUCACGCGGCAGAGCGGCGGAGGCGCAGCCACCGUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCAGGCGUUUGCCGUGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUCGGUUUUCCUAUUUUGUUGGUGUUGUGAGGGGCGAGUAAUGAUUAAGAGGGACAGUUGGGGGCACUUGUAUUCCGGCGCUAGAGGUGAAAUUCUUAGAUUGCCGGAAGACAAACCGCUGCGAAAGCGUCUGCCAAGGAUGUUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACUAUAAACGAUGAGGACUGGGGAUCGGGCGUGGAAUUGCGAUGACCCGCCCGGCACCCUCCGGGAAACCAAAGUUUUUGCUUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUUACCAGGUCAGGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAGCGAGACCUGGGCGUGCUAAAUAGGGGCUAUUACCGCUUUUUUUGGUAGUGAGAGCUUUUUUGACCCCUUCUUAGACGGACUGCGGGCGUCUAGUCCGCGGAAGCUCCAGGCAAUAACAGGUCUGAGAUGCCCUUAGAUGUUCUGGGCCGCACGCGUGCUACACUGAGCGGAUCAGCGGGCGAGGAUGCGCGAAAGCGUUUCCUAAUCCCCAAAUCCGCUCGUGCUGGGGAUAGAGGGUUGCAAUUCUCCCUCUUGAACGAGGAAUACCUUGUAAGCGUGGGUCAUCAUCCCGCGCUGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGGUCCGGUGAGGCCUUGGGAUUGUCGUGAGGGGAGCGUUUGCGCUCGUUUCGUGAAGAAAACUUGGUCGAACCUUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAAGCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.R.leptophylla.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.R.leptophylla.seq new file mode 100644 index 0000000..99deaaf --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.R.leptophylla.seq @@ -0,0 +1,2 @@ +>d.16.e.R.leptophylla +CACCUGGUUGAUCCUGCCAGUGGUAUAUGCUUGUCUCAAGGACUAAGCCAUGCAAGUGUAAGUAUGAGUGAAUUGUACAACGAAACUGCGAAUGGCUCGGUAAAACAGCUAUAGUUUCUUCGAUGAUAUACUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCCACAAGACGACUCAAGUCGUGGUAUAAAUUGGAGAUACAAACCAAUAUUUGGUGAUUCACAAUUUCUUUUCUGAUUGCACUUUCGUGCGACGCAUCGUUCAAAUUUCUGACCUAUCAACUUUGGAUGGUAAGGUAUUGUCUUACCAUGGUUUUGACGGGUAACGGACCGUGGGUGCGGGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCGGACACCGGGAGGUAGUGACAAGAAAUAUCAAUAGAGGGCCCGAUGGGUUUUCUAAUUGGAAUGAGAACAAGGUAAACAGCUUAUCGAGGAGCCAGCAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUGUAAGCGUAUACCAAAGUUGUUGCAGUUAAAACGCUCGUAGUCGGAACUUGGCGGGCGACUUGCCUCGUCCUCGCGGAUGUUGGCAGGUCGGCCGCCUUUGUGGAGGGGGGCCUAGUGGUUCUUUACUGCAUCGCUAGGUCGCUGCCACCGUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCAGGCGUUUGCCGUGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACCUGUUUUCUAUUUUGUUGGUUUGUUAGAAUCGGGUAAUGAUUAAGAGGGAUGGUUGGGGGCAUUUGUAUUCCAGCGUCAGAGGUGAAAUUCUUGGAUUGUUGGAAGACAAACAGCUGCGAAAGCGUCUGCCAAGGACAUUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACUAUAAACGAUGAGGACUGGAGAUCGGGCGGGGCUGUCAUUUGGCCCGCCCGGCAUCCUUCGGGAAACCAAAGUGUUUGCUUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGGAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCGGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUCUGUCUGGUUAAUUCCGUUAACGAGCGAGACCUGGGCGUGUUAGCUAGGCGCCAUUACCGCUUUUGGUAGUGAGGCUAGCCUUCCUAAACGGACUGCGGGCGUCUAGCCCGCGGAAGCUCCAGGCAAUAACAGGUCUGAGAUGCCCUUAGAUGUUCUGGGCCGCACGCGUGCUACACUGAGCGGGUCAACGGGCGAGGAUGUGCGAGAGCAUUUCCAAAUCUCUAAAUCCGCUCGUGCUGGGGAUCGAGGCUUGCAAUUUUCCCUCUUGAACGAGGAAUACCUUGUAAGCACGGGUCAUCAUCCCGUGCUGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGGUCCGGUGAGGCCUUGGGAGGGCUAAAUGGACUGUGUUCUCACGGACCGUUUGGCCCAAACUUGGCCAAGCCUUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAAGCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.R.norvegicus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.R.norvegicus.seq new file mode 100644 index 0000000..8a1603d --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.R.norvegicus.seq @@ -0,0 +1,2 @@ +>d.16.e.R.norvegicus +UACCUGGUUGAUCCUGCCAGUAGCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUACGCACGGCCGGUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUGGUUCCUUUGGUCGCUCGCUCCUCUCCUACUUGGAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCCGACGGGCGCUGACCCCCCUUCCCGUGGGGGGGACGCGUGCAUUUAUCAGAUCAAAACCAACCCGGUCAGCCCCCUCCCGGCUCCGGCCGGGGGUCGGGCGCCGGCGGCUUUGGUGACUCUAGAUAACCUCGGGCCGAUCGCACGCCCUCCGUGGCGGCGACGACCCAUUCGAACGUCUGCCCUAUCAACUUUCGAUGGUAGUCGCCGUGCCUACCAUGGUGACCACGGGUGACGGGGAAUCAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCACUCCCGACCCGGGGAGGUAGUGACGAAAAAUAACAAUACAGGACUCUUUCGAGGCCCUGUAAUUGGAAUGAGUCCACUUUAAAUCCUUUAACGAGGAUCCAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGCUGCAGUUAAAAAGCUCGUAGUUGGAUCUUGGGAGCGGGCGGGCGGUCCGCCGCGAGGCGAGUCACCGCCCGUCCCCGCCCCUUGCCUCUCGGCGCCCCCUCGAUGCUCUUAGCUGAGUGUCCCGCGGGGCCCGAAGCGUUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCCCGAGCCGCCUGGAUACCGCAGCUAGGAAUAAUGGAAUAGGACCGCGGUUCUAUUUUGUUGGUUUUCGGAACUGAGGCCAUGAUUAAGAGGGACGGCCGGGGGCAUUCGUAUUGCGCCGCUAGAGGUGAAAUUCUUGGACCGGCGCAAGACGGACCAGAGCGAAAGCAUUUGCCAAGAAUGUUUUCAUUAAUCAAGAACGAAAGUCGGAGGUUCGAAGACGAUCAGAUACCGUCGUAGUUCCGACCAUAAACGAUGCCGACUGGCGAUGCGGCGGCGUUAUUCCCAUGACCCGCCGGGCAGCUUCCGGGAAACCAAAGUCUUUGGGUUCCGGGGGGAGUAUGGUUGCAAAGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAACCUCACCCGGCCCGGACACGGACAGGAUUGACAGAUUGAUAGCUCUUUCUCGAUUCCGUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGAUAACGAACGAGACUCUGGCAUGCUAACUAGUUACGCGACCCCCGAGCGGUCGGCGUCCCCCAACUUCUUAGAGGGACAAGUGGCGUUCAGCCACCCGAGAUUGAGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCGGGGCUGCACGCGCGCUACACUGACUGGCUCAGCGUGUGCCUACCCUACGCCGGCAGGCGCGGGUAACCCGUUGAACCCCAUUCGUGAUGGGGAUCGGGGAUUGCAAUUAUUCCCCAUGAACGAGGAAUUCCCAGUAAGUGCGGGUCAUAAGCUUGCGUUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGGAUGGUUUAGUGAGGCCCUCGGAUCGGCCCCGCCGGGGUCGGCCCACGGCCCUGGCGGAGCGCUGAGAAGACGGUCGAACUUGACUAUCUAGAGGAAGUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.S.alba.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.S.alba.seq new file mode 100644 index 0000000..b728e04 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.S.alba.seq @@ -0,0 +1,2 @@ +>d.16.e.S.alba +UACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUGUAAGUAUGAACGAAUUCAGACUGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUAGUUUGUUUGAUGGUAACUACUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCAACAAACCCCGACUUCUGGAAGGGAUGCAUUUAUUAGAUAAAAGGUCGACGCGGGCUCUGUGCUGCUCUGAUGAUUCAUGAUAACUCGACGGAUCGCAUGGCCUUUGUGCUGGCGACGCAUCAUUCAAAUUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGUGGCCUACCAUGGUGGUAACGGGUGACGGAGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACGGGGAGGUAGUGACAAUAAAUAACAAUACCGGGCUCAUUGAGUCUGGUAAUUGGAAUGAGUACAAUCUAAAUCCCUUAACGAGGAUCCAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUUAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGAACCUUGGGAUGGGUCGCCCGGUCCGCGUUUGGUGAGCACCGGUCGGCUUGUCCCUUCUGUCGGCGAUACGCUCCUGGCCUUAAUUGGCCGGGUCGUGCCUCCGGCGCUGUUACUUUGAAGAAAUUAGAGUGCUCAAAGCAAGCCUACGCUCUGUAUACAUUAGCAUGGGAUAACAUCAUAGGAUUUCGGUCCUAUUGUGUUGGCCUUCGGGAUCGGAGUAAUGAUUAACAGGGACAGUCGGGGGCAUUCGUAUUUCAUAGUCAGAGGUGAAAUUCUUGGAUUUAUGAAAGACGAACAACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGGACGAAAGUUGGGGGCUCGAAGACGAUCAGAUACCGUCCUAGUCUCAACCAUAAACGAUGCCGACCAGGGAUCAGCGGAUGUUGCUUUUAGGACUCCGCUGGCACCUUAUGAGAAAUCAAAGUUUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAAGUCCAGACAUAGUAAGGAUUGACAGACUGAGAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUCAGCCUGCUAACUAGCUACGUGGAGGCAUCCCUUCACGGCCGGCUUCUUAGAGGGACUAUGGCCGUUUAGGCCAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCGCACGCGCGCUACACUGAUGUAUUCAACGAGUUCACACCUUGGUCGACAGGCCCGGGUAAUCUUUGAAAUUUCAUCGUGAUGGGGAUAGAUCAUUGCAAUUGUUGGUCUUCAACGAGGAAUUCCUAGUAAGCGCGAGUCAUCAGCUCGCGUUGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAAUGAUCCGGUGAAGUACUCGGAUCGCGGCGACGUGGGUGGUUCGCCGUCCGCGACGUCGCGAGAAGUUUUCUAAACCUUAUCAUUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUG diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.S.cerevisiae.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.S.cerevisiae.seq new file mode 100644 index 0000000..7eb6818 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.S.cerevisiae.seq @@ -0,0 +1,2 @@ +>d.16.e.S.cerevisiae +UAUCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAGCAAUUUAUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUCGUUUAUUUGAUAGUUCCUUUACUACAUGGUAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCUUAAAAUCUCGACCCUUUGGAAGAGAUGUAUUUAUUAGAUAAAAAAUCAAUGUCUUCGGACUCUUUGAUGAUUCAUAAUAACUUUUCGAAUCGCAUGGCCUUGUGCUGGCGAUGGUUCAUUCAAAUUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGUGGCCUACCAUGGUUUCAACGGGUAACGGGGAAUAAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUAAUUCAGGGAGGUAGUGACAAUAAAUAACGAUACAGGGCCCAUUCGGGUCUUGUAAUUGGAAUGAGUACAAUGUAAAUACCUUAACGAGGAACAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGAACUUUGGGCCCGGUUGGCCGGUCCGAUUUUUUCGUGUACUGGAUUUCCAACGGGGCCUUUCCUUCUGGCUAACCUUGAGUCCUUGUGGCUCUUGGCGAACCAGGACUUUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCGUAUUGCUCGAAUAUAUUAGCAUGGAAUAAUAGAAUAGGACGUUUGGUUCUAUUUUGUUGGUUUCUAGGACCAUCGUAAUGAUUAAUAGGGACGGUCGGGGGCAUCAGUAUUCAAUUGUCAGAGGUGAAAUUCUUGGAUUUAUUGAAGACUAACUACUGCGAAAGCAUUUGCCAAGGACGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGAUGAUCAGAUACCGUCGUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUCGGGUGGUGUUUUUUUAAUGACCCACUCGGCACCUUACGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUCACCAGGUCCAGACACAAUAAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUUUGUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGCUUAAUUGCGAUAACGAACGAGACCUUAACCUACUAAAUAGUGGUGCUAGCAUUUGCUGGUUAUCCACUUCUUAGAGGGACUAUCGGUUUCAAGCCGAUGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGACGUUCUGGGCCGCACGCGCGCUACACUGACGGAGCCAGCGAGUCUAACCUUGGCCGAGAGGUCUUGGUAAUCUUGUGAAACUCCGUCGUGCUGGGGAUAGAGCAUUGUAAUUAUUGCUCUUCAACGAGGAAUUCCUAGUAAGCGCAAGUCAUCAGCUUGCGUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUAGUACCGAUUGAAUGGCUUAGUGAGGCCUCAGGAUCUGCUUAGAGAAGGGGGCAACUCCAUCUCAGAGCGGAGAAUUUGGACAAACUUGGUCAUUUAGAGGAACUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.S.lemnae.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.S.lemnae.seq new file mode 100644 index 0000000..3697105 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.S.lemnae.seq @@ -0,0 +1,2 @@ +>d.16.e.S.lemnae +AACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGACUAAGCCAUGCAUGUCUAAGUAUAAAUGUUAUACAGUGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUAAUCGAAUUUACAUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCUGUUAAGCCCGACUUUGAGGAAGGGCUGUAUUUAUUAGAUAACAAAUCAAUAUUCCUUGUGUCUAUUGUGAUGACUCAUAAUAACUGAUCGAAUCGCAUGGGCUUUGCCCGCGAUACAUCAUUCAAGUUUCUGCCCCAUCAGCUUUCGAUGGUAGUGUAUUGGACUACCAUGGCUUUCACGGGUAACGGAGGAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGACUCAGGGAGGUAGUGACAAGAAAUAACGGACCGAAGCAUUUGUUUCGGGAUUGCAAUGAGUAGAAUUUAAACCCCUUUACGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCUGGAGGGGCGCCAAUGUCCGAUGUUUCGUGUGCAGCGGUGCCUCUCCAUCCUUCAGUUAACGUUUCUGAUAUUCAUUUAUUGGUCUCGGGCUCUGAUAUUUUACCUUGAGAAAAUUAGAGUGUUCCAGGCAGGCUUGCGCCGGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUUUAGUCUCCUUUGUUGGUUUGAGGGACUGAAGUAAUGAUUAAUAGGGAUAGUUGGGGGCAUUAGUAUUUAAUUGUCAGAGGUGAAAUUCUCGGAUUUGUUAAAGACUAACUUAUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCAAAGACGAUCAGAUACCGUCCUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUCGGAGGCGCGCCUUAUCCGCCUUCGGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCUUGCGGCUCAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAGCCUACUAACUAGUCGAUCCGUUGUUAAGCGGACUUGACUUCUUAGAGGGACUUUGUGACUAAACACAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCCGCACGCGUGCUACACUGACGCAUACAGCGAGUACUUCCCAGCUCCGUGAGGCAGCUGGUAAUCAGCAAUAUGCGUCGUGAUGGGGAUAGAUCUUUGGAAUUAUAGAUCUUGAACGAGGAAUUCCUAGUAAGCGCAAGUCAUUAGCUUGCGCUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUUCGAGUGAUCCGGUGAACCAUUUGGACUGCGCGGUCCUCGUGACUGUGUGGAAAAUCUAGUAAACCAUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAUGA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.S.lophii.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.S.lophii.seq new file mode 100644 index 0000000..2908cfd --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.S.lophii.seq @@ -0,0 +1,2 @@ +>d.16.e.S.lophii +CACCAGGUUGAUUCUGCCUGACGUGGAUGCUAGUCUCAUAGAUUUAGCCAUGCAUGUGUAAGCGAAGCGAUUAGUGAAGCGGCGGAAGGCUCAGUAACGGGCGAGUAUUUUAAUCUCUAGAACCGGACAACCUCAGGAAACAGAGGGGAAAACGGAGUAAGAGCAUGUGUUGUUAGCAUGUGAUGAGAACAACAGUGCAGGAGAGUAAGAAGCCAUCCCAUCAGUUAGUAAGUAGGGUAAGGGCCUAUUUAGACGUAGACGGGUACGGGGGAUUAGGGUUUGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCAGGUCCAAGGACAGCAGCAGGCGCGAAAAUUACCGAAGCCUCCAAGAGGGCGGUAGUGAAGAGACGUGAAAACAAGUGUGUGUAAAAACCACAUGAGUAACUGUGGAGGGUCAAGGCUGGUGCCAGCAUCCGCGGUAAUACCAGCUCCAGGAGUGUCUAUGAUGAUUGCUGCGAUUAAAAGGUCCGUAGUCGAAGAACAGUACUUGUUUGUAAUGUGGCUUAUCGAGAGCCGAAUAGAACGAGAAGAGUUCAGAGUAAGGAGYGAAGGAGGGCUAGAUUAUUGAGCAGCGAGAGGUGAAAUUUGAUGACCUGCUUUAGGAGUAACAGAGGCGAAAGCGCUAGUCAAGAACGAAUCCGAUGAUCAAGGACGUAGGCUGGAGGAUCGAAGACGAUUAGAGAGACCGUAGUAGUUCCAGCAGUAAACGAUGCCUACGCUGUUGUGGUUAUGAGCACGGCAGAAGAGAAAUCUAGUAGGGCUUUGGGGAGAGUACGCGCGCAAGCGAUAAAUUUAAAGGAAAUUGACGGAAGAACACCACAAGGAGUGGAGUGUGCGGCUUAAUUUGACUCAACGCGGGACAGCUUACCAUACCCGAUGGCCGUGUGAGCGUAGUACGCGAUAGGUCAGAGAGUGGUGCAUGGCCGUUAACGACGAGUGGGGUGACCUUUGGGUUAAGUCCGCCGAAGUAGUGAGAUCCCUAGGAUACGAAAGUUAUCGACAGGUGUUAAAAACACAGGAAGGAAGGGGCAAGAACAGGGUCAGUGAUGCCCUUAGAUGGUAUGGGCUGCACGCGCACUACAGUGGUCACAGCAGAAACGGAUAGAAGUAAAUGUGAUCGAGAGGGAAUGAGCACUGUAAUGUGCACAGGAACGAGGAAUUGCUAGUAAUCGUUAUCUCAUUAAGAAGCGAUGAAUGUGUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCGAAGAUGGAACCAGGUGCGAACAAGUGAAAGCGAGUGAGUGCAGGGUUCYAGAUCUGAUACAAGUCGUAACAAGGCAGCUGUAGGAGAACCAUUAGCAGGAAGCUUG diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.S.mytilus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.S.mytilus.seq new file mode 100644 index 0000000..022bce8 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.S.mytilus.seq @@ -0,0 +1,2 @@ +>d.16.e.S.mytilus +AACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGACUAAGCCAUGCAUGUCUAAGUAUAAAUGUUAUACAGUGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUAAUCGAAUUUACAUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCUGUUAAGCCCAACUUUUAGGAAGGGCUGUAUUUAUUAGAUAACAAACCAAUAUUCCUUGUGUCUAUUGUGAUGACUCAUAAUAACUGAUCGAAUCGCAUGGGCUUUGCCCGCGAUACAUCAUUCAAGUUUCUGCCCCAUCAGCUUUCGAUGGUAGUGUAUUGGACUACCAUGGCUUUCACGGGUAACGGAGGAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGACUCAGGGAGGUAGUGACAAGAAAUAACGGACCGAAGCCUAUGUUUCGGGAUUGCAAUGAGUAGAAUUUAAACCCCUUUACGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCUGGAGGGGUGCCAAUGUCCGAUUGUUUCGUGUGCAGCGGCGCCCUUCCAUCCUUCUGUUAACGUUUCUGAUAUUCAUUUAUUGGUCUCGGGCUCAGAUAUUUUACCUUGAGAAAAUUAGAGUGUUCCAGGCAGGCUUGCGCCGGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUUUAGUCUCCUUUGUUGGUUUGAGGGACUGAAGUAAUGAUUAAUAGGGAUAGUUGGGGGCAUUAGUAUUUAAUUGUCAGAGGUGAAAUUCUCGGAUUUGUUAAAGACUAACUUAUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCAAAGACGAUCAGAUACCGUCCUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUCGGAGGCGCGCCUUAUCCGCCUUCGGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCUUGCGGCUCAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAGCCUACUAACUAGUCGAUCCGUUGUUAAGCGGACUUGACUUCUUAGAGGGACUUUGUGACUAAACACAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCCGCACGCGUGCUACACUGACGCAUACAGCGAGUACUUCCCAGCUCCGUGAGGCAGCUGGUAAUCAGCAAUAUGCGUCGUGAUGGGGAUAGAUCUUUGGAAUUAUAGAUCUUGAACGAGGAAUUCCUAGUAAGCGCAAGUCAUUAGCUUGCGCUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUUCGAGUGUUCCGGUGAACCAUUUGGACCACGCGGUCUUCGUGACUGUGAGGAAAAUCUAGUAAACCAUAACACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAUGA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.S.tuberosum.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.S.tuberosum.seq new file mode 100644 index 0000000..3e571a9 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.S.tuberosum.seq @@ -0,0 +1,2 @@ +>d.16.e.S.tuberosum +UACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUGUAAGUAUGAACAAAUUCAGACUGUGAAACUGCGAAUGGCUCAUAAAUCAGUUAUAGUUUGUUUGAUGGUAUCUACUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCAACAAACCCCGACUUCUGGAAGGGAUGCAUUUAUUAGAUAAAAGGUCGACGCGGGCUCUGCCCGUUGCUGCGAUGAUUCAUGAUAACUCGACGGAUCGCACGGCCAUCGUGCCGGCGACGCAUCAUUCAAAUUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGUGGCCUACCAUGGUGGUGACGGGUGACGGAGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACGGGGAGGUAGUGACAAUAAAUAACAAUACCGGGCUCUAUGAGUCUGGUAAUUGGAAUGAGUACAAUCUAAAUCCCUUAACGAGGAUCCAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUUAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGACUUUGGGAUGGCACGGCCGGUCCGCCCUAGGUGUGCACCGGUCGUCUUGUCCCUUCUGUCGGCGAUGCGCUCCUGGCCUUAAUGUGCCGGGUCGUGCCUCCGGCGCUGUUACUUGAAGAAAUUUAGAGUGCUCAAAGCAAGCCUACGCUCUGUAUACAUUAGCAUGGGAUAACAUUAUAGGAUUCGGUCCUAUUUACGUUGGCCUUCGGGAUCGGAGUAAUGAUUAACAGGGACAGUCGGGGGCAUUCGUAUUUCAUAGUCAGAGGUGAAAUUCUUGGAUUUAUGAAAGACGAACAACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACCGAAAGUUGGGGGCUCGAAGACGAUCAGAUACCGUCCUAGUCUCAACCAUAAACGAUGCCGACCAGGGGUCGGCGGAUGUUGCUUUUAGGACUCCGCCGGCACCUUAUGAGAAAUCAAAGUUUUUGGGUUCCGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCAGACAUAGUAAGGAUUGACAGACUGAGAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUCAGCCUGCUAACUAGCUAUGCGAAGGUAUCCCUUCGCGGCCAGCUUCUUAGAGGGACUACGGCCUUUUAGGCCGCGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAUGUAUUCAACGAGCUUAUAGCCUUGGCCGACAGGCCCGGGUAAUCUUUGAAAUUUCAUCGUGAUGGGGAUAGAUCAUUGCAAUUGUUGGUCUUCAACGAGGAAUUCCUAGUAAGCGCGAGUCAUCAGCUCGCGUUGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAAUGAUCCGGUGAAAUGUUCGGAUCGCGGCGACGUGGGCGGUUCGCUGCCCGCGACGUCGCGAGAAGUCCAUUGAACCUUAUCAUUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUG diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.T.cruzi.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.T.cruzi.seq new file mode 100644 index 0000000..9a3b981 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.T.cruzi.seq @@ -0,0 +1,2 @@ +>d.16.e.T.cruzi +AACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUUUCAAGGACUUAGCCAUGCAUGCCUCAGAAUCACUGCAUUGCAGGAAUCUGCGCAUGGCUCAUUACAUCAGACGUAAUCUGCCGCAAAAAUCUUGCGGUCUCCGCAAAAUUGGAUAACUUGGCGAAACGCCAAGCUAAUACAUGAACCAACCGGAUGUUCUCUGUUCCGGCGGCAGGGCAACCUGCUGCCAUGGGACGUCCAGCGAAUGAAUGAAAGUAAAACCAAUGCCUUCACCGGGCAGUAACACUCAGAAGUGUUGAUUCAAUUCAUUCCGUGCGAAAGCCGGGUUUUUUAUCCGGCGUCUUUUGACGAACAACUGCCCUAUCAGCCAGCGAUGGCCGUGUAGUGGACUGCCAUGGCGUUGACGGGAGCGGGGGAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAAUAGCUACCACUUCUACGGAGGGCAGCAGGCGCGCAAAUUGCCCAAUGUCAAAAAAAAAAGAUGAGGCAGCGAAAAGAAAUAGAGCCGACAGUGCUUUUGCAUUGUCGUUUUCAAUGGGGGAUAUUUAAACCCAUCCAAAAUCGAGUAACAAUUGGAGGACAAGUCUGGUGCCAGCACCCGCGGUAAUUCCAGCUCCAAAAGCGUAUAUUAAUGCUGUUGCUGUUAAAGGGUUCGUAGUUGAAUUGAGGGCCUCUAAGGCGCAAUGGUUUAGUCCCAUCCACUUCGGAUUGGUGACCCAUGCCCUUGUGGUCCGUGAACAGACAUAUUCAGAAACAAAAAACACGGGAGUGGUACCUUUUCUGAUUAUCGCAUGUCAUGCAUGCCAGAGGGCGCCCGUGAUUUUUUACUGUGACUAAAAAAGUGUGACCAAAGCAGUCAUUCGACUUGAAUUAGAAAGCAUGGGAUAACAAAGGAGCAGCCUCUGGGCCACCGUUUCGGCUUUUGUUGGUUUUAAAAGUCCAUUGGAGAUUAUGGGGCAGUGUGACAAGCGGCUGGGUGGUUAUUCCACACACACGCACACUCCUUUUUUGGAUGUUGUGUCUCUGUGUGUGUGGCACUCGUCGCCUUUGUGGGAAAUCCGUGUGGCACUUGUUUGGUGUUGUUGGCAGACUUCGGUCUUGCCUUCACACACGUUUCACAUGUGUCAUGCCUUCCCUCAACUCACGGCAUCCAGGAAUGAAGGAGGGUAGUUCGGGGGAGAACGUACUGGUGCGUCAGAGGUGAAAUUCUUAGACCGCACCAAGACGAACUACAGCGAAGGCAUUCUUCAAGGAUACCUUCCUCAAUCAAGAACCAAAGUGUGGGGAUCGAAGAUGAUUAGAGACCAUUGUAGUCCACACUGCAAACGAUGACACCCAUGAAUUGGGGAGUUUUUGGUCGUAGGCGUGGUCGGGCUUGAUUAUAUUAUUUUUCAUCCCGUUCCUCGUCUCGCCAAUGAAUAUAUUAAAUUUACGUGCAUAUUCUUUUUGGUCUUCGUUUUUUUACGGCGAGGACCUUUAACGGGAAUAUCCUCAGCACGUUAUCUGACUUCUUCACGCGAAAGCUUUGAGGUUACAGUCUCAGGGGGGAGUACGUUCGCAAGAGUGAAACUUAAAGAAAUUGACGGAAUGGCACCACAAGACGUGGAGCGUGCGGUUUAAUUUGACUCAACACGGGGAACUUUACCAGAUCCGGACAGGGUGAGGAUUGACAGAUUGAGUGUUCUUUCUCGAUCCCCUGAAUGGUGGUGCAUGGCCGCUUUUGGUCGGUGGAGUGAUUUGUUUGGUUGAUUCCGUCAACGGACGAGAUCCAAGCUGCCCAGUAGGAUUCAGAAUUGCCCAUAGGAUAGCAAUCCCUUCCGCGGGUUUUACCCAAGGGGGGGCGGUAUUCGCUUGUAUCCUUCUCUGCGGGAUUCCUUGUUUUGCGCAAGGUGAGAUUUUGGGCAACAGCAGGUCUGUGAUGCUCCUCAAUGUUCUGGGCGACACGCGCACUACAAUGUCAGUGAGAACAAGAAAAACGACUCUUGUCGGACCUACUUGAUCAAAAGAGUGGGAAAACCCCGGAAUCACGUAGACCCACUUGGGACCGAGUAUUGCAAUUAUUGGUCGCGCAACGAGGAAUGUCUCGUAGGCGCAGCUCAUCAAACUGUGCCGAUUACGUCCCUGCCAUUUGUACACACCGCCCGUCGUUGUUUCCGAUGAUGGUGCAAUACAGGUGAUCGGACAGUCGAGUGCUUCACUUGACCGAAAGUUCACCGAUAUUUCUUCAAUAGAGGAAGCAAAAGUCGUAACAAGGUAGCUGUAGGUGAACCUGCAGAAGGAUCAAGCUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.T.gondii.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.T.gondii.seq new file mode 100644 index 0000000..c3f9ae2 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.T.gondii.seq @@ -0,0 +1,2 @@ +>d.16.e.T.gondii +AACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUUAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAGCUUUUAUACGGCUAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUGGUCUUUACUACAUGGAUAACCGUGGUAAUUCUAUGGCUAAUACAUGCGCACAUGCCUCUUCCCCUGGAAGGCAGUGUUUAUUAGAUACAGAACCAACCCACCUUCCGGUGGUCCUCAGGUGAUUCAUAGUAACCGAACGGAUCGCGUUGACUUCGGUCUGCGACGGAUCAUUCAAGUUUCUGACCUAUCAGCUUUCGACGGUACUGUAUUGGACUACCGUGGCAGUGACGGGUAACGGGGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGAUUCAGGGAGGUAGUGACAAGAAAUAACAACACUGGAAAUUUCAUUUCUAGUGAUUGGAAUGAUAGGAAUCCAAACCCCUUUCAGAGUAACAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCUGCUGGAAGCAGCCAGUCCGCCCUCAGGGGUGUGCACUUGGUGAAUUCUAGCAUCCUUCUGGAUUUCUCCACACUUCAUUGUGUGGAGUUUUUUCCAGGACUUUUACUUUGAGAAAAUUAGAGUGUUUCAAGCAGGCUUGUCGCCUUGAAUACUGCAGCAUGGAAUAAUAAGAUAGGAUUUCGGCCCUAUUUUGUUGGUUUCUAGGACUGAAGUAAUGAUUAAUAGGGACGGUUGGGGGCAUUCGUAUUUAACUGUCAGAGGUGAAAUUCUUAGAUUUGUUAAAGACGAACUACUGCGAAAGCAUUUGCCAAAGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGCUCGAAGACGAUCAGAUACCGUCGUAGUCUUAACCAUAAACUAUGCCGACUAGAGAUAGGAAAACGUCAUGCUUGACUUCUCCUGCACCUUAUGAGAAACCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGCGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUCACCAGGUCCAGACAUAGGAAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAACCUGCUAAAUAGGAUCAGGAACUUCGUGUUCUUGUAUCACUUCUUAGAGGGACUUUGCGUGUCUAACGCAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCUGCACGCGCGCUACACUGAUGCAUCCAACGAGUUUAUAACCUUGGCCGAUAGGUCUAGGUAAUCUUGUGAGUAUGCAUCGUGAUGGGGAUAGAUUAUUGCAAUUAUUAAUCUUCAACGAGGAAUGCCUAGUAGGCGCAAGUCAGCACGUUGCGCCGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGUUCCGGUGAAUUAUUCGGACCGUUUUGUGGCGCGUUCGUGCCCGAAAUGGGAAGUUUUGUGAACCUUAACACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.T.hominis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.T.hominis.seq new file mode 100644 index 0000000..22f2555 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.T.hominis.seq @@ -0,0 +1,2 @@ +>d.16.e.T.hominis +CACCAGGUUGAUUCUGCCUGACGUGGAUGCUAGUCUCAUAGGUUAAGCCAUGCAUGUGCAAGCGAAGCCGGUGGUGGGGCGGCGCAAGGCUCAGUAACGGGCGACUGAUUUGAUCUCCCGGUGUGGACAACCUCUGUAAACGGAGGCCAAAACACAGGAGCGCCGUGUACAGAGACGGUGCGAGAACCGGAGGUGCGGGAGAGUAAGGAGCCAUCCCAUCAGUUAGUAAGUAGGGUAAGGGCCUACUUAGACGAAGACGGGUACGGGGAAUUAGAGUUCGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCAGGUCCAAGGACAGCAGCAGGCGCGCAAAUUACCGAAGCCCGCGUUCGGGGCGGUAGUAAGGAGACGUGUAAGCGAUGUGCAGGUAAAAUAUGCACUGGUAACAGGAGGUAAAGACUGGUGCCAGCAUCCGCGGUAAUACCAGCUCCUGGAGUGUCUAUGAUGAUUGCUGCAGUUAAAGAGUUCGUAGUCGGGCUGCGUGACUGGGGUUUAAGGCCCGCUAUCGAGGCGGGCAGUGCGCCAGAAAAGCAGAGGAUGAGGAGCGGCCGGGGGCCAGGUUAUUAAGCGACGAGAGGUGAAAUUUGAUGACUCGCUUAGGAGCAGCAGAGGCGAAAGCGCUGGCCAGGGGCGAAUCCGAUGAUAAAGGACGUAGGCUAGAGGAUCGAAGACGAUUAGAGACCGUUGUAGUUCUAGCAGUAAACGAUGCCGAUGCCGUGGGGCGGUGAGCCGCCACGCGGAGGAGAAAUUGAGUAGGGCCCUGGGGAGAGUACACGCGCAAGCGAGAAAUUUAAAGGAAAUUGACGGAAGAACACCACAAGGAGUGGAGUGUGCGGCUUAAUUUGACUCAACGCGGGACAGCUUACCAGGCCCGACGGUCGCAUGAGUGUUGUACACGAUAGGCCGGAGAGUGGUGCAUGGCCGUUAACGACAAGUGGGGUGACCUUUGGGUUAAGUCCGGGAAGUAGUGAGACCCCUGCCGGCGUGCCGGGACAGGUGCGCAAAGCACAGGAAGGAAGGGUCAAGAACAGGUCAGUGAUGCCCUUAGAUGGUCUGGGCUGCACGCGCACUACAGUGGUCGCAGAAAUGGCAGAGGUAGCCUGAAUGGCGAUCGAGAGGGAACGAGCUCUGGAAGGGGCUCGGGAACGAGGAAUUGCUAGUAAUCGUGGGCUCAUUAAGACGCGAUGAAUACGUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCGAAGAUGGAGUCAGGCGCGAACAAGCGAGAGCGAGUGAGUGCAGGGUUCUAGAUGUGAUACAAGUCGUAACAAGGUAGCUGUAGGAGAACCAGCAGCAGGAUCAUAA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.T.thermophila.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.T.thermophila.seq new file mode 100644 index 0000000..15995cb --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.T.thermophila.seq @@ -0,0 +1,2 @@ +>d.16.e.T.thermophila +AACCUGGUUGAUCCUGCCAGUUACAUAUGCUUGUCUUAAAUAUUAACCCAUGCAUGUGCCAGUUCAGUAUUGAACAGCGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUAAUUAAAGAUUACAUGGAUAACCGAGCUAAUUGUUGGGCUAAUACAUGCUUAAAAUUCCGUGUCCUGCGACCGGAACGUAUUUAUUAGAUAUUAGACCAAUCGCAGCAAUGUGAUUGAGAUGAAUCAAAGUAACUGAUCGGAUCGAGGUUUACCUCGAUAAAUCAUCUAAGUUUCUGCCCUAUCAGCUCUCGAUGGUAGUGUAUUGGACUACCAUGGCAGUCACGGGUAACGGAGAAUUAGGGUUCGAUUCCGGAGAAGGAGCCUGAGAAACGGCUACUACAACUACGGUUCGGCAGCAGGGAAGAAAAUUGGCCAAUCCUAAUUCAGGGAGCCAGUGACAAGAAAUAGCAAGCUGGGAAACUUACGUUUCUACGGCAUUGAAAUGAGAACAGUGUAAAUCUCUUAGCGAGGAACAAUUGGAGGGCAAGUCAUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGAACUUCUGUUCAGGUUCAUUUCGAUUCGUCGUGUGAAACUGGACAUACGUUUGCAAACUAAAAUCGGCCUUCACUGGUUCGACUUAGGGAGUAAACAUUUUACUGUGAAAAAAUUAGAGUGUUCCAGGCAGGUUUUAGCCCGAAUACAUUAGCAUGGAAUAAUGGAAUAGGACUAAGUCCAUUUUAUUGGUUCUUGGAUUUGGUAAUGAUUAAUAGGGACAGUUGGGGGCAUUAGUAUUUAAUAGUCAGAGGUGAAAUUCUUGGAUUUAUUAAGGACUAACUAAUGCGAAAGCAUUUGCCAAAGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCAAAGACGAUCAGAUACCGUCGUAGUCUUAACUAUAAACUAUACCGACUCGGGAUCGGCUGGAAUAAAUGUCCAGUCGGCACCGUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGGAAGUAUGGUACGCAAGUCUGAAACUUAAAGGAAUUGACGGAACAGCACACCAGAAGUGGAACCUGCGGCUUAAUUUGACUCAACACGGGGAAACUCACGAGCGCAAGACAGAGAAGGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUUUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAACCUGCUAACUAGUCUGCUUGUAAAUAACAGGUUGUACUUCUUAGAGGGACUAUUGUGCAAUAAGCCAAUGGAAGUUUAAGGCAAUAACAGGUCUGUGAUGCCCCUAGACGUGCUCGGCCGCACGCGCGUUACAAUGACUGGCGCAAAAAGUAUUUCCUGUCCUGGGAAGGUACGGGUAAUCUUAUUAAUACCAGUCGUGUUAGGGAUAGUUCUUUGGAAUUGUGGAUCUUGAACGAGGAAUUUCUAGUAAGUGCAAGUCAUCAGCUUGCGUUGAUUAUGUCCCUGCCGUUUGUACACACCGCCCGUCGCUUGUAGUAACGAAUGGUCUGGUGAACCUUCUGGACUGCGACAGCAAUGUUGCGGAAAAAUAAGUAAACCCUACCAUUUGGAACAACAAGAAGUCGUAACAAGGUAUCUGUAGGUGAACCUGCAGAUGGAUCAUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.T.violacea.1.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.T.violacea.1.seq new file mode 100644 index 0000000..627b884 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.T.violacea.1.seq @@ -0,0 +1,2 @@ +>d.16.e.T.violacea.1 +CACCUGGUUGAUCCUGCCAGUGGUAUAUGCUUGUCUCAAGGACUAAGCCAUGCAAGUGUAAGUAUAAGUAAUUUUUACGACGAAACUGCGAAUGGCUCGGUAAAACAGCUAUAGUUUCUUCGAUGCUAACUUACUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCCAACACGCGGGGCAACCCGUGGUACCAAUUAGAUAUCAAGCCAACAUAUGGUGAUUCAUGAUUGUUUUUCUGAUCGCACGCGCAGUGCGACGCAUCGUUCAAGUUUCUGACCUAUCAACUUUCGAUGGUAAGGUAUUGUCUUACCAUGGUUGUGACGGGUAACGGACCGUGGGUGCGGGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUAACACAGGGAGGUAGUGACAAGAAAUAUCAAUAGAGGGCGUUUCUACGUCUUCUAAUUGGAAUGAGAACAAGGUAAACAGCUUAUCGAGGAUCCAGCAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUGUAAGCGUAUACCAAAGUUGUUGCAGUUAAAACGCUCGUAGUCGGAUUUUGGCGCGGCCGGCGCUGUGCGCGUAAAUGCGUGCGGCGUUAAAGAAAAAAUUUAUUUUUUUUCGGGCGUGCUUUUGUGGAGGGCGACACGUGGUGGCUUGAUUGUUGCUGCGGGUCGGCGCCACUUUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCAGGCGUUUGUCGUGAAUACGUUAGCAUGGGAAAAUGGAAUAGGACUUGGUUUCUAUUUUGUUGGUUUGUGAGAGCCGAGUAAUGAUUAAGAGGGACGGUUGGGGGCAUUUGUAUUCCGGCGUCAGAGGUGAAAUUCUUGGAUUGCCGGAAGACAAACCGCUGCGAAAGCGUCUGCCAAGGACGUUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACUAUAAACGAUGAGAACUGGGGAUCGGGCGAGCAUUACGAUGACUCGUCCGGAACCCUCCGGGAAACCAAAGUGUUUGCUUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUUACCAGGUCCGGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAGCGAGACCUGGGCGUGCUAACUAGGGGCUGUUACACAUGUUUGUGUAGCUCAGAAGCAAUAGAGGUUUUUUCUUUUCUUUUCUUUUCUUUCUUUUUUUCCUUUGAGCAAUUGAAGGGGGAGAGGUUUGAAAAAGGAAUGGAACGGAGACUCCUUACUCAUGUUGUUUUGUGCUCCUUCUUAGACGGACUGCGGGCGUCUAGUCCGCGGAAGCUCCAGGCAAUAACAGGUCUGAGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAGCGGACCAACGGGUUUGGAUGCGCGAGAGCGUUUCCUAAUCCCUAAAUCCGCUCGUGCUGGGGAUAGAGGCUUGCAAUUUUCCCUCUUGAACGAGGAAUACCUUGUAAGCGUGGGUCAUCAGCCCGCGCUGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGAUCCGGUGAGGCUUUGGGAUUGCUGCGAUCGGAGUGUUUACGCUCUGGCCGCGGUGAAAACUUAUCCGAACCUUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAAGCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.U.gallina.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.U.gallina.seq new file mode 100644 index 0000000..f847076 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.U.gallina.seq @@ -0,0 +1,2 @@ +>d.16.e.U.gallina +AACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGACUAAGCCAUGCAUGUCUAAGUAUAAAUGUUAUACAGUGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUAAUCGAAUUUACAUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCUGGUUAGCCUGACUUUUGAGGAAGGGCUGUAUUUAUUAGAUAACAAACCAAUAUUCCCCGUGUCUAUUGUGACGACUCAUAAUAACUGAUCGAAUCGCAUGGACUUUGUCCGCGAUACAUCAUUCAAGUUUCUGCCCCAUCAGCUUUCGAUGGUAGUGUAUUGGACUACCAUGGCUUUCACGGGUAACGGAGGAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGACUCAGGGAGGUAGUGACAAGAAAUAACGGACCGAAGCCUAUGUUUCGGGAUUGCAAUGAGUAGAAUUUAAACCCCUUUACGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCAUAUAUUAAAUUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCUGGGAGGGUGCCAAUGUCCGCUCGUUCGCGUGUGCAGCGGCGCCCUUCCAUCCUUCUGUUAACGUUUCUGGUAUUCAGUUACUGGACUCGGGCUCAGAUAUUUUACCUUGAGAAAAUUAGAGUGUUCCAGGCAGGCUUGCGCCGGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUUUAGUCUCCUUUGUUGGUUUGAGGGACUGAAGUAAUGAUUAAUAGGGAUAGUUGGGGGCAUUAGUAUUUAAUUGUCAGAGGUGAAAUUCUCGGAUUUGUUAAAGACUAACUUAUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCAAAGACGAUCAGAUACCGUCCUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUCGGAGGCGCGUUUUAUCCGCCUUCGGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCUUGCGGCUCAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAGCCUGCUAACUAGUCGACUCAAUCUCGAUUGAAUCCGACUUCUUAGAGGGACUUUGUGACUAAACACAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCCGCACGCGUGCUACACUGACGCAUACAGCGAGUACUUCCCAGCUCCGUGAGGCAGCUGGUAAUCAGCAAUAUGCGUCGUGAUGGGGAUAGAUCUUUGGAAUUAUAGAUCUUGAACGAGGAAUUCCUAGUAAGCGCAAGUCAUUACCUUGCGCUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUUCGAGUGAUCCGGUGAACCUUUUGGACUGCGUGGGGUCUCGUGCCUCGUGUGGAAAAUCAAGUAAACCAUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAUGA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.U.grandis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.U.grandis.seq new file mode 100644 index 0000000..8506647 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.U.grandis.seq @@ -0,0 +1,2 @@ +>d.16.e.U.grandis +AACCUGGUUGAUCCUGCCAGUAGUCAUACGCUUGUCUCAAAGACUAAGCCAUGCAUGUCUAAGUAUAAAUGAUAUACAGUGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUAAUCAAAUUUACAUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCUGGUUAGCCUGACUUCAAGGAAAGGCUGUAUUUAUUAGAUAACAAACCAAUAUUCCUCGUGUCUAUUGUGAUGAUUCAUAAUAACUGAUCGAAUCGCAUAGUCUUUGGCUGCGAUACAUCAUUCAAGUUUCUGCCCCAUCAGCUUUCGAUGGUAGUGUAUUGGACUACCAUGGCUUUAACGGGUGACGGAGGAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUAAUUCAGGGAGGUAGUGACAAGAAAUAACGGACUGAGCCUUUGGUUCAGGAUUGCAAUGAGUAGAAUUUAAACCCCUUUACCAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCUGAGGGGGUGACAAAGUCCGCUGAUGCGUGUGCUGCGUCGCCCCUUCAUCCUUCUGUUAACGUUUCUUGGUAUUCAGUUACUGGUUUCGGGCUCAGAUAUUUUACCUUGAGAAAAUUAGAGUGUUUCAGGCAGGCUUGCGCCGGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUUGGGUCUCCUUUGUUGGUUUGAGGGACUCUAGUAAUGAUUAAUAGGGAUAGUUGGGGGCAUUAGUAUUUAAUUGUCAGAGGUGAAAUUCUCGGAUUUGUUAAAGACUAACUUAUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCAAAGACGAUCAGAUACCGUCGUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUCGGAGGUGUGUAUUAUCCACCUUCGGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCUUGCGGCUCAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUUAUGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAGCCUACUAACUAGUCAACGCAAUCUUAUUGCAUUUGACUUCUUAGAGGGACUUUGUGAUUAAACACAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCCGCACGCGUGCUACACUGAUGCAUACAGCGAGUACUUUCCAGCUCCGAGAGGCUGCUGGUAAUCAGCAAUAUGCAUCGUGCUUGGGAUUGAUCUUUGGAAUUAUAGAUCAUCAACGAGGAAUUCCUAGUAAGCGCAAGUCAUUAGCUUGCGUUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUUCGAGUGAUUCGGUGAACCUUUUGGACAGCGUUAGUUUCGGCUGAUGCUGAAAAUCAAGUAAACCAUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAUGA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.U.maydis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.U.maydis.seq new file mode 100644 index 0000000..e4d1fb5 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.U.maydis.seq @@ -0,0 +1,2 @@ +>d.16.e.U.maydis +UACCUGGUUGAUUCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUAUACGCAAAUUAUACUGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUAGUUUAUUUGAUGUUUCUUGCUACAUGGAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCGUAAAAAGCCCCGACUUCUGGAAGGGGUGUAUUUAUUAGAUAAAAACCAUCCUCCUCGGAGUUUGGUGAUUCAUAAUAACUUCUCGAAUCGCACGGCCUUGUGCUGGCGAUGCUUCAUUCAAAUAUCUGCCCUAUCAACUGUCGAUGGUAGGAUAGAGGCCUACCAUGGUUGCAACGGGUAACGGGGAAUAAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCCGACACGGGGAGGUAGUGACAAUAAAUAACAAUGCAGGGCCCUUUUGGGUCUUGUAAUUGGAAUGAGUACAAUUUAAAUCCCUUAACGAGGAACGAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGAAGUUUGGUCUCGGACGCUGGGUCUGCUUAAUUGCAUGUACUUGACGGUCCGAGACUUCCUUCUUGGUGAACGGCCGCCCUCGGGUGGUCCGGAACCAGGACUAUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCCAUAGGCCCGAAUAUAUUAGCAUGGAAUAACAGAAUAGGACGUGCGGUUCUAUUUUGUUGGUUUCUAGAACUGCCGUAAUGAUUAAAAGGGACAGCCGGGGGCAUUAGUAUUUGCACGCUAGAGGUGAAAUUCUUGGAUUGUGCAAAGACUUCCUACUGCGAAAGCAUUUGCCAAGAAUGUUUUCAUUAAUCAAGAACGAAGGUUAGGGUAUCGAAAACGAUUAGAUACCGUUGUAGUCUUAACAGUAAACUAUGCCGACUCCGAAUCGGUCGAUGCUCAUUUCACUGGCUCGAUCGGCGCGGUACGAGAAAUCAAAGUUUUUGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGAAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUCACCGGGUCCGGACAUAGUAAGGAUUGACAGAUUGAUGGCGCUUUCAUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGAUAACGAACGAGACCUUGACCUGCUAAAUAGACGGGUUGACAUUUUGUUGGCCCCUUAUGUCUUCUUAGAGGGACAAUCGACCGUCUAGGUGAUGGAGGCAAAAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCCGGGCUGCACGCGCGCUACACUGACAGAGACAACGAGUGGAGCCCCUUGUCCGAAAUGACUGGGUAAACUUGUGAAACUUUGUCGUGCUGGGGAUGGAGCUUUGUAAUUUUUGCUCUUCAACGAGGAAUUCCUAGUAAGCGCAAGUCAUCAGCUUGCGUUGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGAAUGGCUUAGUGAGGACUUGGGAGAGUACAUCGGGGAGCCAGCAAUGGCACCCUGACGGCUCAAACUCUUACAAACUUGGUCAUUUAGAGGAAGUAAAAGUCGUAACAAGGUAUCUGUAGGUGAACCUGCAGAUGGAUCAUUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.U.pisces.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.U.pisces.seq new file mode 100644 index 0000000..7e0d307 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.U.pisces.seq @@ -0,0 +1,2 @@ +>d.16.e.U.pisces +AACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGACUAAGCCAUGCAUGUCUAAGUAUAAAGGUUAUACAAUGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUAAUCGAAAUUACAUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCUGGUUAGCCUGACUUUUAGGAAGGGCUGUAUUUAUUAGAUAACAAACCAAUAUUCCUUGUGUCUAUUGUGACGACUCAUAAUAACUGAUCGAAUCGCAUGGACUUUGUCCGCGAUACAUCAUUCAAGUUUCUGCCCCAUCAGCUUUCGAUGGUAGUGUAUUGGACUACCAUGGCUUUCACGGGUAACGGAGGAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGACUCAGGGAGGUAGUGACAAGAAAUAACGGACCGAGGCUAUGCUUCGGGAUUGCAAUGAGUAGAAUUUAAACCCCUUUACGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCUGGGAGGGUGCCAAUGUCCGCAUGUUGCGUGUGCAGCGGCGCCCUUCCAUCCUUCUGUUAACGUUUCUGGUAUUCAGUUACUGGACUCGGGCUCAGAUACUUUACCUUGAGAAAAUUAGAGUGUUCCAGGCAGGCUUGCGCCGGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUUUAGUCUCCUUUGUUGGUUUGAGGGACUGAAGUAAUGAUUAAUAGGGAUAGUUGGGGGCAUUAGUAUUUAAUUGUCAGAGGUGAAAUUCUCGGAUUUGUUAAAGACUAACUUAUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCAAAGACGAUCAGAUACCGUCGUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUCGGAGGCUCGUUUUAUCAGCCUUCGGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCUUGCGGCUCAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAGCCUGCUAACUAGUCGACUCAAUCUCGAUUGGGAACGACUUCUUAGAGGGACUUUGUGACUAAACACAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCCGCACGCGUGCUACACUGACGCAUACAGCGAGUACUUCCCAGCUCCGAGAGGCAGCUGGUAAUCAGCAAUAUGCGUCGUGAUGGGGAUAGAUCCUUGGAAUUAUGGAUCUUGAACGAGGAAUUCCUAGUAAGCGCAAGUCAUCACCUUGCGCUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUUCGAGUGAUCCGGUGAACCUUUUGGACUGCGGGUGGCUUCGUGCCAACUGUGGAAAAUCAAGUAAACCAUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAUGA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.V.acridophagus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.V.acridophagus.seq new file mode 100644 index 0000000..9cf06ee --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.V.acridophagus.seq @@ -0,0 +1,2 @@ +>d.16.e.V.acridophagus +CACCAGGUUGAUUCUGCCUGUUAUAUGUACUAGUGUCGAAGAUUUAGCCAUGCAUGCUUUACGAAUUCACAAGAAGAAGUGGCGGACAGCUCAGUAAUACAGUUAUAAUAUACUCUCUACUAAAGGAUAACCGCGGUAAGCUGCGGGUAAAACUUCAAGCUAUGUGUUUCAUGAAAGAAUUUAUAGUUCAGAGUGUUAGUUUCUGGCCUAUUAGUUAGUAGGUAAUGUAAGGGAUUACCUAGACUAUUAUGGGUAACGGGAGAUGAAUGUCUGAUACCGGAGAGGAAGCCUUAGAAACCGCUUUCACGUCCAAGGAUGGCAGCAGGCGCGAAACUUACCCAAUCGUUUUUUAAGACGGAGGUAGUUAUGACACAUGUGAAUUAUUCACGAGGAAGAUCAAUAAAUCAGAUUUUUUUUACUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAGUAGUGCAUAUACAUGCUGUAGUUAGAAAGUUUGUAGCCGUAUAAGCUUGAAUCAGAGGAAAGGAGGACUCUUAAGGUAAACUUUAACUCUGGUCAAUGCUUAUAUUCGAAGCGGAUGGAGGCACUUGUAUUCAAUAGCGAGAGGUAAAAUUUGAUGACCUAUUGAGGACAAUCAGUAGCGAAAGCGAGUGUCUAGUACGCGUUUGAGGGUCAAGAACGUUAGCCGGAGGAUCGAAGAUGAUUAGAUACCGUUGUAGUUCCGGCCGUAAACCAUGCCUACUUGCCUUGUACAUAGUAUGAAGCAUAGAGAAAUUAAGAGUUUUUGGGCUCUAGGGAUAGUAAUCCGGCAACGGACAAACUUAAAGAAAUUGGCGGAAGGACACCACAAGGAGUGGAUUGUGCGGCUCAACUUGACUCAACACGGGAAAUCUUACCAGGGUCUGUAUAUGUGAGACUGUCCCAUUUAUGGUGGUACACGAUAAUAUACUGAGUGGUGCAUGGCCGUUUUCAACACGUGGGGUGACCUGUCAGGUUUAUUCCGGUAACGUGUGAGGUCACAGUAUUAAUAAGUAUUUUAAUAGACAGCUAAUGGUAAAUUAGAGGAAGUGUGACGAUAACAGGUCAGUGAUGCCCUUAGAUACCCUGGGCUGCACGCGCAAUACAUUGAGUAAGUCAUUUACAAUAGUAAUUUUGAAACUUACUCGCUACUGGGAUCAUCCUUUGUAAUUGGGAUGUGAACGUGGAAUUCCUAGUAAUCGUAGCUCACUAAGUUACGAUGAAUGUGUCCCUGUUCUUUGCACACACCGCCCGUCGCUAUCUAAGAUGGAUGUUGAUAUGAAAUUGCUGCUUGAAUGUGAGGUACUUGAGUAUUAACAACUAGAUAAGAUAUAAGUCGUAACAAGGCUGCUAUAGAAGAAUCUGUGGCAAGAUCAUAC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.V.corneae.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.V.corneae.seq new file mode 100644 index 0000000..b9bf68b --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.V.corneae.seq @@ -0,0 +1,2 @@ +>d.16.e.V.corneae +CACCAGGUUGAUUCUGCCUGACGUAGAUGCUAGUCUCUAAGAUUAAGCCAUGCAUGUUUCCUCAAUCAGGGACGAAUAGCUCAGUAAAACUGCGAUGAUUUAGUCUGGCUGUGUAGAUAACACGUGAAAAUGUAGCUAAGGGAAGGCAGAAUAAGACGCAGGACUAUCAGUUAGUUGGUAGUGUAAUGGACUACCAAGACAGUGACGGUUGACGGGAAAUUAGGGUUUUGUACCGGAGAGGGAGCCUGAGAGAUUGCUCCCACGUCCAAGGACGGCAGCAGGCGCGAAAAUUGCCCACUCUUUGCAGGAGGCAGUUAUGAGACGUGAAGAUGAGUAUCUUGUAAAGAGGGAUAGGAGAAUUGGAGGGCAAGUUUGGUGCCAGCAGCCGCGGUAAUACCGACUCCAAGAGUGUGUAUGAGAGAUGCUGCAGUUAAAAAGUCCGUAGUCAUAGAAGGGCAAAGAGAGAUGCGAGGUCUCACAGUGCGAUGAUGGAGGAGCCGAUGGGGAACAUAGUAUACCAGGGCGAGAGAUGAAAUGCCAAGACCCCUGGUGGACUGAGCGAGGCGAAGGCGAUGUUCUUGUAGGCAUUCGGUGAUCAAGGACGAAGGCUGGAGUAUCGAAAGUCAUUAGAUACCGCAGUAGUUCCAGCAGUAAAAGAUGCCGACAUGCUCAUUGGACACAGUGGGCAGGGAGAAAUCUUAGAGUUCGGGCUCUGGGGAUAGUAUGCUCGCAAGGGUGAAAAUUAAAGAAAUUGACGGAGCUACACCACAAGGAGUGGAUUGUGCGGCUUAAUUUGACUCAACGCGAGGAAACUUACCAGGGCCAAGUACUUGUGUAGAAACGAGCAAUACAGGAGUGGUGCAUGGUCGUUGGAAAUUGAUGGGAUGACUUUGACCUUAAAUGGUUGAAUGAGUGAGAUCUUUUGGACAUGUUCCGCACGGAACAGGAAGGAAAAGGCUAUAACAGAUCCGAGAUGCCCUCAGAUGCCCUGGGCUGCACGCGCAAUACAAUAGCAGGUAGAGAGAGAGACAGGAAGGUGCUCAGAUGGACUAUGUGCUGUAAGGCACAUACGAAAGAGGAAUUCCUAGUAAGUGUGUAUCAACAAUGGAUAUUGAAUAAGUCCCUGUAGCUUGUACACACCGCCCGUCACUAUCUCAGAUGUUUUUCAGGAUGAAGAGUCCAGGCUCUGAAUAAUGAAAAGUAGAUAAGAUGUAAGUCGUAACAAGGUUGCGGUUGGUGAACCAUUAGCAGGAUCAUAA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.V.culicis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.V.culicis.seq new file mode 100644 index 0000000..32ce19a --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.V.culicis.seq @@ -0,0 +1,2 @@ +>d.16.e.V.culicis +CACCAGGUUGAUUCUGCCUGACGUGGAUGCUAGUCUCAUAGGUUAAGCCAUGCAUGUGCAAGCGAAGCCGGUGGUGGAGCGGCGCAAGGCUCAGUAACGGGCGACUGAUUUGAUCUCCCGGUGUGGACAACCUCUAUAACCGGAGGCCAAAACACAGGAGGCGCGUGACACGGGCACGGGCGUGCAACCGGCAGGUGCGGGAGAGUAAGGAGCCAUCCCAUCAGUUAGUAAGUAGGGUAAGGGCCUACUUAGACGAAGACGGGUACGGGGAAUUAGAGUUCGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCAGGUCCAAGGACAGCAGCAGGCGCGGAAAUUACCGAAGCCCGCGUUCGGGGCGGUAGUAAGGAGACGUGAAUACGAUGUGCAGGUAAAAUAUGCACUGGUAACAGGAGGUCAAGACUGGUGCCAGCAUCCGCGGUAAUACCAGCUCCUGGAGUGUCUAUGACGAUUGUUGCAGUUAAAGAGUUCGUAGUCGGGCUGCAUGACCGGCGCUGAAGGCUCCCUAUCGAGGGGGGCAGGGCGCCGGAAAAGCAGAGGAUGAGGAGCGGCCGGGGGCCAGGUUAUUAAGCGACGAGAGGUGAAAUUUGAUGACUCGCUUAGGAGCAGCAGAGGCGAAAGCGCUGGCCAGGGGCGAAUCCGAUGAUAAAGGACGUAGGCUAGAGGAUCGAAGACGAUUAGAGACCGUUGUAGUUCUAGCAGUAAACGAUGCCGAUGCCGUGGGGCGGUGCAGCCGCCACGCGGAGGAGAAAUUGAGUAGGGCCCUGGGGAGAGUACACGCGCAAGCGGGAAAUUUAAAGGAAAUUGACGGAAGAACACCACAAGGAGUGGAGUGUGCGGCUUAAUUUGACUCAACGCGGACAGCUUACCAGGCCCGACGGUCGCACGAGUGUGGUACACGAUAGGCCGGAGAGUGGUGCAUGGCCGUUAACGACAAGUGGGGUGACCUUUGGGUUAAGUCCGGGAAGUAGUGAGACCCCUGCCGGCGCGCCGGGACAGGUGCUCAAAGCACAGGAAGGAAGGGUCAAGAACAGGUCAGUGAUGCCCUUAGAUGGUCUGGGCUGCACGCGCACUACAGUGGUCGCAGAAAUCAGUGCCCGAGCGGCAAUGGCGAUCGAGAGGGAACGAGCUCUGGAAGGGGCUCGGGAACGAGGAAUUGCUAGUAAUCGUGGGCUCAUUAAGACACGGUGAAUACGUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCGAAGAUGGAGUCAGGCGCGAACAAGCGAGAGCGAGUGAGUGCAGGGUUCUAGAUGUGAUACAAGUCGUAACAAGGUAGCUGUAGGAGAACCAGUAGCAGGAUCAUAA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.V.imperfecta.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.V.imperfecta.seq new file mode 100644 index 0000000..ddad56b --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.V.imperfecta.seq @@ -0,0 +1,2 @@ +>d.16.e.V.imperfecta +CACCAGGUUGAUUCUGCCUGACGUAGACGCUAUACUCUAAGAUUAACCCAUGCAUGUUAUUGAAUAUAAAGAAAAGACGAACAGCUCAGUAACUCUUAUUUGAUUUGAUGUAUUAGGACUCUAACUAUGUUAAAUUAUAGGUAACAAUAAUACAAUAAGAAUAAGAUCUAUCAGUUAGUUGUUAAGGUAAUGGCUUAACAAGACUAUGACGGAUAACGGUAUUACUUUGUAAUAUUCCGGAGAAGGAGCCUGAGAGAUUGCUACUAAGUCUAAGGAUUGCAGCAGGGGCGAAACUUGACCUAUGAUAUUAUAUUGAGGCAGUUAUGAGUAGUAUUUUAUAAUUAUUGUAAUAUUGUAAGUACAUAUUACAAGAUAAAUCGGAGGGCAAAUCGAGUGCCAGCAGCCGCGGUAAUACUUGUUCCGAUAGUGUGUAUGAUGAUUGAUGCAGUUAAAAAGUCUGUAGUUUAUUUAUAAUAAGCAUUGUAAGGUAUACUGUAUGGUUAGGAGAGAGAUGAAAUGUGAUAACCCUAACUGGAUGAACAGAAGCGAAAGCUGUAUACUUAAAUGUAUUAUUAGAACAAGGACGUAAGCUAGAGGAUCGAAGAUGAUUAGAUACCAUUGUAGUUCUAGCAGUAAACUAUGUUGAAUCAUAGAUAUAUUUUGAUAUAUAUUUGUGUAGAGAAAUUAAGAUUAUAUUGACUCUGGGGAUAGUAUGAUCGCAAGAUUGAAAAUUAAAGAAAUUGACGGAAGAAUACCACAAGGAGUGGAUUGUGCGGCUUAAUUUGACUCAACGCGGGGUAAUUUACCAGGUAUAACAUGGUAUAAUAUUUUAUCAUGAUAGUGGUGCAUGGCCGUUUCCAAUGGAUGCUGUGAAGUAAUGAUUAAUUUCAACAAGAUGUGAGACCCUCAUUUAGACAGAUGUAGUGAUACAUAUGAAGGAGAGGAUUAAAACAGGUCCGUUAUGCCCUAAGAUAAUCUGGGUUGCACGCGCAAUACAAUAAUAUUUGAUAUUAUAAGGGAUAAUAUAAUGUAAGAUAUAUUUGAACAUGGAAUUGCUAGUAAAUUUUAUUUAAUAAGUAGAAUUGAAUGAGUCCCUGUUCUUUGUACACACCGCCCGUCGCUAUCUAAGAUGGUAUUAUCUAUGAACAAAUUUAUAAAGUGAAUAGAUAGUACUAGAUCUGAUAUAAGUCGUAACAUGGUUGCUGUUGGAGAACCAGCAGCAGGAUCAUAA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.V.necatrix.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.V.necatrix.seq new file mode 100644 index 0000000..1ae37da --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.V.necatrix.seq @@ -0,0 +1,2 @@ +>d.16.e.V.necatrix +CACCAGGUUGAUUCUGCCUGACGUAGACGCUAUUCCCUAAGAUUAACCCAUGCAUGUUUUUGAUAUGGAAAAAUGGACUGCUCAGUAAUACUCACUUUAUUUAAUGUAUUAAAUUAGUAUAACUGCGUUAAAGUGUAGCAUAAGACAUAUACAGUAAGAGUGAGACCUAUCAGCUAGUUGUUAAGGUAAUGGCUUAACAAGGCAAUGACGGGUAACGGUAUUACUUUGUAAUAUUCCGGAGAAGGAGCCUGAGAGACGGCUACUAAGUCUAAGGAUUGCAGCAGGGGCGAAACUUGACCUAUGGAUUUUAUCUGAGGCAGUUAUGGGAAGUAAUAUUCUAUUGUUUCAUAUUGUAAAAGUAUAUGAGGUGAUUAAUUGGAGGGCAAAUCAAGUGCCAGCAGCCGCGGUAAUACUUGUUCCAAGAGUGUGUAUGAUGAUUGAUGCAGUUAAAAAGUCCGUAGUUUAUAUUUAAGAAGCAAUAUGAGGUGUACUGUAUAGUUGGGAGAGAGAUGAAAUGUGACGACCCUGACUGGACGAACAGAAGCGAAAGCUGUACACUUGUAUGUAUUUUUUGAACAAGGACGUAAGCUGGAGGAGCGAAGAUGAUUAGAUACCAUUGUAGUUCCAGCAGUAAACUAUGCCGACGAUGUGAUAUGAUAUUAAUUGUAUUAGAUGAUAGAAAUUUGAGUUUUUUGGCUCUGGGGAUAGUAUGAUCGCAAGAUUGAAAAUUAAAGAAAUUGACGGAAGAAUACCAGAAGGAGUGGAUUGUGCGGCUUAAUUUGACUCAACGCGAGGUAACUUACCAAUAUUUUAUUCAGAGAAGAUUUUCGAUCUGAGAAUGAUAAUAGUGGUGCAUGGCCGUUUUCAAUGGAUGCUGUGAAGUUUUGAUUAAUUUCACCAAGACGUGAGACCCUUUUAUUAAUAGACAGACACAAUCAGUGUAGGAAGGAAAGGAUUAAAACAGGUCCGUUAUGCCCUCAGACAUUUUGGGCUGCACGCGCAAUACAAUAGAUAUAUAAUCUUUAUGGGAUAAUAUUUUGUAAGAGAUAUUUGAACUUGGAAUUGCUAGUAAAUUUUAUUAAAUAAGUAGAAUUGAAUGUGUCCCUGUUCUUUGUACACACCGCCCGUCGCUAUCUAAGAUGAUAUGUGUUGUGAAAUUAGUGAAAACUACUUGAACAAUAUGUAUUAGAUCUGAUAUAAGUCGUAACAUGGUUGCUGUUGGAGAACCAUUAGCAGGAUCAUAA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.Vairimorpha.sp.C21.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.Vairimorpha.sp.C21.seq new file mode 100644 index 0000000..ae6d794 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.Vairimorpha.sp.C21.seq @@ -0,0 +1,2 @@ +>d.16.e.Vairimorpha.sp.C21 +CACCAGGUUGAUUCUGCCUGACGUAGACGCUAUUCCCUAAGAUUAACCCAUGCAUGUUUUUGACAUUUGAAAAAUGGACUGCUCAGUAAUACUUACUUUAUUUAAUGUACAUUUGAAAAUAACUACGUUAAAGUGUAGAUAAGAUGUGUACAGUAAGAGUAAGACCUAUCAGCUAGUUGUUAAGGUAAUGGCUUAACAAGGCAGUGACGGGUAACGGUAUUACUUUGUAAUAUUCCGGAGAAGGAGCCUGAGAGACGGCUACUAAGUCUAAGGAUUGCAGCAGGGGCGAAACUUGACCUAUGGAUUUUUUCUGAGGCAGUUAUGGGAAGUAAUAUUAUAUUGUUUCAUAUUGUAAAAGUAUAUGAGGUGAUUAAUUGGAGGGCAAAUCAAGUGCCAGCAGCCGCGGUAAUACUUGUUCCAAGAGUGUGUAUGAUGAUUGAUGCAGUUAAAAAGUCCGUAGUUUAUGAUUAAGAAGCAAUAUGAGGUGUACUGUAUAGUUGGGAGAAAAAUGAAAUGUGACGACCCUGACUGGACGAACAGAAGCGAAAGCUGUACACUUGUAUGUAUUUUUUGAACAAGGACGUAAGCUGGAGGAGCGAAGAUGAUUAGAUACCAUUGUAGUUCCAGCAGUAAACUAUGCCAACGAUGUGAUAUGAUAUUAAUUGUAUUACAUGAUAGAAAUUUGAGUUUUUUGGCUCUGGGGAUAGUAUGAUCGCAAGAUUGAAAAUUAAAGAAAUUGACGGAAGAAUACCACAAGGAGUGGAUUGUGCGGCUUAAUUUGACUCAACGCGAGGUAACUUACCAAUAUUUUAUUAUUCUGAGAUAAUUUUCCAAUUUGAGAAUGAUAAUAGUGGUGCAUGGCCGUUUUCAAUGGAUGCUGUGAAGUUUUGAUUAAUUUCAACAAGACGUGAGACCCUUUUUUAUAUAAGACAGACACAAUCAGUGUAGGAAGGAAAGGAUUAAAACAGGUCCGUUAUGCCCUCAGACAUUUUGGGCUGCACGCGCAAUACAAUAGAUAUAUAAUCUUUAUGGGAUAAUAUUUUGUAAGAGAUAUUUGAACUUGGAAUUGCUAGUAAAUUUUAUUAAAUAAGUAGAAUUGAAUGUGUCCCUGUUCUUUGUACACACCGCCCGUCGCUAUCUAAGAUGAUAUGUGUUAUGAAAAUAGUGAAAACUACUUGAACAAUAUGUAUUAGAUCUGAUAUAAGUCGUAACAUGGUUGCUGUUGGAGAACCAUUAGCAGGAUCAUAA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.X.borealis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.X.borealis.seq new file mode 100644 index 0000000..780471c --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.X.borealis.seq @@ -0,0 +1,2 @@ +>d.16.e.X.borealis +UACCUGGUUGAUCCUGCCAGUAGCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCACGUGUAAGUACGCACGGCCGGUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUGGUUCCUUUGAUCGCUCCAUCUGUUACUUGGAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCCGACGAGCGCUGACCCCCAGGGAUGCGUGCAUUUAUCAGAUCAAAACCAACCCGGGGCCCCCGCGCCCCGGCCGCUUUGGUGACUCUAGAUAACCUCGGGCCGAUCGCACGUCCCCGUGACGGCGACGAUACAUUCGGAUGUCUGCCCUAUCAACUUUCGAUGGUACUUUCUGCGCCUACCAUGGUGACCACGGGUAACGGGGAAUCAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCACUCCCGACGCGGGGAGGUAGUGACGAAAAAUAACAAUACAGGACUCUUUCGAGGCCCUGUAAUUGGAAUGAGUACACUUUAAAUCCUUUAACGAGGAUCUAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGCUGCAGUUAAAAAGCUCGUAGUUGGAUCUUGGGAUCGAGCUGGCGGUCCGCCGCAAGGCGAGCUACCGCCUGUCCCAGCCCCUGCCUCUCGGCGCCUCCCCGAUGCUCUUGACUGAGUGUCCCGGGGGCCCGAAGCGUUUACUUUGAAAAAAUUAGAGUGUUCCAAGCAGGCCGCGUCGCCUGGAUACUUCAGCUAGGAAUAAUGGAAUAGGACUCCGGUUCUAUUUUGUUGGUUUUCGGAACUGGGGCCAUGAUUAAGAGGGACGGCCGGGGGCAUUCGUAUUGUGCCGCUAGAGGUGAAAUUCUUGGACCGGCGCAAGACGAACCAAAGCGAAAGCAUUUGCCAAGAAUGUUUUCAUUAAUCAAGAACGAAAGUCGGAGGUUCGAAGACGAUCAGAUACCGUCGUAGUUCCGACCAUAAACGAUGCCGACUAGCGAUCCGGCGGCGUUAUUCCCAUGACCCGCCGAGCAGCUUCCGGGAAACCAAAGUCUUUGGGUUCCGGGGGGAGUAUGGUUGCAAAGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAACCUCACCCGGCCCGGACACGGAAAGGAUUGACAGAUUGAUAGCUCUUUCUCGAUUCUGUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGAUAACGAACGAGACUCCUCCAUGCUAACUAGUUACGCGACCCCCGGCGGUCGGCGUCCAACUUCUUAGAGGGACAAGUGGCGUUCAGCCACACGAGAUCGAGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCGGGGCUGCACGCGCGCUACACUGAACGGAUCAGCGUGUGUCUACCCUGCGCCGACAGGUGCGGGUAACCCGCUGAACCCCGUUCGUGAUAGGGAUCGGGGAUUGCAAUUAUUUCCCAUGAACGAGGAAUUCCCAGUAAGUGCGGGUCAUAAGCUCGCGUUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGGAUGGUUUAGUGAGGUCCUCGGAUCGGCCCCGCCGGGGUCGGCAACGGCCCUGGCGGAGCGCCGAGAAGACGAUCAAACUUGACUAUCUAGAGGAAGUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.X.laevis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.X.laevis.seq new file mode 100644 index 0000000..ec9c5bb --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.X.laevis.seq @@ -0,0 +1,2 @@ +>d.16.e.X.laevis +UACCUGGUUGAUCCUGCCAGUAGCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCACGUGUAAGUACGCACGGCCGGUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUGGUUCCUUUGAUCGCUCCAUCUGUUACUUGGAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCCGACGAGCGCUGACCCCCAGGGAUGCGUGCAUUUAUCAGACCAAAACCAAUCCGGGGCCCCCGCGCCCCGGCCGCUUUGGUGACUCUAGAUAACCUCGGGCCGAUCGCACGUCCCCGUGACGGCGACGAUACAUUCGGAUGUCUGCCCUAUCAACUUUCGAUGGUACUUUCUGCGCCUACCAUGGUGACCACGGGUAACGGGGAAUCAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCACUCCCGACGCGGGGAGGUAGUGACGAAAAAUAACAAUACAGGACUCUUUCGAGGCCCUGUAAUUGGAAUGAGUACACUUUAAAUCCUUUAACGAGGAUCUAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGCUGCAGUUAAAAAGCUCGUAGUUGGAUCUUGGGAUCGAGCUGGCGGUCCGCCGCGAGGCGAGCUACCGCCUGUCCCAGCCCCUGCCUCUCGGCGCCUCCCCGAUGCUCUUGACUGAGUGUCCCGGGGGCCCGAAGCGUUUACUUUGAAAAAAUUAGAGUGUUCCAAGCAGGCCGCGUCGCCUGGAUACUUCAGCUAGGAAUAAUGGAAUAGGACUCCGGUUCUAUUUUGUUGGUUUUCGGAACUGGGGCCAUGAUUAAGAGGGACGGCCGGGGGCAUUCGUAUUGUGCCGCUAGAGGUGAAAUUCUUGGACCGGCGCAAGACGAACCAAAGCGAAAGCAUUUGCCAAGAAUGUUUUCAUUAAUCAAGAACGAAAGUCGGAGGUUCGAAGACGAUCAGAUACCGUCGUAGUUCCGACCAUAAACGAUGCCGACUAGCGAUCCGGCGGCGUUAUUCCCAUGACCCGCCGAGCAGCUUCCGGGAAACCAAAGUCUUUGGGUUCCGGGGGGAGUAUGGUUGCAAAGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAACCUCACCCGGCCCGGACACGGAAAGGAUUGACAGAUUGAUAGCUCUUUCUCGAUUCUGUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGAUAACGAACGAGACUCCUCCAUGCUAACUAGUUACGCGACCCCCGGCGGUCGGCGUCCAACUUCUUAGAGGGACAAGUGGCGUUCAGCCACACGAGAUCGAGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCGGGGCUGCACGCGCGCUACACUGAACGGAUCAGCGUGUGUCUACCCUGCGCCGACAGGUGCGGGUAACCCGCUGAACCCCGUUCGUGAUAGGGAUCGGGGAUUGCAAUUAUUUCCCAUGAACGAGGAAUUCCCAGUAAGUGCGGGUCAUAAGCUCGCGUUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGGAUGGUUUAGUGAGGUCCUCGGAUCGGCCCCGCCGGGGUCGGCCACGGCCCUGGCGGAGCGCCGAGAAGACGAUCAAACUUGACUAUCUAGAGGAAGUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.Z.mays.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.Z.mays.seq new file mode 100644 index 0000000..6dcff46 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.Z.mays.seq @@ -0,0 +1,2 @@ +>d.16.e.Z.mays +UACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUGCAAGUAUGAACUAAUUCGAACUGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUAGUUUGUUUGAUGGUACGUGCUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCAACAAACCCCGACUUCCGGGAGGGGCGCAUUUAUUAGAUAAAAGGCUGACGCGGGCUCUGCCCGCCGAUCCGAUGAUUCAUGAUAACUUGACGGAUCGCACGGCCUUCGUGCCGGCGACGCAUCAUUCAAAUUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGGGGCCUACCAUGGUGGUGACGGGUGACGGAGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACGGGGAGGUAGUGACAAUAAAUAACAAUACCGGGCGCGUUAGUGUCUGGUAAUUGGAAUGAGUACAAUCUAAAUCCCUUAACGAGGAUCCAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUUAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGACCUUGGGCCGGGCCGGGUGCCGCCGCCGUACGGGCAGAACCGACCGGCUCGACCCUUCUGCCGGCGAUGCGCUCCUGGCCUUAACUGGCCGGGUCGUGCCUCCGGGCCGUUACUUUGAAGAAAUUAGAGUGCUCAAAGCAAGCCAUCGCUCUGGAUACAUUAGCAUGGGAUAACAUCAUAGGAUUCCGGUCCUAUUGUGUUGGCCUUCGGGAUCGGAGUAAUGAUUAAUAGGGACAGUCGGGGGCAUUCGUAUUUCAUAGUCAGAGGUGAAAUUCUUGGAUUUAUGAAAGACGAACAACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUGGGGGCUCGAAGACGAUCAGAUACCGUCCUAGUCUCAACCAUAAACGAUGCCGACCAGGGAUCAGCGGUGUUACUAAUAGGACCCCGCUGGCCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGCGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCAGACAUAGCAAGGAUUGACAGACUGAGAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGUCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUCAGCCUGCUAACUAGCUAUGCGGAGCCAUCCCUCCGUAGUUAGCUUCUUAGAGGGACUAUGGCCGUUUAGGCCGCGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAUGUAUCCAACGAGUAUAUAGCCUUGGCCGACAGGCCGGUAAUCUUGGGAAAUUUCAUCGUGAUGGGGAUAGAUCAUUGCAAUUGUUGGUCUUCAACGAGGAAUGCCUAGUAAGCGCGAGUCAUCAGCUCGCGUUGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAAUGGUCCGGUGAAGUGUUCGGAGCUCGGCCGCACCGGUUCGCCGCCCCCGACGUCGCGAGAAGUCCAUUGAACCUUAUCAUUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUG diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.A.americana.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.A.americana.seq new file mode 100644 index 0000000..3994c56 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.A.americana.seq @@ -0,0 +1,2 @@ +>d.16.m.A.americana +CAUAGGUUUGGUCCCAGCCUUCCUAUUGACUACUAAUAGACUUACACAUGCAAGCAUCCGCACCCCAGUGAAGACGCCCUUUAAAUCCACCUGAACCAAAAGGAGCUGGUAUCAAGCACACAUUUGUAGCUUAUGACGCCUUGCUCAGCCACACCCCCACGGGAGACAGCAGUGAUAAAAAUUAAGCUAUGGACGAAAGUCUGACUAAGUCAUAUUGAUAAGGGUCGGUAAAUCUCGUGCCAGCCACCGCGGUCAUACGAUUGACCCUAGUUAAUAGGAAUACGGCGUAAAGAGUGUUAAAGCAUCACACUAAAUAGAGUUAAAUUAUAACUAAGCUGUAAAAAGCCACAGCUGUAAUAAAAAUAGACAACGAAAGUGACUCUACAACCGCUGAUCACACUACAGCUAAGACCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCAUAAACACAGGUAAUUGUAUAAACAAAAUUAUUCGCCAGAGUACUACUAGCAACUGCUUAAAACUCAAAGGACUUGGCGGUGCUUUACACCCUUCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGAUAAACCUCACCAACCCUUGCUAAUACAGUCUAUAUACCGCCAUCUUCAGCAAACCCUAAAAAAGGAACAAGAGUAAGCAUAAUAAUAGCACAUAAAAACGUUAGGUCAAGGUGUAACCUAUGGGUUGGAAAGAAAUGGGCUACAUUUUCUAUUUCAAGAACACUCAACACGAAAGUUAUUAUGAAACUGAUGACUAAAGGAGGAUUUAGUAGUAAACUAAGAAUAGAGCGCUUAGUUGAAUUAGGCUAUGAAGCACGCACACACCGCCCGUCACCCUCCUCAAGUAAACACGAUACACCUAAACUUAUUCACACGUAUUAACCGUACAAGAGGAGAUAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGAUAAAU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.A.cahirinus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.A.cahirinus.seq new file mode 100644 index 0000000..487d01e --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.A.cahirinus.seq @@ -0,0 +1,2 @@ +>d.16.m.A.cahirinus +AAUAGGUUUGGUCCUAGCCUUAUAAUUAGCUGAAAGUAAAAUUACACAUGCAAGACUCCCCACACCAGUGUCAAAUCCCUUAGAACUAGACAGCUAACCUAAGGAGAGGAUAUCAAGCACAUUAAUAUAGCUCAAGACAUCUCGCCAAGCCACACCCCCACGGGAAACAGCAGUGAUAAAAAUUAAGCAAUGAACGAAAGUUUGACUUAGUUAUACUUCCAAGGGUUGGUAAAUUUCGUGCCAGCCACCGCGGUCAUACGAUUAACCCAAACUAAUUAUUUUACGGCGUAAAAGGUGUUAUAUCUAAAACAAAUAGAAUUAAAACCUGACUUAUAUGUGAAAAUUCAUUGUCAGACAAAAACACAACCACGAAAGUGAUUCUAAUAAACCAAACACGAAAGCUAAGACCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAACUUAAAUAAUUAAUAACAAAAUUAUUUGCCAGAGAACUACUAGCCAUAGCUUAAAACUCAAAGGACUUGGCGGUACUUUAUAUCCACCUAGAGGAGCCUGUUCUAUAAUCGAUAUACCCCGUUACACCUCACCACCCCUUGCUAAUCCAGCCUAUAUACCGCCAUCUUCAGCAAACCCUCAAAAGGACACACAGUAAGCAAGAGCACAAACAUAAAAAAGUUAGGUCAAGGUGUAGCCCAUGAGGUGGGAAGUAAUGGGCUACAUUUUCUUAAAAAGAACACACGAAACCCUUUAUGAAAUUAAAGGAUAAAGGAGGAUUUAGUAGUAAAUUAAGAAUAGAGAGCUUAAUUGAAUAGAGCAAUGAAGUGCGCACACACCGCCCGUCACCCUCCUCAAACUAAUCUUCAAGUAAAAUAAAUAAAAUUAAACUAACUAGAAUACGAGAGGAGACAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.A.fulgens.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.A.fulgens.seq new file mode 100644 index 0000000..eeb9896 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.A.fulgens.seq @@ -0,0 +1,2 @@ +>d.16.m.A.fulgens +CAAAGGUUUGGUCCUAGCCUUCCCGUUAGUUCUUAAUAAAAUUACACAUGCAAGUAUCUACACCCCAGUGAAAAUGCCCUCCAAAUCACUAGUUGAUUAAAAGGAGCAGGUAUCAAGCACACUUUACAUAAGUAGCUCACAACACCUUGCUUAGCCACACCCCCACGGGAUACAGCAGUGAUAAAAAUUAAGCUAUAAACGAAAGUUUGACUAAGUUAUAUUAAUAGAGGGUUGGUAAAUUUCGUGCCAGCCACCGCGGCCAUACGAUUAACCCAAACUAACGGGCAUCCGGCGUAAAACGUGUUAAAGAAUCUACUCACAUUAAAGUUAAAACUUAAUCAGGCCGUAAAAAGCUACCGUUAACAUAAAAUACCUUACGAAAGUAACUUUAUUAAUUCUGAUUACACGACAGCUAAGGCCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAACAUAAAUAGUUUAGUAUAACAAAACUAUUCGCCAGAGAACUACUAGCAAUAGCCUAAAACUCAAAGGACUUGGCGGUGCUUUACACCCCUCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGAUAAACCUUACCACUUCUAGCUACUUCAGUCUAUAUACCGCCAUCUUCAGCAAACCCUCAAAAGGAAGCAAAGUAAGCAUAAUGAUUCCUGCAUAAAAAAGUUAGGUCAAGGUGUAACCCAUGAAGUGGAAAGAAAUGGGCUACAUUUUCUAAACAAGAACACUAUACGAAAAUUUUUAUGAAAUUAAAACCUAAAGGUGGAUUUAGUAGUAAAUUAAGAAUAGAGAGCUUAGUUGAAUUGGGCUAUAAAGCACGCACACACCGCCCGUCACCCUCCUCAAACGUCAAGAUUUAAACCCAAUAUAUAAUCACAACAGACUAAACGCAAGAGGAGACAAGUCGUAACAAGGUAAGCGUACUGGAAGGUGUGCUUGGAUAAAC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.B.brevicauda.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.B.brevicauda.seq new file mode 100644 index 0000000..2249b46 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.B.brevicauda.seq @@ -0,0 +1,2 @@ +>d.16.m.B.brevicauda +UAAAGGUUUGGUCCCAGCCUUCCUAUUAAUUGUUAGCAAAUUUACACAUGCAAGUAUCCGCGCCCCUGUGAGAAUACCCUUUAAAUCACCUAUGACUGAAAGGAGUAGGUAUCAAGCACACUUAUUUAUAAGUAGCUAAUCACACCUUGCUUAGCCACACCCCCACGGGAAACAGCAGUGAUAAAAAUUAAGCCAUGAACGAAAGUUCGACUAAGUUAUGCUAAUAUUUAGGGUUGGUAAAUUUCGUGCCAGCCACCGCGGUCAUACGAUUAACCCAAAUUAAUAGGUAGCGGCGUAAAGCGUGUUAAAGAACACUAAAUAAAAUAAAGAUAAAACUUGACUAGGCUGUAGAAAGCAACAGUCAAGACUAAAAUAAACUACGAAAGUGACUUUAUUACUUUUGAUCACACGAUAGCUAAGACCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAACUUAGGUAAUUUAAUUAACAAAACUACUCGCCAGAGGACUACUAGCAACAGCUUAAAACUCAAAGGACUUGGCGGUGCUUUAUAUCCAUCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGAUAAACCUCACCGCCCCUUGCUAAUACAGCUUAUAUACCGCCAUCUUCAGCAAACCCUUAAAAGGAAUAACAGUAAGCUUAAAUAUUUCACAUAAAAACGUUAGGUCAAGGUGUAGCUUAUGGGGCGGGAAGAAAUGGGCUACAUUUUCUAUAACUAGAAUAUUCACGAAAGUUUCUAUGAAACUAGAAACCAAAGGAGGAUUUAGUAGUAAGUUAAGAAUAGAGCGCUUAACUGAACCAGGCCAUGAAGCACGCACACACCGCCCGUCACCCUCCUCAAGUAUUUUAAGUCUACUGAUAUAUAAUCUCAGACUAACUAAUAUUAGAGGAGAUAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGACGAAU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.B.taurus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.B.taurus.seq new file mode 100644 index 0000000..f3a2a28 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.B.taurus.seq @@ -0,0 +1,2 @@ +>d.16.m.B.taurus +CAUAGGUUUGGUCCCAGCCUUCCUGUUAACUCUUAAUAAACUUACACAUGCAAGCAUCUACACCCCAGUGAGAAUGCCCUCUAGGUUAUUAAAACUAAGAGGAGCUGGCAUCAAGCACACACCCUGUAGCUCACGACGCCUUGCUUAACCACACCCCACGGGAAACAGCAGUGACAAAAAUUAAGCCAUAAACGAAAGUUUGACUAAGUUAUAUUAAUUAGGGUUGGUAAAUCUCGUGCCAGCCACCGCGGUCAUACGAUUAACCCAAGCUAACAGGAGUACGGCGUAAAACGUGUUAAAGCACCAUACCAAAUAGGGUUAAAUUCUAACUAAGCUGUAAAAAGCCAUGAUUAAAAUAAAAAUAAAUGACGAAAGUGACCCUACAAUAGCCGACGCACUAUAGCUAAGACCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAACACAGAUAAUUACAUAAACAAAAUUAUUCGCCAGAGUACUACUAGCAACAGCUUAAAACUCAAAGGACUUGGCGGUGCUUUAUAUCCUUCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGAUAAACCUCACCAAUUCUUGCUAAUACAGUCUAUAUACCGCCAUCUUCAGCAAACCCUAAAAAGGAAAAAAAGUAAGCGUAAUUAUGAUACAUAAAAACGUUAGGUCAAGGUGUAACCUAUGAAAUGGGAAGAAAUGGGCUACAUUCUCUACACCAAGAGAAUCAAGCACGAAAGUUAUUAUGAAACCAAUAACCAAAGGAGGAUUUAGCAGUAAACUAAGAAUAGAGUGCUUAGUUGAAUUAGGCCAUGAAGCACGCACACACCGCCCGUCACCCUCCUCAAAUAGAUUCAGUGCAUCUAACCCUAUUUAAACGCACUAGCUACAUGAGAGGAGACAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGAUAAAU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.C.elegans.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.C.elegans.seq new file mode 100644 index 0000000..ca47b03 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.C.elegans.seq @@ -0,0 +1,2 @@ +>d.16.m.C.elegans +UAAAGUUUUCUUUCAGGGAAUUAAAAUUUGAUCAUGGUUUAAGAUGAUUUAAAAUGGUAUUAUCUAAAUUUGAUUUACAGAGUAGGCAAUAAAAAUUUACCUCGGCAAUUUAUCGCUUGUAAAAUACUUGUUCCAGAAUAAUCGGCUAGACUUGUUAAAGCUUGUACUUUAAUUGAUGUUAAUUAUGAAAUUAUUAUAUUUUCUUUUAGAUCUAUGGUAGAAUUUGGAUUUAUAUUAGUGAAUUUUCAUAAUUUUAAGAUUUGUUGAACAAAGCAGAUUAGUACCUGGUUAGACAAAAAUUAAAAGAGCAGGAGUAAAGUUGUAUUUAAACUGAAAAGAUAUUGGCAGACAUUCUAAAUUAUCUUUGGAGGCUGAGUAGUAACUGAGAACCCUCAUUAACUACUUAAUUUUUUGACUCGUGUAUGAUCGUUUAUUUUAUUCUUAAGGAUUAUAAUAAAAAAUUUUUAAUUUAUUAAAAUAGAUAUAUACCCGGUUUAUGAUUUAAGAAACAUUUGGCCUACAAUAUUUUAUAUUAUGGAUUUUAGUUUUAGUUAACUAAAUGAAAUUGUAAAAGACAGUAAAAAAUUCUUAAUGUAUUUUUGAAGAUUAUCUAGAAGUGGUACAAAUCAUCCAUCAAUUGCCCAAAGGGGAGUAAGUUGUAGUAAAGUAGAUUUAGGGGAACCUGAAUCUAGUAAUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.D.dugon.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.D.dugon.seq new file mode 100644 index 0000000..9bb815f --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.D.dugon.seq @@ -0,0 +1,2 @@ +>d.16.m.D.dugon +UAAAGGUUUGGUCCUGGCCUUCUUAUUGGUUCUUAGCGAGCUUACACAUGCAAGUAUCCGCGCGCCAGUGAGAAUGCCCUUUAAAUCACUCCCGAUCAUAAAGGAGCAGGUAUCAAGCACACACUCAUGUAGCUCAUAACGCCUUGCUUAGCCACACCCCCACGGGAUACAGCAGUGAUAGAAAUUUAGCCAUAAACGAAAGUUUGACUAAGCUACGCUAUAUAGGGUUGGUAAAUUUCGUGCCAGCCACCGCGGUCACACGAUUAACCCAAAUUAAUAAGUACCGGCGUAGAGCGUGUUUAGGAGAAGACCCAUAAAUAAAGUUAAAUCAGAUCCAAGCCGUAGAAAGCUAAAGAUCAGACAAAAAUAAUCCACGAAAGUGACUUUAUCAGCUCUGAACACACGAUAGCUAAGACACAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAACCUCGAUAGCUUCCAACAAAGCUACCCGCCAGAGAACUACUAGCAAAAGCUUAAAACUCAAAGGACUUGACGGUGCUUCACAUCCCCCUAGAGGAGCCUGUCCCAUAAUCGAUAAACCCCGAUAAACCUCACCCCCACUUGCUAAUUCAGCCUAUAUACCGCCAUCUUCAGCCAACCCUUAAAAGGUGCAAAAGUAAGCUCAAUGAUAGCCAUAAAAAAGUUAGGUCAAGGUGUAGCCCAUGUGGAGGUCUAAGAUGGGCUACAUUUUCUCUUAGAGAACAAUCAACCAACGGACGUCACUAUGAAACAAGUGACCAAAGGAGGAUUUAGCAGUAAAUUAAGAAUAGAGAGCUUAAUUGAACUAGGCCAUGAAGCACGCACACACCGCCCGUCACCCUCCUCAAGUAUUCAUAACCAUUCCACCAUAUAUGAUCCUAAUAGCAUAUGAGAGGAGACAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGAUUACU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.D.geoffroii.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.D.geoffroii.seq new file mode 100644 index 0000000..a39ca60 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.D.geoffroii.seq @@ -0,0 +1,2 @@ +>d.16.m.D.geoffroii +CAGAGGUUUGGUCCUGGCCUUACUGUUAAUUUUUAUUAGACCUACACAUGCAAGUUUCCGCAUCCCAGUGAGUAUGCCCUUUUAGCUUCACUGAAGUAUAAAGGAGCUGGUAUCAGGCACACUUAAUUAAGCAGCCCAUGACACCUUGUUUAACCACACCCCCACGGGUAACAGCAGUGACUAACAUUGAGCUAUAAACGAAAGUUUGACUAAAUCAUAAUAAAUAAGGGUUGGUAAAUCUCGUGCCAGCCACCGCGGUCAUACGAUUAACCCAAAUUAACAGAAAAACGGCGUAAAGGGUGUUUAAGCAUAAACCUCAUAAAUAAAGUUAAAACUCAACUAUGCUGUAAUACGCCCUAGUUGGCAUUAAAAUAUACAACUUACGUGACUUUACUACUGCUGAAGACACUAAAGCUAAGGUACAAACUGGGAUUAGAGACCCCACUAUGCUUAGCCGUAAACCUAGGUAAUUAAAUAACAAAAUUACUCGCCAGAGAACUACUAGCCACUGCUUAAAACUCAAAGGACUUGGCGGUGCCCUAGACCCUCCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGAUACACCUCACCCCUUCUAGCUUAACAGUCUAUAUACCGCCAUCGUCAGCUCACCCCAAUAGGGCCCCAAAGUGAGCAAAAUCAUCUAAACCAUAAAAACGUUAGGUCAAGGUGUAGCAUAUGAAGGGGGAAGCAAUGGGCUACAUUUUCUAUAUUAGAACAUAACGGAUUGUCUACUGAAAUAGAGGCAUGAAGGAGGAUUUAGUAGUAAAUUAAGAGUAGAGAGCUUAAUUGAAAUAGGCAAUAGGGUGCGUACACACCGCCCGUCACCCUCCUCGAUAAAGUAACCUUCAAUACCUAAUUAGAAUACGCUAAAAAGAGGAGAAAAGUCGUAACAUGGUAAGUGUACUGGAAAGUGCACUUGGACAAUC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.D.novemcinctus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.D.novemcinctus.seq new file mode 100644 index 0000000..e7d211c --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.D.novemcinctus.seq @@ -0,0 +1,2 @@ +>d.16.m.D.novemcinctus +CACAGGUCUGGUCCUAGCCUUACUAUUAAUUCAUAACAAAAUUACACAUGCAAGUAUCAGCACACCAGUGAGAAUGCCCUCUAACUCUUAUAGAUCAAAAGGAGCAAGCAUCAAGUACACACAGCCCUUACAGUAGCUCAUAACGCUUUGCUCAACCACACCCCCACGGGAUACAGCAGUGAUAAAAAUUAAGCAAUAAGCGAAAGCUUGACUAAGUUAUGUUAUUAUAAGGGUUGGUAAAUUUCGUGCCAGCAACCGCGGUCAUACGAUUAACCCAAAUUAAUAGUUAUCGGCGUAAAGCGUGUUUAAGACACCUAGACAAUAGAGUUAAACCCUUACUACGCUGUAAAAAGCCUUAGUAGGACCAUAAACCCUUCAACGAAAGUGACUCUAAUUUAUCUGACUACACGAUAGCUAGGACCCAAACUGGGAUUAGAUACCCCACUAUGCCUAGCCCUAAACUAAAACAGUUCACAAACAAAACUGUUCGCCAGAGUACUACUAGCAACAGCUUAAAACUCAAAGGACUUGGCGGUGCUUUACAUCCUUCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGAUAUACCUCACCACCCCUUGCUAAUACAGCCUAUAUACCGCCAUCUUCAGCAGACCCUAGUAAGGCACCACAGUGAGCACAAUAACAUACAUAAAGACGUUAGGUCAAGGUGUAGCUUAUGGGGUGGGAAGAAAUGGGCUACAUUUUCUAAUAAAGAGCAAAUACAAAAAACUUAAUGAAACAAUUUAAGACUAAGGUGGAUUUAGUAGUAAGCUAAAAAUAGAGAGUUUAGCUGAACCAGGCCAUAAAGCACGCACACACCGCCCGUCACCCUCUUCAAUUAUAAGCGCCACAUAAACUAAAACACAUUAAUUCAGUAGCAACUAUAUAAGAAGAGACAAGUCGUAACAAGGUAAACAUACUGGAAAGUGUGUUUGGAUAAC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.D.virilis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.D.virilis.seq new file mode 100644 index 0000000..5620601 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.D.virilis.seq @@ -0,0 +1,2 @@ +>d.16.m.D.virilis +AUAAAGUUUUAUUUUGGCUUAAAAGUUUGUUAUUAAUUUGAUUUAUAUGUAAAUUUUUGUGUGAAUAUUUAAUAAUUUAAAAAAUUAUUAAAUUUAUUAUAAUCGCAGUAAUUAAUUUUAUUAGUUAAAGAAAUUUAGAAAUAGCAAUAUUAAAGAGUAUAGAUUAAAUUGGUGCCAGCAAUCGCGGUUACACCAAUUAUACAAAUGAAUUUUUUUAGUAAAAGUUAAAUUGGUUUAAUUUAAAUAUAAUUAAAUUUAUUAAGUGAAAUUUUAAAUUUAAAAUUUUUAUUAAGUGAAUAAUUGAAACUUGAAAAUUUUAAAUAAAAACUAGGAUUAGAUACCCUAUUAUUUAAAAUGUAAAUAUAAAUACUUAAGUAGUAAUAGUUAAGUUCUUGAAACUUAAAAAAUUUGGCGGUAUUUUAGUCUAUCCAGAGGAACCUGUUUUGUAAUCGAUAAUCCACGAUGGACCUUACUUAAGUUUGUAAUCAGUUUAUAUACCGUCGUUAUCAGAAUAUUUUAUAAGAAUAUUAAUAUUCAAUAAUUUUUAUUAAAAUUUAUAUCAGAUCAAGGUGUAGCUUAUAUUUAAGUAAUAAUGGGUUACAAUAAAUUUAUUUAAACGGAUAAAAUUAUGAAAAAAUUUUUGAAGGUGGAUUUGGUAGUAAAAUUAUAAAGAUUAAUAAUUUGAUUUUAGCUCUAAAAUAUGUACACAUCGCCCGUCGCUCUUAUUAUUAAGGUAAGAUAAGUCGUAACAUAGUAGAUGUACUGGAAAGUGUAUCUAGAAUGA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.E.rufescens.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.E.rufescens.seq new file mode 100644 index 0000000..52bb4a4 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.E.rufescens.seq @@ -0,0 +1,2 @@ +>d.16.m.E.rufescens +CAAAGGUUUGGUCCUAGCCUUAUUAUUAGUUGUCAGUAAGAUUAUACAUGCAAGUAUCCGCCAACCAGUGAAAAUGCCCUCAUACUCGUCCACUACAAACGAUCCCAAAGGAGCCGAUAUCAAGCACACCCACGGUAGCUCAAGACAUCUUGCUCAGCCACACCCCCACGGGAUACAGCAGUAGUAAAAAUUAAGCAAUAAACGAAAGUUUGACUAAGUUAUACUGAUUAGGGUUGGUCAAUCUCGUGCCAGCCACCGCGGUCAUACGAUUGACCCAAAUUAAUGAUUAAACGGCGUAAAGUGUGGUUAAACACUUACCAAUGUAAAUAAAGUUAAACUAGCUCUCAGCUGUAAAAAGCUAAAGAUCUAUGGUAAAUAGACUAUUAAUGUAACUUUACUUAUAGUGAACCCACGAUAGCUAAGAUACAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCGUAAACUUUGAUAAUUACUAACAAAAAUAUCCGCCAGAGAACUACAAGCCACUGCUUAAAACUCAAAGGACUUGGCGGUGCUUUAUACCCCCUAGAGGAGCCUGUUGCAUAAUCGAUAAACCCCGAUAAACCCUACCAUCACUUGCUAAAUCAGUCUAUAUACCGCCAUCUUCAGCAAACCCUUAUAAGGAACAAUAGUAAGCUUAAACGCCCCCGCAAAAACGUUAGGUCAAGGUGUAACCUAUGUGAUGGAAAACAAUGGGCUACAUUUUCUACAUAAGAACACACGAACUCUUAUAUGAAAUUAUCAGAUAAAGGAGGAUUUAGAAGUAAGCCAGGAAUAGAGAGCCUGACUGAACUUGGCUAUGAAGCACGCACACACCGCCCGUCACCCUCCUCAAGUGUUUAAGACUAACAACCCUAUUACACUAAUACAAACAUAAGAGGAGACAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGAGUAUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.G.gorilla.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.G.gorilla.seq new file mode 100644 index 0000000..ec6581f --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.G.gorilla.seq @@ -0,0 +1,2 @@ +>d.16.m.G.gorilla +AAUAGGUUUGGUCCUAGCCUUUCUAUUAACUCUUAGUAGGAUUACACAUGCAAGCAUCCCCGCCCCAGUGAGUCACCCUCUAAAUCACCACGAUCAAAAGGAACAAGCAUCAAGUACGCAGAAAUGCAGCUCAAAACGCUUAGCCUAGCCACACCCCCACGGGAGACAGCAGUGAUAAACCUUUAGCAAUAAACGAAAGUUUAACUAAGCCAUACUAACCCCAGGGUUGGUCAAUUUCGUGCCAGCCACCGCGGUCACACGAUUAACCCAAGCCAAUAGAAAUCGGCGUAAAGAGUGUUUUAGAUCAAUCCCCCAAUAAAGCUAAAAUUCACCUGAGUUGUAAAAAACUCCAGCUGAUAUAAAAUAAACUACGAAAGUGGCUUUAAUAUAUCUGAACACACAAUAGCUAGGACCCAAACUGGGAUUAGAUACCCCACUAUGCCUAGCCCUAAACUUCAACAGUUAAAUUAACAAGACUGCUCGCCAGAACACUACGAGCCACAGCUUAAAACUCAAAGGACCUGGCGGUGCUUCACAUCCUUCUAGAGGAGCCUGUUCUGUAAUCGAUAAACCCCGAUCAACCUCACCACCUCUUGCUCAGCCUAUAUACCGCCAUCUUCAGCAAACCCUGACGAAGGCCACAAAGUAAGCACAAGUACCCACGUAAAGACGUUAGGUCAAGGUGUAGCCCAUGAGGUGGCAAGAAAUGGGCUACAUUUUCUACUUCAGAAAACUACGAUAACCCUUAUGAAACCUAAGGGUAGAAGGUGGAUUUAGCAGUAAACUAAGAGUAGAGUGCUUAGUUGAACAGGGCCCUGAAGCGCGUACACACCGCCCGUCACCCUCCUCAAGUAUACUUCAAAGGACAUUUAACUAAAACCCCUACGCAUCUAUAUAGAGGAGAUAAGUCGUAACAUGGUAAGUGUACUGGAAAGUGCACUUGGACGAAC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.amphibius.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.amphibius.seq new file mode 100644 index 0000000..bb4f2d2 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.amphibius.seq @@ -0,0 +1,2 @@ +>d.16.m.H.amphibius +UACAGGUUUGGUCCCAGCCUUUCUGUUAAUUUUUAAUAGAAUUACACAUGCAAGUAUCCACACCCCAGUGAGAAUGCCCUCUAAAUCACCCAGAUCAAAAGGAGCGGGUAUCAAGCACACCAUACACCGUAGCUCAAAACGCCCUGCUCAGCCACACCCCCACGGGAAACAGCAGUGACCAAAAUUAAGCCAUGAACGAAAGUUUGACUAAGCCAUAUUAACCAGAGUUGGUAAAUCUCGUGCCAGCCACCGCGGUCAUACGAUUGACUCAAACUAACAGAAAUACGGCGUAAAGCGUGUUAAAGAAUUAAAAGUACAAAUAAAGUUAAAUUCUAACUAAACUGUAAAAAGCCCUAACUAGAAUAAAAAUCUACUACAAAAGUGACUUUAACAAUACUGACCACACGAUAGCUAAGACCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAACACAGAUAAUUCCAAAAACAAAACUAUUCGCCAGAGUACUACUAGCAACAGCUUAAAACUCAAAGGACUUGGCGGUGCUUCAUACCCCUCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGAUAAACCUCACCAACCCUUGCUAAUCCAGUCUAUAUACCGCCAUCUCCAGCAAACCCUAAAAAGGACUAAAAGUAAGCUCAACUAUUACACAUAAAGACGUUAGGUCAAGGUGUAACCUAUGGGCUGGGAAGAAAUGGGCUACAUUUUCUAGAACAAGAACACAACCCACCCGAACGAAAACUCCUAUGAAAGCUAGGAACUAAAGGAGGAUUUAGUAGUAAAUCAAGAGUAGAGUGCUUGAUUGAACAAGGCUAUGAAGCACGCACACACCGCCCGUCACCCUCCUCAAAUAACACAAACCCAUAAACAUAAUAGCUAGACAAAACCAAAUGAGAGGAGACAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGACAAAU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.auropunctatus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.auropunctatus.seq new file mode 100644 index 0000000..5a42913 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.auropunctatus.seq @@ -0,0 +1,2 @@ +>d.16.m.H.auropunctatus +CAAGGGUUUGGUCCUGGCCCUUCCAUUAGUUACUAAUAGGAUUACACAUGCAAGCCUCCGCAUCCCGGUGAAAAUGCCCUCUAAGUCAUAACUGACCUAAAGGAGCAGGUAUCAAGCACACAAAAUGUAGCUCAUAACGCCUUGCUCAGCCACACCCCCACGGGCUACAGCAGUGACAAAAAUUAAGCCAUGAAUGAAAGUUCGACUAAGCCAUAUUAAAUCAGGGUUGGUAAAUUUCGUGCCAGCCACCGCGGCCAUACGAUUAACCCAGACUAAUAGACACACGGCGUAAAGCGUGUUCCAGAAACAACCUACCACUAAAGUUAAACCUUAACUAAGCCGUAAAAAGCCACAGUUAACAUGAAAAUACAACACGAAAGUAACUUUAAUACCCCAACUACACGACAGCUAAGACCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAAUCUAGAUAGUUAACUUAACAAACCUAUCCGCCAGAGAACUACUAGCAACAGCUUAAAACUCAAAGGACUUGGCGGUGCUUCACAUCCCUCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGAUAAACCUCACCACCUCUUGCUAAUACAGUCUAUAUACCGCCAUCUUCAGCAAACCCUUAAAAGGAAUAACAGUAAGCAAAAGUAUCUUAACAUAAAAAAGUUAGGUCAAGGUGUAACCCAUGAGGUGGAAAGCAAUGGGCUACAUUUUCUACACAAGAACAUCUUACGAAAGUUUUUAUGAAAUCAAAAACUAAAGGAGGAUUUAGCAGUAAGCUGAGAAUAGAGCGCUCAGCUGAAUCGGGCCAUGAAGCACGCACACACCGCCCGUCACCCUCCUCAAGUACACAAACCCAAACAUAACCUAUUAAAAUCACACUUAAUACAAGAGGAGAUAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGAUUAAA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.lar.2.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.lar.2.seq new file mode 100644 index 0000000..d10d756 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.lar.2.seq @@ -0,0 +1,2 @@ +>d.16.m.H.lar.2 +AAUAGGUUUGGUCCUAGCCUUUCUAUUAGCCCCUGGCAAGAUUACACAUGCAAGCAUCCCCGCCCCGGUGAAAUCGCCCUUCAAAUCACCCGUGAUCAAAAGGAGCAGGUAUCAAGCACGCAGUAAUGCAGCUCAAAACACCCUGCCUAGCCACACCCCCACGGGAGACAGCAGUGAUAAACCUUUAGCAAUAAACGAAAGUUUAACUAAGCUAUGCCAACCCAGGGUUGGUCAACUUCGUGCCAGCCACCGCGGUCAUACGAUUAACCCCAGUUAAUAGAGCCCGGCGUAAAGAGUGUUUUAGAUUGCUCCCUAAUAAAGCUAAGCUCCAUCCAAGUCGUAAAAAACUCUGGCUGCUAUAAAAUAAACUACGAAAGUGGCUUUAACACCUCUGAAUACACAAUAGCUGAGACCCAAACUGGGAUUAGAUACCCCACUAUGCUCAGCCCUAAACUUCAACAGUCAAAUCAACAAGACUGCUCGCCAGAACACUACGAGCAACAGCUUAAAAAUCAAAGGACCUGGCGGUGCUUCACACCCCCCUAGAGGAGCCUGUCCUAUAAUCGAUAAACCCCGUUCAACCUCACCAUCUCUUGCUCAGCCUAUAUACCGCCAUCUUCAGCAAACCCUGACAAAGGCUAUAAAGUAAGCACAAACACCCACAUAAAGACGUUAGGUCAAGGUGUAGCCCAUGAGAUGGGAAGAGAUGGGCUACAUUUUCUAUGCCAGAAAACCACGAUAACCCUCAUGAAACUUGAGCGGUCGAAGGAGGAUUUAGCAGUAAAUUAAGAAUAGAGUGCUUAGUUGAACAAGGCCCUGAAGCGCGUACACACCGCCCGUCACCCUCCUCAAGCAUAUUUCAAGGAACCCCUAACUAAAUACUCCACGCAUCUAUGUAGAGGAGACAAGUCGUAACAUGGUAAGUGUACUGGAAAGUGCACUUGGACAAAC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.lar.geno.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.lar.geno.seq new file mode 100644 index 0000000..88f8a65 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.lar.geno.seq @@ -0,0 +1,2 @@ +>d.16.m.H.lar.geno +AAUAGGUUUGGUCCUAGCCUUUCUAUUAGCCCCUGGCAAGAUUACACAUGCAAGCAUCCCCGCCCCGGUGAAAUCGCCCUUCAAAUCACCCGUGAUCAAAAGGAGCAGGUAUCAAGCACGCAGUAAUGCAGCUCAAAACACCCUGCCUAGCCACACCCCCACGGGAGACAGCAGUGAUAAACCUUUAGCAAUAAACGAAAGUUUAACUAAGCUAUGCCAACCCAGGGUUGGUCAACUUCGUGCCAGCCACCGCGGUCAUACGAUUAACCCCAGUUAAUAGAGCCCGGCGUAAAGAGUGUUUUAGAUUGCUCCCUAAUAAAGCUAAGCUCCAUCCAAGUCGUAAAAAACUCUGGCUGCUAUAAAAUAAACUACGAAAGUGGCUUUAACACCUCUGAAUACACAAUAGCUGAGACCCAAACUGGGAUUAGAUACCCCACUAUGCUCAGCCCUAAACUUCAACAGUCAAAUCAACAAGACUGCUCGCCAGAACACUACGAGCAACAGCUUAAAAAUCAAAGGACCUGGCGGUGCUUCACACCCCCCUAGAGGAGCCUGUCCUAUAAUCGAUAAACCCCGUUCAACCUCACCAUCUCUUGCUCAGCCUAUAUACCGCCAUCUUCAGCAAACCCUGACAAAGGCUAUAAAGUAAGCACAAACACCCACAUAAAGACGUUAGGUCAAGGUGUAGCCCAUGAGAUGGGAAGAGAUGGGCUACAUUUUCUAUGCCAGAAAACCACGAUAACCCUCAUGAAACUUGAGCGGUCGAAGGAGGAUUUAGCAGUAAAUUAAGAAUAGAGUGCUUAGUUGAACAAGGCCCUGAAGCGCGUACACACCGCCCGUCACCCUCCUCAAGCAUAUUUCAAGGAACCCCUAACUAAAUACUCCACGCAUCUAUGUAGAGGAGACAAGUCGUAACAUGGUAAGUGUACUGGAAAGUGCACUUGGACAAAC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.moschatus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.moschatus.seq new file mode 100644 index 0000000..6d7bbbc --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.moschatus.seq @@ -0,0 +1,2 @@ +>d.16.m.H.moschatus +CAUAGGUUUGGUCCUGGCCCUACUGUUAAUUGUAAUUAGACCUACACAUGCAAGCUUCCACAAUCCGGUGAGAUAUGCCCUACAGAUUACUUACCAUAAUCGUUAAGGAGCGGGCAUCAGGCACACCACAGGUAGCCCAUCACGCCUUGCUUAGCCACACCCCCACGGGAUACAGCAGUGACUAAUAUUAAGCCAUAAACGAAAGUUUGACUAAAUCAUAAUUAAAUCAGGGUUGGUAAAUUUCGUGCCAGCCGCCGCGGUCAUACGAUUAACCCAAGUUAACAGAAAACCGGCGUAAAGCGUGUUUAAGCACAAACCUACAAAUAAAGCUAAGACGCAACUAAGCUGUAAUACGCUAUAGUCAACAUUAAAAUACACUACAAAAGUGGCUUUAAUACCGCUGAAGACACGACAGCUAAGACACAAACUGGGAUUAGAUACCCCACUAUGCUCAGCUUUAAACCAAGAUAAUUAAACAACAAAAUUAUUCGCCAGAGAACUACUAGCAAUCGCUUAAAACUCAAAGGACUUGGCGGUGUCCUAAACCCACCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCACGAUACACCUCACCCCUUCUUGCCAAUACAGCCUAUAUACCGCCAUCGUCAGCUGGCCCCAACACGGGUAAUAAAGCAGCAAGAUUACUCAACCGUAAAAACGUUAGGUCAAGGUGUAGCAUAUGAAGGGGGAAGCAAUGGGCUACAUUUUCUAAAUUAGAACAAACGAAUUAUCUUAUGAAACCUAAGACAUAUGAAGGAGGAUUUAGCAGUAAAUUAAGAAUAGAGAGCUUAAUUGAAACAGGCAAUAGGACGCGCACACACCGCCCGUCACCCUCCUCGAUAAAACUGGAUAAAUAACUAAUAACUCCGAGCACAAAAAGAGGAGAAAAGUCGUAACAUGGUAAGUGUACUGGAAAGUGCACUUGGAACAU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.sapiens.5.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.sapiens.5.seq new file mode 100644 index 0000000..790ca18 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.sapiens.5.seq @@ -0,0 +1,2 @@ +>d.16.m.H.sapiens.5 +AAUAGGUUUGGUCCUAGCCUUUCUAUUAGCUCUUAGUAAGAUUACACAUGCAAGCAUCCCCGUUCCAGUGAGUUCACCCUCUAAAUCACCACGAUCAAAAGGAACAAGCAUCAAGCACGCAGCAAUGCAGCUCAAAACGCUUAGCCUAGCCACACCCCCACGGGAAACAGCAGUGAUUAACCUUUAGCAAUAAACGAAAGUUUAACUAAGCUAUACUAACCCCAGGGUUGGUCAAUUUCGUGCCAGCCACCGCGGUCACACGAUUAACCCAAGUCAAUAGAACCCGGCGUAAAGAGUGUUUUAGAUCACCCCCUCCCCAAUAAAGCUAAAACUCACCUGAGUUGUAAAAAACUCCAGUUGACACAAAAUAGACUACGAAAGUGGCUUUAACAUAUCUGAACACAGAAUAGCUAAGACCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAACCUCAACAGUUAAAUCAACAAAACUGCUCGCCAGAACACUACGAGCCACAGCUUAAAACUCAAAGGACCUGGCGGUGCUUCAUAUCCCUCUAGAGGAGCCUGUUCUGUAAUCGAUAAACCCCGAUCAACCUCACCACCUCUUGCUCAGCCUAUAUACCGCCAUCUUCAGCAAACCCUGAUGAAGGCUACAAAGUAAGCGCAAGUACCCACGUAAAGACGUUAGGUCAAGGUGUAGCCCAUGAGGUGGCAAGAAAUGGGCUACAUUUUCUACCCCAGAAAACUACGAUAGCCCUUAUGAAACUUAAGGGUCGAAGGUGGAUUUAGCAGUAAACUAAGAGUAGAGUGCUUAGUUGAACAGGGCCCUGAAGCGCGUACACACCGCCCGUCACCCUCCUCAAGUAUACUUCAAAGGACAUUUAACUAAAACCCCUACGCAUUUAUAUAGAGGAGACAAGUCGUAACAUGGUAAGUGUACUGGAAAGUGCACUUGGACGAAC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.sapiens.geno.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.sapiens.geno.seq new file mode 100644 index 0000000..7292f31 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.sapiens.geno.seq @@ -0,0 +1,2 @@ +>d.16.m.H.sapiens.geno +AAUAGGUUUGGUCCUAGCCUUUCUAUUAGCUCUUAGUAAGAUUACACAUGCAAGCAUCCCCGUUCCAGUGAGUUCACCCUCUAAAUCACCACGAUCAAAAGGGACAAGCAUCAAGCACGCAGCAAUGCAGCUCAAAACGCUUAGCCUAGCCACACCCCCACGGGAAACAGCAGUGAUUAACCUUUAGCAAUAAACGAAAGUUUAACUAAGCUAUACUAACCCCAGGGUUGGUCAAUUUCGUGCCAGCCACCGCGGUCACACGAUUAACCCAAGUCAAUAGAAGCCGGCGUAAAGAGUGUUUUAGAUCACCCCCUCCCCAAUAAAGCUAAAACUCACCUGAGUUGUAAAAAACUCCAGUUGACACAAAAUAGACUACGAAAGUGGCUUUAACAUAUCUGAACACACAAUAGCUAAGACCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAACCUCAACAGUUAAAUCAACAAAACUGCUCGCCAGAACACUACGAGCCACAGCUUAAAACUCAAAGGACCUGGCGGUGCUUCAUAUCCCUCUAGAGGAGCCUGUUCUGUAAUCGAUAAACCCCGAUCAACCUCACCACCUCUUGCUCAGCCUAUAUACCGCCAUCUUCAGCAAACCCUGAUGAAGGCUACAAAGUAAGCGCAAGUACCCACGUAAAGACGUUAGGUCAAGGUGUAGCCCAUGAGGUGGCAAGAAAUGGGCUACAUUUUCUACCCCAGAAAACUACGAUAGCCCUUAUGAAACUUAAGGGUCGAAGGUGGAUUUAGCAGUAAACUGAGAGUAGAGUGCUUAGUUGAACAGGGCCCUGAAGCGCGUACACACCGCCCGUCACCCUCCUCAAGUAUACUUCAAAGGACAUUUAACUAAAACCCCUACGCAUUUAUAUAGAGGAGACAAGUCGUAACAUGGUAAGUGUACUGGAAAGUGCACUUGGACGAAC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.L.catta.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.L.catta.seq new file mode 100644 index 0000000..dfde3d8 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.L.catta.seq @@ -0,0 +1,2 @@ +>d.16.m.L.catta +UAUAGGUUUGGUCCUGGCCUUACUAUUAGUUUACAGUAAGAUUACACAUGCAAGUAACCGCAUCCCAGUGAGAAUGCCCUCCAAAUCCCCUGAUUAAAAGGAGCAGGUAUCAAGCACACCAAUAGGUAGCUCACCACACCUUGCUAAACCACACCCCCACGGGAUACAGCAGUGAUUGAACUUAAGCAAUAAACGAAAGUUUGACUAAGCUAUACUGACACUUAGGGUUGGUAAAUCUCGUGCCAGCCACCGCGGUCAUACGAUUAACCCAAACUAAUAUUUCCCGGCGUAAAGUGUGUUUAAGAUUUAUAUAAAUAAAGUUAAUUUUUAUCCAAGCCGUAAAACGCCCCAGCUAAAACAAAACUAACCUACGAAAGUGACUUUAAUACUCUGAAGACACGACAACUAAGAUCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCGUAAACCUAAGUAAUUAACAAACAAAAUUACUCGCCAGAGCACUACAAGCAACAGCUUAAAACUCAAAGGACUUGGCGGUGCUUUAUAUCCCUCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGAUAAACCUCACCACUUCUUGCUAAUUCAACUUAUAUACCGCCAUCCCCAGCAAACCCUAUUAAGGCCCCAAAGUAAGCAAAAACACAUACAUAAAGACGUUAGGUCAAGGUGUAGUCAAUGAAGUGGAAAGAAAUGGGCUACAUUUUCUAAUAUUAGAACAACACCCCAACAGAAGCCUUUAUGAAACUAAAAGCCAAAGGAGGAUUUAGCAGUAAAUUAAGAAUAGAGAGCUUAAUUGAAUAGGGCCAUGAAGCACGCACACACCGCCCGUCACCCUCCUCAAUCACCAAUUAUUAAUUCACUAAUUCUACUAAACUCUAAACAAGAGGAGAUAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGAAUAUUC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.M.auratus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.M.auratus.seq new file mode 100644 index 0000000..5f34aee --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.M.auratus.seq @@ -0,0 +1,2 @@ +>d.16.m.M.auratus +AAAAGGUUUGGUCCUAGCCUUAUAGUUAGUUAGAGGUAGAGUUACACAUGCAAAUCUCUAUAAACCAGUGUCAAAUCCCUAGGUUUUACUUUAAACCCUAAGGAGAGGGUAUCAAGCACAUACACAUAUAUAGCUAAAGACACCUUGCCUAGCCACACCCCCACGGGACUCAGCAGUGAUAAAAAUUAAGCCAUAAACGAAAGUUUGACUUAGUCAUACCUCAUCAGGGUUGGUAAAUUUCGUGCCAGCCACCGCGGUCAUACGAUUAACCCAAACUAACUAUUCUCCGGCGUAAAAUGUGUUUUUAUUACGAACAUAAUAGAAUUAAAACCCAACUAAUAUGUGAAAAUUCAUUGUUGGACUUAAAAUCAAUAACGAAAGUAAUUCUAAUUAUAUUAAUACACGAUAGCUAAGAUCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAACCUAAGUGAUUAAAUAACAAAAUCACUUGCCUGAGAACUACUGGCCACAGCUUAAAACUCAAAGGACUUGGCGGUACUUUAUAUCCAUCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGUUAUACCUUACCACCCCUUGCUAAUUCAGCCUAUAUACCGCCAUCUUCAGCAAACCUUAAAAAAGAACAAGAGUAAGCAAGAGAAUACCCAUAAAAACGUUAGGUCAAGGUGUAGCCUAUGGGCUGGGAAGUAAUGGGCUACAUUUUCUUCUAAAGAACAGUUACGCUAUCCUCUAUGAAACUUAGAGGACAAAGGAGGAUUUAGUAGUAAAUUAAGAAUAGAGAGCUUAAUUGAAUAGAGCAAUGAAGUACGUACACACCGCCCGUCACCCUCCUCAAAUUAAGCUAACUGUUAACUAUACCUAAUAUUGACUCAUAAACUUAUGAGAGGAGAUAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.M.musculus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.M.musculus.seq new file mode 100644 index 0000000..1091d21 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.M.musculus.seq @@ -0,0 +1,2 @@ +>d.16.m.M.musculus +AAAGGUUUGGUCCUGGCCUUAUAAUUAAUUAGAGGUAAAAUUACACAUGCAAACCUCCAUAGACCGGUGUAAAAUCCCUUAAACAUUUACUUAAAAUUUAAGGAGAGGGUAUCAAGCACAUUAAAAUAGCUUAAGACACCUUGCCUUAGCCACACCCCCACGGGACUCAGCAGUGAUAAAUAUUAAGCAAUAAACGAAAGUUUGACUAAGUUAUACCUCUUAGGGUUGGUAAAUUUCGUGCCAGCCACCGCGGUCAUACGAUUAACCCAAACUAAUUAUCUUCGGCGUAAAACGUGUCAACUAUAAAUAAAUAAAUAGAAUUAAAAUCCAACUUAUAUGUGAAAAUUCAUUGUUAGGACCUAAACUCAAUAACGAAAGUAAUUCUAGUCAUUUAUAAUACACGACAGCUAAGACCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCAUAAACCUAAAUAAUUAAAUUUAACAAAACUAUUUGCCAGAGAACUACUAGCCAUAGCUUAAAACUCAAAGGACUUGGCGGUACUUUAUAUCCAUCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGCUCUACCUCACCAUCUCUUGCUAAUUCAGCCUAUAUACCGCCAUCUUCAGCAAACCCUAAAAAGGUAUUAAAGUAAGCAAAAGAAUCAAACAUAAAAACGUUAGGUCAAGGUGUAGCCAAUGAAAUGGGAAGAAAUGGGCUACAUUUUCUUAUAAAAGAACAUUACUAUACCCUUUAUGAAACUAAAGGACUAAGGAGGAUUUAGUAGUAAAUUAAGAAUAGAGAGCUUAAUUGAAUUGAGCAAUGAAGUACGCACACACCGCCCGUCACCCUCCUCAAAUUAAAUUAAACUUAACAUAAUUAAUUUCUAGACAUCCGUUUAUGAGAGGAGAUAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGAAUAAU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.M.putorius.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.M.putorius.seq new file mode 100644 index 0000000..276037b --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.M.putorius.seq @@ -0,0 +1,2 @@ +>d.16.m.M.putorius +CAAAGGUUUGGUCCUAGCCUUCCUAUUGAUUAUUAACAGAAUUACACAUGCAAGUCUCUACACCCCAGUGAGAAUGCCCUCCAAAUCUAUAUGUUGAUUAAAAGGAGCGGGUAUCAAGCACACUAAAUUAGUAGCUCAUAACGCCUUGCUCAACCACACCCCCACGGGAUACAGCAGUGAUAAAAAUUAAGCCAUAAACGAAAGUUUGACUAAGCCAUGUUAACAAAGAGCUGGUAAAUUUCGUGCCAGCCACCGCGGUCAUACGAUUAGCCCGAAUCAAUAGGCAAACGGCGUAAAACGUGUUAAGGAUUAUAUUAUAUUAAAGUUAAAAUUUGACAAGGCUGUAAAAAGCUACUGUUAAUAUAAGAUAAACCACGAAAGUGACUUUAUUACUUCCAUCAACACGAUAGCUGAGACCCAAACUGGGAUUAGAUACCCCACUAUGCUCAGCCCUAAACAUAAAUAAUUAUCACAACAAAAUUAUCUGCCAGAGAACUACUAGCAAUAGCUUAAAACUCAAAGGACUUGGCGGUGCUUUACAUCCCUCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGAUAGACCUCACCACUUCUAGCUUAAUCAGUCUAUAUACCGCCAUCUUCAGCAAACCCUUAAAGGGAAGAAAAGUAAGCACAAUAAUAUUACAUAAAAAAGUUAGGUCAAGGUGUAACCUAUGAAGUGGGAAGAAAUGGGCUACAUUUUCUAACCAAGAACACACUCACGAAAGUUUUUAUGAAAACUAAAAACUAAAGGUGGAUUUAGUAGUAAAUUAAGAAUAGAGAGCUUAAUUGAAUAGGGCCAUAAAGCACGCACACACCGCCCGUCACCCUCCUCAAGCAACACACUCAAAUACUACAUAAUAAAAGUAAACCUAAAGCAAGAGGAGACAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGGUAAAU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.Manis.sp.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.Manis.sp.seq new file mode 100644 index 0000000..c971496 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.Manis.sp.seq @@ -0,0 +1,2 @@ +>d.16.m.Manis.sp +CAUAGGUUUGGUCCCAGCCUUUUUAUUAGUUUAUGAUAAAAUUACACAUGCAAGUAUCCGCCCUACGGUGAAAACGCCCUUUAGCCUUUACAAGUCAAAAGGAGCUGGUAUCAAGCACGCCAAUUUAAGGCAGCUAGUGACACCUUGCUUACGCCACACCCCCACGGGAGACAGCAGUGAUAAAAAUUAAACCAUUAACGAAAGUUAGAUUUAGUUAUAUCAUUUAUGGGUUGGUAAAUCUCGUGCCAGCCACCGCGGUCAUACGAUUAACCCUAAUUAAUAAAAAACCGGCGUAAAAAGUGUCAAAGUGUAUUUAAAUCAAAUAAAAUUAAGCCCUAAUCAAGCUGUAAAAAGCCUCGAUUAUAGUAAAAAUAAACUAUGAAAAUAAUUUUAAUAAAACCCACACACGAUAGCUAAGAUCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCUUAAACCUAAAUAAUUAAUUAAACAAAAUUAUUCGCCAGAGUACUACUAGCAAUAGCUUGAAACUCAAAGGACUUGGCGGUGCUUCAUAUCCCUCUAGAGGAGCCUGUCCUAUAAACGAUAAACCCCGAUAAACCUCACCAAUCCUAGCUAAUGCAGCCUAUAUACCGCCAUCCUCAGCAAACCCUAAUAAAGGAACCAUAGUAAGCAAGAUCAUUGAAACAUAAAAACGUUAGGUCAAGGUGUAGCUUAUGGAUUGGGAAGAGAUGGGCUACAUUUUCUAAAACAGAAUAAGACGAAUACCCUUAUGAAAAUAAGGGUUAAAGGAGGAUUUAGUAGUAAGACAAGAAUAGAGAGCUUGACUGAAUUAGGCCCUGAAGCACGCACACACCGCCCGUCACCCUCUUCAAAUUUCCAAAAAACAGUAAAUAUAUUAAUGAAUAACAAGAAUGAGAAGAGAUAAGUCGUAACAAGGUAAGCAUACUGGAAGGUGUGCUUGGAUAAU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.O.afer.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.O.afer.seq new file mode 100644 index 0000000..4a5338a --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.O.afer.seq @@ -0,0 +1,2 @@ +>d.16.m.O.afer +AUAAAGGUUUGGUCCUAGCCUUUCUAUUAGUUGACAGUAAAUUUAUACAUGCAAGUAUCUGCCUCCCAGUGAAAUAUGCCCUCUAAAUCCUUACCGGAUUAAAAGGAGCCGGUAUCAAGCUCACCUAGAGUAGCUCAUGACGCCUUGCUAAACCACGCCCCCACGGGAUACAGCAGUAAUAAAAAUUUAGCAAUGAACGAAAGUUUGACUAAGUUAUACUAUAACUAGGGUUGGUAAAUUUCGUGCCAGCCACCGCGGUCAUACGAUUAACCCAAAUUAAUAGUAAUACGGCGUAAAGCAUGAUUAGGGAAUAAUAUAAAUAAAGUUAAAUGUAAAUCAAAGCUGUAAAAAGCUCCUGAUUAACUUAAAAUAAAACACGAAAGUUACUUUACCACUCCUGAAUUCAUGAUAGCUAGGAUACAAACUGGGAUUAGAUACCCCACUAUGCCUAGCCAUAAACUUAAAUAUUUCUCAACAAAAUUAUUCGCCAGAGAACUACAAGCAACAGCUUAAAACUCAAAGGACUUGGCGGUGCUUUAUAUCCAUCUAGAGGAGCCUGUUAUGUAAUCGAUAAACCCCGAUAUACCUCACCAUCACUUGCCAAUACAGCCUAUAUACCGCCAUCUUCAGCAAACCCUUACAAGGAAUAAUAGUAAGCCAAAUUAUUACCAUAAAAACGUUAGGUCAAGGUGUAGCCAAUGUGAUGGCAAUAAAUGGGCUACAUUUUCUAUUUUAAGAACAUAUCCCUACGAAAACCCAAAUGAAACCAAGGCUAAAGGAGGAUUUAGUAGUAAAUUAAGAAUAGAGAGCUUAAUUGAAUAAGGCCAUGAAGCACGCACACACCGCCCGUCACCCUCCUCAACUACUAGUAUUACUAAAAAUAUUUCACUACAUAAACGUACUAGAGGAGACAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGAUAAUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.O.anatinus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.O.anatinus.seq new file mode 100644 index 0000000..fb058b0 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.O.anatinus.seq @@ -0,0 +1,2 @@ +>d.16.m.O.anatinus +UAAAGGUUUGGUCCUAGCCUUACUGUUAGAUUUGAUUAGAUUUAUACAUGCAAGUAUCCGCAACCCAGUGAGAAUACCCUAAAAACUCUUAACAAGUUAGAAGGAGUAGAUAUCAGGCACACUAAAGUAGCCCACAACAUCUUGCCCUAGCCACACCCCCACGGGACACAGCAGUAAUAGAAAUUAGUCAAUAAACGCAAGUUUGAACAAGUCAUAAUCAAUAAGAGUCGGUAAAUUUCGUGCCAGCCACCGCGGUCAUACGAUUGACUCAACCUAACAAAUAACGGUGUAAAACGUGUUUAAAAACUUAAACUAAUAAGAUUAAAGUAGAACUAAACUGUGAUAAGUCAUAGUUAAUACUAAAGCCAUCUACGAAAGUGAUCUUAGACUAAUUGAAUACACGAUAGCUAAGGUACAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAACUCAAGUCGUUUAAUAACAAAACUACUCACCAGAGAACUACUAGCAACAGCUUAAAACUCAAAGGACUUGGCGGUGCUUCACCCCUCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGAUACACCUCACCAUCUUUUGCCACUACUGUCUAUAUACCGCCAUCGUCAGCCAACCCUAAAAAGGAACAAAAGUAGGCGUAAUCAUUUUUCAUAAAAACGUUAGGUCAAGGUGUAGCCUAUAAGAUGGAAGAAAUGGGCUACAUUUUCUACAUUAGAACAUACGAAAAACUCUAUGAAACUAGAGUAUUAAGGAGGAUUUAGUAGUAAGCCAAGAAUAGAGAGCUUGACUGAACUGGGCAAUGAAGCACGCACACACCGCCCGUCACCCUCCUCAAUCAAGCAACACAAACAUUCCUAAAAUCCCAACGCUUUUCAAGAGGAGAUAAGUCGUAACAAGGUAAGCAUACCGGAAGGUGUGCUUGGAAUAUC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.O.aries.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.O.aries.seq new file mode 100644 index 0000000..d11a7f6 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.O.aries.seq @@ -0,0 +1,2 @@ +>d.16.m.O.aries +UAUAGGUUUGGUCCCAGCCUUCCUGUUAACUUUCAAUAGACUUAUACAUGCAAGCAUCCACGCCCCGGUGAGUAACGCCCUUCGAAUCACACAGGACUAAAAGGAGCAGGUAUCAAGCACACACUCUUGUAGCUCACAACGCCUUGCUUAACCACACCCCCACGGGAGACAGCAGUAACAAAAAUUAAGCCAUAAACGAAAGUUUGACUAAGUCAUAUUGACCAGGGUUGGUAAAUCUCGUGCCAGCCACCGCGGUCAUACGAUUGACCCAAGCUAACAGGAGUACGGCGUAAAGCGUGUUAAAGCAUCAUACUAAAUAGAGUUAAAUUUUAAUUAAACUGUAAAAAGCCAUAAUUAUAACAAAAAUAAAUGACGAAAGUAACCCUACAAUAGCUGAUACACCAUAGCUAAGACCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAACACAAAUAAUUAUAAAAACAAAAUUAUUCGCCAGAGUACUACCGCAACAGCCCGAAACUCAAAGGACUUGGCGGUGCUUUAUACCCUUCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGAUAAACCUCACCAAUCCUUGCUAAUACAGUCUAUAUACCGCCAUCUUCAGCAAACCCUAAAAAAGGGACAAAAGUAAGCUCAAUAAUAACACAUAAAGACGUUAGGUCAAGGUGUAACCUAUGGAGUGGGAAGAAAUGGGCUACAUUUUCUACCCAAGAAAAUUUAAUACGAAAGCCAUUAUGAAAUUAAUAGCCAAAGGAGGAUUUAGCAGUAAACUAAGAAUAGAGUGCUUAGUUGAAUCAGGCCAUGAAGCACGCACACACCGCCCGUCACCCUCCUCAAGUAAAUAUGAUAUACUUAAACCUAUUUACAUAUAUCAACCACACGAGAGGAGACAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGAUAAAC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.O.cuniculus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.O.cuniculus.seq new file mode 100644 index 0000000..018a895 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.O.cuniculus.seq @@ -0,0 +1,2 @@ +>d.16.m.O.cuniculus +UAAAGGUUUGGUCCUGGCCUUUUUAUUGUUUUGUAGCAACCUUACACAUGCAAGACUCCUCACGCCAGUGAGAAUGCCCUUAACAUCAAACUAGAUCAAGAGGAGCGGACAUUAAGCACACUAAUCAGUAGCUCAAGAUGCCUUGCUUAACCACACCCCCAAGGGAUACAGCAGUGAUAAAUAUUUAGCAAUGAACGUAAGUUUGACUAAGUUAUGCUACUUUAGGGUUGGUAAAUCUCGUGCCAGCCACCGCGGUCAUACGAUUAACCCAAAUUAAUAAAUAUCCGGCGUAAAGCGUGAUUAGAAUAAACAACAAAAUAAAAUCAAAUAACAACUAAGCUGUAGAAAGUAAUAGUUGCAAACAAAAAUAAACAACGAAAGUGAUUUUAUACUCUUCGAACUCACGAUAGCUAAGGCCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAACUUUGAUAAUUUCAUAACAAAAUUAUUCGCCAGAGAACUACAAGCCAAAGCUUAAAACUCAAAGGACUUGGCGGUGCUUUAUACCCACCUAGAGGAGCCUGUUCCGUAAUCGAUAAACCCCGAUAAACCCUACCACUCUUUGCCAACUCAGCCUAUAUACCGCCAUCUUCAGCGAACCCUAAAAAGGAGCAAAAGUAAGCUCAAUUACCACCGUAAAAACGUUAGGUCAAGGUGUAGCCCAUAGAGUGGAGAGCAAUGGGCUACAUUUUCUACUUCAGAAUAUACGAAAGCCCUUAUGAAACUCUAAGGGCCAAAGGAGGAUUUAGUAGUAAAUUAAGAAUAGAGUGCUUAAUUGAACAAGGCCAUGAAGCACGCACACACCGCCCGUCACCCUCCUCAAGUGACAAAUAUUUACUUAUACCUAAUUACAUAAAUAGACAAGCAUAAGAGGAGAUAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGACAUUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.O.virginianus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.O.virginianus.seq new file mode 100644 index 0000000..bfc3821 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.O.virginianus.seq @@ -0,0 +1,2 @@ +>d.16.m.O.virginianus +CAGAGGUUUGGUCCCAGCCUUCCUAUUAAUCCCUAGCAGACUUACACAUGCAAGUAUCCUCAUCCCAGUGAAAAUGCCCUCCAAGUCAAUAAAACUAAGAGGAGCUGGUAUCAAGCUCACACCCGUAGCUCAUGACGCCUUGCUCAGCCACACCCCCACGGGAGACAGCAGUGAUAAAAAUUAAGCUAUAAACGAAAGUUUGACUAAGUCAUGCUAAUUAGGGUUGGUAAAUUUCGUGCCAGCCACCGCGGUCAUACGAUUAACCCAAGUUAAUAGGCACACGGCGUAAAGCGUGUUUAAGCACUAUGCCAAAUAGAGUUAAACUCCAAUUAAGCUGUAAAAAGCCAUAAUCAAGACGAAAAUAAAUAACGAAAGUAACUUUACAACCGCUGAAACACGAUAGCUAAGAUCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAACAUAAAUAGUUAUAUAAACAAAACUAUUCGCCAGAGUACUACCGGCAAUAGCUUAAAACUCAAAGGACUUGGCGGUGCUUUAUACCCUUCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGAUAGACCUUACCACCCCUUGCUAAUACAGUCUAUAUACCGCCAUCUUCAGCAAACCCUAAAAAGGAACAAAAGUAAGCACAAUCAUUAUACAUAAAAACGUUAGGUCAAGGUGUAACCUAUGGAGUGGAAAGAAAUGGGCUACAUUUUCUAAUCUAAGAAAACUCUUUACGAAAGUUACUAUGAAAUUAGUAACCAAAGGAGGAUUUAGCAGUAAACUAAGAAUAGAGUGCUUAGUUGAAUUAGGCCAUGAAGCACGCACACACCGCCCGUCACCCUCUUCAAAUAGGCACAAUACACUUAAAUUUAAUUAUACGUAUUAAUCAUAUGAGAAGAGAUAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGAUAA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.P.cinereus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.P.cinereus.seq new file mode 100644 index 0000000..d59ad6b --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.P.cinereus.seq @@ -0,0 +1,2 @@ +>d.16.m.P.cinereus +UAAAGGUUUGAUCCUAGCCUUACUGUUAGUUUUAAUUAAACUUACACAUGCAAGUUUCCGCAACCCAGUGAGAAUGCCCCCAAAAUUUAUACACAAUUUAGCAGGAGCAGACAUCAGGUUCACUACAAAGUAGCCCAUAACGUCUUGUCCAACCACACCCCCACGGGAUACAGCAGUGAUUAACAUUAAGCUAUAAACGAAAGUUUGACUAAAUUAUAAUUAUCUAGGGCCGGUAAAUUUCGUGCCAGCCACCGCGGCCAUACGAUUGACCCAAACUAACAGAUGUCGGCGUAAAGCGUGUACAAUCCAACAACCAAAAUAAGGCUAAAACUCAAUCAUGCUGUAAUACGCUAUAGCUAACAUUAAAAAAUGCAACCAAAGUGGCCUUAAUACUGACCAAAACACGACAGCUAAGACUCAAACUGGGAUUAGAUACCCCAUUAUGCUUUAGCGUAAACUUAGAUAGUUUAAUAACGAAACUAUUCGCCAGAGAACUACUAGCCAGCGCUUAAAACUCAAAGGACUUGACGGUGUCCUAAGCCCAUCUAGAGGAGCCUGUCCUAUAACCGAUGAACCCCGAUACACCCCACCUCUUCUUGCCAAUACAGCCUAUAUACCGCCAUCGUCAGCCUACCCCAAUAGGGACCAAAAGUAAGCAAAAUCAUCAACCAUAAAAACGUUAGGUCAAGGUGUAGCAUAUGAAGAGGAAAGUGAUGGGCUACAUUUUCUAACAUAGAAAAUUACGGACUAUCUUAUGAAACCUAAGAUAUACGAAGGAGGAUUUAGCAGUAAAUUAAGAAUAGAGAGCUUAAUUGAAACAGGCAAUAGGACGCGUACACACCGCCCGUCACUCUCUUCAACAUAAACAAACCAAAUAACUAAUAAAAUAAAUAAAUAAAGAAGAGAAAAGUCGUAACAUGGUAAGUGUACCGGAAGGUGCACUUGGAUCAUC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.P.polycephalum.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.P.polycephalum.seq new file mode 100644 index 0000000..f347a38 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.P.polycephalum.seq @@ -0,0 +1,2 @@ +>d.16.m.P.polycephalum +GUUUUAAUAUAAUAAUGAGUUUGAUCCUGGCUCCGAGAGAAUGCUAGCAACUUACUUGAUACAUGCUAGUCGAACGCUUAUAUGAGCGUGGCGUACGAGCGACAAGGGCAAAGAUAGAAAAUACAUCAGUCAAGGGAAAUCCUAGAUUUAAAAGAUUAUAUCGCUGAAUGUAAGGUCUUUGUGAGAUUAGGUUGUUGGUAAGAUAAAAGCCUACCAAGCCGAUGAUCUCUAGCUGGUCUGAGAGGAUGUACAGCCGCGUCGGAAAUGCAAUAAGGUCCGGACUCCCUCGGGAGGCUGCAGUAGGGAAUCGUGAACAAUGUGCUAACGCUUGAUUCUAUAAUGUUGCGUGGGGGAUACAAAAAACAUUAUUUUAUACUUAUUGUUUUAUAAACAAAUUUAUAUAUAAAAUAGUGAUAAUUCUAGCAACGACUUAAGCGCAAUAAAAGUUUCCGUAAAAAGAGAUUUUUAUCUGUGUCUUCUGUAGCGUGCCUUUCUAGUAGACGGCAAGUUGUCUUAAACCCCUUUUUUUACGAUUAUAAUGACUGUAGUUAGUAUAUAUCUAUUUAUCAAGAUGAGGGUUGGUAAAUUACAUUUUGUUUGUUAGACUAAAAUACUCGAGCAAAAAUGCCUUAUGCUGCUUUGCUUAAAAAUAUCAAACCCCGGCUAACUUCGUGCCAGCAGCCGCGGUAAAACGGGGGGGGUUAGUGUUAUUCGUGAUGACUGGGCGUAAAGGGUACGUAGGCAGAUAAUUGAAAAUACAGUAAAAAACUGAGGUAAACCCUCUUCAUUCUGUAUUCACUCAUUAUCUUGAGUUCAGAAGGCGGUUUAUUGAAUUCUCGAAGGAAGGGUGAAAUCUGUUGAUAUCUGGAAGACAUUCGAUAGCGAAAGCAACAUCCGAUUCUGAUCUAACGCUCAGGUACUAAAGUAUGGGGAUCAAAUAGGAUUAGAGACCCUAGUAGUCCAUACCUUAAACAAUGAGUGUUCAACGUCUUUAAUAUAGUCAAUAUAUUUAGGGGGUUUAAAGCUAACGCGUGAAACACUCCGCCUGGGGAAUGUGGCCGCAAGGUCUAAACUCAAAGGAAUUGACGGUGACUUAUACAAGGGGUGGAGCAUGUGGUUUAAUUCGACAUACCGCGCAAAACCUUACCAAUUUUUGUAUCUGGUUUCUUUUCGUUAGCCAUUUAUUUGGUUAGCCUUCUUCUUUCUGUUGAAGGUCUACUACGAUAUCGAUUGAAGAUGUGGGUGUUUCUAUGCGUAAGCAUGAUCUAGCUAUUUUCAAUUAACGGUAACCAAUGACAAGAGCUGCAUGAUUGUCGUAAGUUCGUGCCGUGAGGUGUUGGGUUCAUUCCAUAAACGAACGCAACCCUUUUGAUUAGUUGCAUAAUGGAUGAAAGUUUAAACUGGAUAUCCAUGUUCACUAGUUCAACCAGCCCUUCUACCUUUAGGGAUUAAGGACAGGUCCACGUCAAAUCAUUAUGGCCUUAAUAGAUUGGGCUACACAUGUGCUACAUUGAUGAUCGACAACAAGAAGCAAUGGCGUGAGCCUGAGCAAAUCUUUAAAAGACAUUUCAGUCCGAAUUGUUCUUUGAAACUCAAGAGCAUGAAGCCGGAAUCUCUUGUAAUCGUGGAUCAUUACGCCACGGUGAAUUAGUACAAAAGUCACGUACAGACCGCCCGUCAUGCUAUGGAAACUAUUUGAAGUAGAAGUUACAAGGUUUCAAUUGUUUCGAUAGACCACCUUAUUGAAAGUUUUCAUAAGGCCUUGACAUUCUGUUGGCUUUGUACACGACUCUUUAUUUAGGGACUGGAGUAAAGUCGAAACAGGGUAGUGGUAGAAGAAUCUGCUGCUGGACCAUUAUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.R.norvegicus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.R.norvegicus.seq new file mode 100644 index 0000000..a016faf --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.R.norvegicus.seq @@ -0,0 +1,2 @@ +>d.16.m.R.norvegicus +AAAGGUUUGGUCCUGGCCUUAUAAUUAAUUGGAGGUAAGAUUACACAUGCAAACAUCCAUAAACCGGUGUAAAAUCCCUUAAAGAUUUGCCUAAAACUUAAGGAGAGGGCAUCAAGCACAUAAUAUAGCUCAAGACGCCUUGCCUAGCCACACCCCCACGGGACUCAGCAGUGAUAAAUAUUAAGCAAUGAACGAAAGUUUGACUAAGCUAGUACCUCUCAGGGUUGGUAAAUUUCGUGCCAGCCACCGCGGUCAUACGAUUAACCCAAACUAAUUAUUUUCGGCGUAAAACGUGCCAACUAUAAAUCUCAUAAUAGAAUUAAAAUCCAACUUAUAUGUGAAAAUUCAUUGUUAGGACCUAAGCCCAAUAACGAAAGUAAUUCUAAUCAUUUAUAUAAUGCACGAUAGCUAAGACCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAACCUUAAUAAUUAAACCUACAAAAUUAUUUGCCAGAGAACUACUAGCUACAGCUUAAAACACAAAGGACUUGGCGGUACUUUAUAUCCGUCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGUUCUACCUUACCCCUUCUCGCUAAUUCAGCCUAUAUACCGCCAUCUUCAGCAAACCCUAAAAAGGCACUAAGUUAGCACAAGACAACAUAAAACGUUAGGUCAAGGUGUAGCCAAUGAAGCGGAAAGAAAUGGGCUACAUUUUCUUUUCCCAGAGAACAUUACGAAACCCUUAUGAAACUAAAGGACAAAGGAGGAUUUAGUAGUAAAUUAAGAAUAGAGAGCUUAAUUGAAUAGAGCAAUGAAGUACGCACACACCGCCCGUCACCCUCCUCAAAUUAGAUUGACAUUCACAUAUACAUAAUUUCACUAACAAAUUUAUGAGAGGAGAUAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGAAUAAU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.R.unicornis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.R.unicornis.seq new file mode 100644 index 0000000..1a6dfd1 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.R.unicornis.seq @@ -0,0 +1,2 @@ +>d.16.m.R.unicornis +CAUAGGUUUGGUCCUAGCCUUUCUAUUAACUAUUAGUAAAAUUACACAUGCAAGUAUCCGCACUCCAGUGAGAAUGCCCUCUAAAUCACCCAUAACGAUUAAAAGGAGCAGGUAUCAAGUACACUAAUAACAGUAGCUAACAACACCUUGCUCAACCACACCCCCACGGGAGACAGCAGUGACAAAAAUUAAGCAAUAAACGAAAGUUUGACUAAGUUAUACUAAGCAGAGCCGGUAAAUUUCGUGCCAGCCACCGCGGCCAUACGAUUGACUCAAAUUAAUAGAACCUCGGCGUAAAGCGUGUCAAAGAUAUAACCCCUAAUAAAGUUAAAAACAUAGUUAAGCUGUAAAAAGCUAUAACCAAGAUAAAAUAAACCACGAAAGUGACUUUAAUAUAUCACCCACACUACAGCUAAGACCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCCCAAACUCAAAUAAUUCUUCCCAACAAAAUUAUUCGCCAGAGUACUACUAGCAACAGCCUAAAACUCAAAGGACUUGGCGGUGCUUUAUAUCCCCCUAGAGGAGCCUGUUCCAUAACCGAUAAACCCCGAUAAACCUUACCAGCCCUUGCUAAUUCAGCCUAUAUACCGCCAUCUUCAGCCAACCCUAAAAAGGAACCAAAGUAAGCACAAGUAUAAGACAUAAAAACGUUAGGUCAAGGUGUAGCUUAUGGGAUGGAGAGAAAUGGGCUACAUUUUCUACUUCAAGAACAACAACUACCCAAACGAAGGCUUUUAUGAAAUUAAAAGCUAAAGGAGGAUUUAGCAGUAAAUUAAGAAUAGAGAGCUUAAUUGAACCAGGCCAUAAAGCACGCACACACCGCCCGUCACCCUCCUUAAAUAUCAUAAACCACAACACAACAUAUUAACGUACGUUGAACAUAUAAAAGGAGACAAGUCGUAACAAGGUAAGUGUACUGGAAAGUGCGCUUGGAUAAU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.S.aestuans.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.S.aestuans.seq new file mode 100644 index 0000000..ec9dd34 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.S.aestuans.seq @@ -0,0 +1,2 @@ +>d.16.m.S.aestuans +UAUAGGUUUGGUCCUAGCCUUUUUAUUAAUUCUUAGUAGACUUACACAUGCAAGUAUCCCCGCCCCAGUGAGAAUGCCCUCUAUCUCCAUAAGGAUCUAAAGGUGCAGGUAUCAAGUACGCUCUCUCGAGCAGCUCAUGACACCUUGCUACACCACACCCCCACGGGACACAGCAGUGAUUAAAAUUGAGACAUAAACGAAAGUUUGACUGAGUUAUACUAAUAAUUAGGGUUGGUAAAUUUCGUGCCAGCCACCGCGGUCAUACGAUUAACCCUAGUUAAUAAAACACGGCGUAAAGCGUGAUUAAGGAAUAACCCCAAAUAAGAUUAAGCUCUGACUAAGCUGUAAAAAGCCUUAGUUAAAAUAAAAAUUUAUAAACGAAAGUAAUCUUACAACCCCUGAAUUCACGAUAGCUAAGGCCCAAACCGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAACAUAAAUACUCAAAUAACAAGAGUAUUCGCCAGAGAACUACUAGCCACUGCUUAAAACUCAAAGGACUUGGCGGUGCUUUAUACCCCUCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGUUAAACCUCACCACUCUUUGCAAUGUCAGCCUAUAUACCGCCAUCUUCAGCAAACCCUAAUAAGGUAUCGCAGUAAGCACAAGAAUUCUGCAUAAAAACGUUAGGUCAAGGUGUAGCCUAUAGAGUGGGAAGAAAUGGGCUACAUUUUCUAAUUUCUUUAGAACAUUUCACGAUAGCUGUCAUGAAACAUGAUCAGCCCAAGGAGGAUUUAGUAGUAAGUUGGGAAUAGAGUGCCCAACUGAAUUGGGCAAUAAAGCACGCACACACCGCCCGUCACCCUCUUCAAGCAUCCAUGAUAACCCAUAUAAAUAAUACAAAAAUCUCCUAAUGCAAGAAGAGACAAGUCGUAACAAGGUAAACAUACUGGAAAGUGUGUUUGGAAUAUC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.S.aquaticus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.S.aquaticus.seq new file mode 100644 index 0000000..e30ce56 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.S.aquaticus.seq @@ -0,0 +1,2 @@ +>d.16.m.S.aquaticus +UAAAAGGUUUGGUCCUGGCCUUUCUAUUAGCUGUCAGUAAAAUUACACAUGCAAGUAUCCGCGCCCCAGUGAAAAUGCCCUUGAAGUCAUCAUAGACAUAAAGGAGCCGGCAUCAAGUACACCAUAAUGGUAGCUAACGACGCCUUGCUUAGCCACGCCCCCACGGGAAACAGCAGUGAUAAAAAUUAAGCUAUGAACGAAAGUUUGACUAAGUUAUACUGAUAUAGGGUUGGUAAAUUUCGUGCCAGCCACCGCGGUCAUACGAAUAACCCAAGUUAAUAGAUACACGGCGUAAAGAGUGUUAAAGAACCUGGCAUUGUAAAUAAAGCUAAGACUUAACUAAGACGUAAAAAUCUCCAGUUAAAGUAAAAACAAACUACGAAAGUGGCUUUAUAUUAUUCUGAUCACACGAUAGCUAAGACCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAACUAAGACAAUCCAACUAACAAGAUUGUUCGCCAGAGAACUACUAGCAAUAGCUUAAAACUCAAAGGACUUGGCGGUGCUUUAUAUCCCUCUAGAGGAGCCUGUUCUGUAAUCGAUAAACCCCGAUAAACCUCACCAACCCUUGCUAAUUCAGCCUAUAUACCGCCAUCUUCAGCAAACCCUUAAAGGGAGCCACAGUAAGCACAAGUAUAUACAUAAAAACGUUAGGUCAAGGUGUAGCUAAUGAGUUGGGAAGAAAUGGGCUACAUUUUCUAUAUCUAGAACACUUUAACGAAAGUCUUUAUGAAACGAAAGACUAAAGGAGGAUUUAGUAGUAAAUUAAGAAUAGAGUGCUUAAUUGAAUUAGGCCAUGAAGCACGCACACACCGCCCGUCACCCUCCUCAAGUACUAAAGCCAGUCAAUAUACAUAAUAUAUAGGCAAUAAAUACAAGAGGAGAUAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGAUUAAC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.S.scrofa.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.S.scrofa.seq new file mode 100644 index 0000000..af65bac --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.S.scrofa.seq @@ -0,0 +1,2 @@ +>d.16.m.S.scrofa +CACAGGUUUGGUCCUGGCCUUUCUAUUAAUUCUUAAUAAAAUUACACAUGCAAGUAUCCGCGCCCCGGUGAGAAUGCCCUCCAGAUCUUAAAGAUCAAAAGGAGCAGGUAUCAAGCACACCUAUAACGGUAGCUCAUAACGCCUUGCUCAACCACACCCCCACGGGAAACAGCAGUGAUAAAAAUUAAGCCAUGAACGAAAGUUUGACUAAGUUAUAUUAAUUAGAGUUGGUAAAUCUCGUGCCAGCCACCGCGGUCAUACGAUUAACCCAAAUUAAUAGAUCCACGGCGUAAAGAGUGUUUAAGAAAAAAAAAUCACAAUAGAGUUAAAUUAUAACUAAGCUGUAAAAAGCCCUAGUUAAAAUAAAAUAACCCACGAAAGUGACUCUAAUAAUCCUGACACACGAUAGCUAGGACCCAAACUGGGAUUAGAUACCCCACUAUGCCUAGCCCUAAACCCAAAUAGUUACAUAACAAAACUAUUCGCCAGAGUACUACUCGCAACUGCCUAAAACUCAAAGGACUUGGCGGUGCUUCACAUCCACCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGAUAGACCUUACCAACCCUUGCCAAUUCAGCCUAUAUACCGCCAUCUUCAGCAAACCCUAAAAAGGAACAAUAGUAAGCACAAUCAUAGCACAUAAAAACGUUAGGUCAAGGUGUAGCUUAUGGGUUGGAAAGAAAUGGGCUACAUUUUCUACAUAAGAAUAUCCACCACACGAAAGUUUUUAUGAAACUAAAAACCAAAGGAGGAUUUAGCAGUAAAUCAAGAAUAGAGUGCUUGAUUGAAUAAGGCCAUGAAGCACGCACACACCGCCCGUCACCCUCCUCAAGCAUGUAGUAAUAAAAAUAACCUAUAUUCAAUUACACAACCAUGCAAGAAGAGACAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGAUUACC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.S.sinuspaulianus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.S.sinuspaulianus.seq new file mode 100644 index 0000000..5a2d1d3 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.S.sinuspaulianus.seq @@ -0,0 +1,2 @@ +>d.16.m.S.sinuspaulianus +AAAAGAAAGAAUUUAAUUUUGGUUCCGAUUGAACGUUUUUCAGUAGUUUUAAGACAUGCAAAUCGUUAUUUCUGAAAGUAAAUUUUUAUUUAAAAUUAUAUAAAUAAUAACUAAAUAAAAAUGAUAAUAUGAAAUAAGGUGUAGAGGUGAGGAUAGUAAAUAAGAUACCCUGUAGUCUUCAUAGAUAGAAGAUAUUAUUCUAAGUAAAUUUUUUAAAUUUAUUACUAGUAUUUUUAAAUUAAUUUGCUUGCAUUAUAUAAAAUUAUAAUUGUUUUUCAUUAAUUGCAAAAAUUUAAAUAAAAAUGACUAAAGCAAAAAAAUUAUUUAAAUAACAAUAAUGUAAAAUAAAUGAAUAAAAUAAAAAAGCUAUUUUUAUUAAAAAAAGGAAAUUUUCUGCUAUAGGAUUCUAUUUAUUUUGAUUAGGUAGUUGGUAUGGGUAAAGGCCUACCAAGCCGACAAUCAAUAGCCAUGCUUGACAGAGCAGAUGGCCACAUUGGGAAUGAAAUCUCCCAAGUAGUUUUAUACUACCAGCAGUCAAGAAUAUUAGUCAAUGCUCGUAAGAGUGAACUAGCUAACUGAAAUCGCAAAUGUGUCAUUUGUGAUAAAGUAAGAGAAAAUUAUGAUAUUAUCUUACUACUAGUGCUGUCCAAAACUGGUGCCAGAAGACUCGGUAAGGCCAGAGGCGCAAACGUUAGUCGUCCUAAUCAGGCGUAAAGGGUUUGUAGGCUGCUUUGAAAGUCUUAUUAUUAUAAUAGCUAUUAAAUGAUAAGAUGAAUUGAAGCUAGAAUCUAAUAGAGGGUAAAACAAAUAAUAUUUAAAGUAAGGAUUAAAUCUCAAGAGUUUAGAUGGAAUACUAACGGUUAAAGCUUUUAUCUAUCUACAGAUUGACGCUGAGAAACGAAAGGGAGGUAAGGAAACAGGAUUAGAUACCCAACUACUGCUCCCUGUCAACGAUGAAUGGUGGUUGCUAGUUAUAACUACUUUAAGUAAAUAUUUUAUAUUAUAUAAGAUAAAAUAAGUAGUUAAAAUGACUGGUAGCGAUGCUAACGCGUUAACCAUUCCGCCUUGUGAGUACGACUGCAAAGUUGAAAACAAAAAAAUUAGUCGGUUUCGAAGCAAACGAAGUGAAGCAUGUUAUUUAAUACGAUAAUCCGCGUAAAAUCUUACCAGUUCUUGCAUACAAACUUUUUUUAUAAUAAUUUAAAUUAAAUUUUAAAUAGUUAUUUAAAAAGGAGUGUUUUUACUUUUUUAAAAAUACUUAGAUACAGGUGUUGCAUGGCUGUCGUCAGUCCGUGCUGUGAGAAGUUUGGUUAAAUCCGCUAACGGACAAAAUCCCUGUUGUUAAUUUAUACUUAACAAUUAAUGAUACUGAUAGAGCAUCAUUUGGGGCGAAGACAAGUCGUUAUGGCCCUCAUGAACUGGGCUAUAGACGUGCCACAAAGACUUUAACAAAGUGAAGCGAUACUGUUCCCUUAAUAUUUUUCUAAAGAAUUUUAUUAGAUUUAAUUAUAACAAUUAAAUUAUAGGGAAUUUAAGGAGGAGCUAAUCAUUAAAAAAAGUCAAACUAUUAAAUAUAGUCGGAUUGUCAUCUGAAACUCGGGGACAUGAAGAAGGAAUUUCGAGUAAUCGUUGAUCACUACGCAACGGUGAAGCUAGCAUUCGGAAUGAACUAACCGUCUGUCGCUGGGAAGGAGCUUAACUUGGUGGAAACUGGAAUGAAGUUUUAACUUUUACAAAAAUUAAAUUUUUAUUUAGUAUCUUUGAUAUUUUAUUUUUAAUUUAUUAGUUUUUUUUUCGUUAGAUUUUUUUUAAUUUAUUGCUUAAUUAAAAAGUAUUAUUUUUGUUUAAAGAAUAAAUACUUGUCUAACAAUGUUAAAUUUAAAACGAUUUUGUUAAGCAAAUUAGCUCUAGUUAAACCAAUUAAGUAACAUCUCAAAAGUCAUAGCAAGGUAGCCGUACUGGAAAGUGCUGCUGUAAAAUAAAACGA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.V.ursinus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.V.ursinus.seq new file mode 100644 index 0000000..e00de33 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.V.ursinus.seq @@ -0,0 +1,2 @@ +>d.16.m.V.ursinus +CAAAGGUUUGGUCCUAGCCUUACUGUUAAUUUUAAUUAAGCCUACACAUGCAAGUUUCCGCUGCCCAGUGAGAAUGCCCUCAAAAUUCUACAAUCGAAUCAACAGGAGCAGGUAUCAGGCACACCCAUCCCGGUAGCCCAUAACACCUUGCUUAGCCACACCCCCACGGGAUACAGCAGUGACUAACUUUAAGAUAUGAACGAAAGUUUGACUAAAUUAUAAUUAUACAGGGUUGGUAAAUUUCGUGCCAGCCGCCGCGGUCAUACGAUUAACCCAAAUUAACAGAACACCGGCGUAAAGCGUGUUUAAGCGCAAAUCUCAAAAUAAAGUUAAUACUUAACUAAACUGUAAUACGCCCUAGUUAACAUUAAAAUAAACAACUAAAGUGACUUUAAUUUCGCUGAAUACACGACAACUAAGACUCAAACUGGGAUUAGAUACCCCACUAUGCUUAGUCAUAAACCUAGGUAAUCCGAUAACAAAAUUAUUCGCCAGAGAACUACUAGCCACCGCUUAAAACUCAAAGGACUUGGCGGUGCUCUAAACCCACCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGAUACACCUCACCCCUUCUUGCCAAUACAGCCUAUAUACCGCCAUCGUCAGCUCACCCCAAUAGGGAACAAAAGUGGGCAAAAUCAUUCACCAUAAAAACGUUAGGUCAAGGUGUAGCAUAUGAAGGGGGAAGUAAUGGGCUACAUUUUCUAAAUUAGAAAACCAACGAACUAUCUCAUGAAACCCUGAGUCAUACGAAGGAGGAUUUAGUAGUAAAUUAAGAAUAGAGAGCUUAAUUGAAAUAGGCAAUAGAGCGCGCACACACCGCCCGUCACCCUCCUCAACACAAACCGUCACAUUAACUAAUAAGUUAUCCAAAAAAAGAGGAGAAAAGUCGUAACAUGGUAAGUGUACUGGAAGGUGCACUUGGAGUAU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.X.laevis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.X.laevis.seq new file mode 100644 index 0000000..dc25fe7 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.X.laevis.seq @@ -0,0 +1,2 @@ +>d.16.m.X.laevis +UAAAGGUUUGGUCCUAGCCUUAUUAUCAACUUUUUCUGAACUUACACAUGCAAGCAUCCGCACUCCCGUGAAAAUGCCCUUAAGCCUCUUAAACAGGGGAUAAGGAGCCGGUAUCAGGCACAACUAAUAGCCCAUGACACCUUGCUCUGCCACACCCACAAGGGAAUUCAGCAGUGAUAAACAUUGAACAUGAGCGACACAAAGCUCGAUUCAGUUACAGUAAAUAGAGUUGGUCAAUCUCGUGCCAGCCGCCGCGGUUAUACGAGAAACUCAAGUUGAUCAUUUUCGGCGUAAAGCGUGAUUAAAGUAACCCAAACUAGAGUCAAACUCCAACCAAGCUGUCGCCGCUUUCGUUGGUUUGAAGAACACUCACGAAAGUAACUCUACCCAUAUUACACUUGAACUCACGACCGCUAGGAAACAAACUGGGAUUAGAUACCCCACUAUGCCUAGCCAUAAACUUUGACUACUUACGCAAAAAUCCGCCAGAACUACGAGCCUAAGCUUAAAACCCAAAGGACUUGGCGGUGCUCCAAACCCACCUAGAGGAGCCUGUUCUGUAAUCGAUACCCCUCGCUAAACCUCACCACUUCUUGCCAAACCCGCCUAUAUACCACCGUCGCCAGCCCACCUCGUGAGAGAUUCUUAGUAGGCUUAAUGAUUUUUCAUCAACACGUCAGGUCAAGGUGUAGCAUAUGAAGUGGGAAGAAAUGGGCUACAUUUUCUAUACCUUAGAAUAAACGCAAGAUCUCUAUGAAACCAGAUCGGAAGGCGGAUUUAGCAGUAAAGAGAAACAAGAGAGUUCUCUUUAAAACGGCCCUGGAGCGCGCACACACCGCCCGUCACCCUCUUCUACAAAAAUCAACCAAUUUUAUAAACACACAAUUAACACAAAGAAGAGGCAAGUCGUAACAUGGUAAGCACACCGGAAGGUGUGCUUGGAAU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.Z.californianus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.Z.californianus.seq new file mode 100644 index 0000000..47e7bd4 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.Z.californianus.seq @@ -0,0 +1,2 @@ +>d.16.m.Z.californianus +CAAAGGUUUGGUCCUAGCCCUUCCGUUAGUUUUUAAUAAAAUUAUACAUGCAAGCUUCCACGCCCCAGUGAGAAUGCCCUUCAGAUCCCUACAGCCGAUCAAAAGGAGCGGGUAUCAAGCACACUCAACGAGUAGCUCACAACGCCUUGCUCAACCACACCCCCACGGGACACAGCAGUAAUAAAAAUUAAGCCAUGAACGAAAGUUCGACUAAGUUAUAUUAAUCAUAAGGGUUGGUAAAUUUCGUGCCAGCCACCGCGGUCAUACGAUUAACCCAAACUAACGGGCUCACGGCGUAAAGCGUGUAAAAGAUCUACCUACACUAAAGUUAAAAUUUAACCAAGCCGUAAAAAGCUGCCGUUAAUACAAAAUAUACUACGAAAGUGACUUUAAUAAUUCUGAUUACACGAUAGCUAAGACCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAACAUAAAUAAUUCACUUAACAAAAUUAUCCGCCAGAGAACUACUAGCAAUAGCUUAAAACUCAAAGGACUUGGCGGUGCUUCACAUCCCCCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGAUAAACCUCACCACCUCUUGCUAAUCCAGUCUAUAUACCGCCAUCCUCAGCAAACCCUUAAAAGGAAAGAAAGUAAGCAUAAUCAUCGCACGUAAAAAAGUUAGGUCAAGGUGUAACCCAUGAGGUGGGAAGAAAUGGGCUACAUUUUCUAAACAAGAACACACCGUACGAAAGUUAUUAUGAAACUAAUAACUAAAGGUGGAUUUAGUAGUAAACUAAGAAUAGAGAGCUUAAUUGAACUGGGCCAUGAAGCACGCACACACCGCCCGUCACCCUCCUCAAAUAAUAACCUCAAAGCACAUACAUAAAUCAAUAUAAAACCAUAAGAGGAGAUAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGAUAAAU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.Z.mays.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.Z.mays.seq new file mode 100644 index 0000000..10bd605 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.Z.mays.seq @@ -0,0 +1,2 @@ +>d.16.m.Z.mays +AAAAUCUGAGUUUGAUCCUGGCUCAGAAGGAACGCUAGCUAUAUGCUUAACACAUGCAAGUCGAACGUUGUUUUCGGGGAGCUGGGCAGAAGGAAAAGAGGCUCCUAGCUAAAGUUGUCUCGCCCUGCCUGCAGGGCGCGCGCAACGGCUUUGACCUAACGGCCUCCGUUUGCUGGAAUCGGAAUAGUUGAGAACAAAGUGGCGAACGGGUGCGUAACGCGUGGGAAUCUGCCGAACAGUUCGGGCCAAAUCCUGAAGAAAGCUCAAAAGCGCUGUUUGAUGAGCCUGCGUAGUAUUAGGUAGUUGGUCAGGUAAAGGCUGACCAAGCCAAUGAUGCUUAGCUGGUCUUUUCGGAUGAUCAGCCACACUGGGACUGAGACACGGCCCGGACUCCCACGGGGGGCAGCAGUGGGGAAUCUUGGACAAUGGGCGAAAGCCCGAUCCAGCAAUAUCGCGUGAGUGAAGAAGGGCAAUGCCGCUUGUAAAGCUCUUUCGUCGAGUGCGCGAUCAUGACAGGACUCGAGGAAGAAGCCCCGGCUAACUCCGUGCCAGCAGCCGCGGUAAGACGGGGGGGGCAAGUGUUCUUCGGAAUGACUGGGCGUAAAGGGCACGUAGGCGGUGAAUCGGGUUGAAAGUGAAAGUCGCCAAAAAGUGGCGGAAUGCUCUCGAAACCAAUUCACUUGAGUGAGACAGAGGAGAGUGGAAUUUCGUGUGUAGGGGUGAAAUCCGUAGAUCUACGAAGGAACGCCAAAAGCGAAGGCAGCUCUCUGGGUCCCUACCGACGCUGGGGUGCGAAAGCAUGGGGAGCGAACAGGAUUAGAUACCCUGGUAGUCCAUGCCGUAAACGAUGAGUGUUCGCCCUUGGUCUGUCUACGCUACGCUACGCGGAUCAGGGGCCCAGCUAACGCGUGAAACACUCCGCCUGGGGAGUACGGUCGCAAGACCGAAACUCAAAGGAAUUGACGGGGGCCUGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUACAACGCGCAAAACCUUACCAGCCCUUGACAUAUGAACAACAAAACCUGUCUUUAACGGGAUGGUACUUACUUUCAUACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUUGGUCAAGUCCUAUAACGAGCGAAACCCUCGUUUUGUGUUGCUGAGACAUGCGCCUAAGGAGAAAUAGCCGAGGAGCCGAGUGACGUGCCAGCGCUACUACUUGAUUGAGUGCCAGCACGUAGCUGUGCUUUCCGCAAGAAUUUCACCAUUGGGAGCCUCGAAGCACUUUCACGUGUGAACCGAAGUCGUCUUGCCGAACUCAAGACCCACGGAGACCUACCUAUAGUGACGUCAAAGUACCAGUGAGCAUGGAGGUUUGGUUAGGCUUGGUUACGACGACGUCGAGUUGGCGGCGGAGGAAGACUCGGCAUGAAGGCCAGCCGCCCGGUGGUGUGGUACGUAGUGGUAAUAGUACGCGCCCCGCUCCGAAACAAAGAAAAAGGUGCGUGCCGCACUCACGAGGGACUGCCAGUGAGAUACUGGAGGAAGGUGGGGAUGACGUCAAGUCCGCAUGGCCCUUAUGGGCUGGGCCACACACGUGCUACAAUGGCAAUGACAAUGGGAAGCAAGGCUGUAAGGCGGAGCGAAUCCGGAAAGAUUGCCUCAGUUCGGAUUGUUCUCUGCAACUCGGGAACAUGAAGUAGAAAUCGCUAGUAAUCGCGGAUCAGCAUGCCGCGGUGAAUAUGUACCCGGGCCCUGUACACACCGCCCGUCACACCCUGGGAAUUGGUUUCGCCCGAAGCAUCGGACCAAUGAUCACCCAUGACUUCUGUGUACCACUAGUGCCACAAAGGCCUUUGGUGGUCUUAUUGGCGCAUACCACGGUGGGGUCUUCGACUGGGGUGAAGUCGUAACAAGGUAGCCGUAGGGGAACCUGUGGCUGGAUUGAAUCCUUC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.y.C.paradoxa.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.y.C.paradoxa.seq new file mode 100644 index 0000000..48e9291 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.y.C.paradoxa.seq @@ -0,0 +1,2 @@ +>d.16.y.C.paradoxa +UACCAUGGAGAGUUUGAUCCUGGCUCAGGAUGAACGCUGGCGGUAUGCUUAACACAUGCAAGUCGAACGAAGAUCGCAAGAUCUUAGUGGCGGACGGGUGAGUAACGCGUGAGAAUCUACCCUUAGGAGGGGGACAACAGUUGGAAACGACUGCUAAUACCCCAUAUGCCAUUCGUGGUGAAAAGAGUAAUCUGCCUGAGGAAGAGCUCGCGUCUGAUUAGCUAGUUGGUGGGGUAAAGGCCUACCAAGGCGACGAUCAGUAGCUGGUCUGAGAGGAUGAUCAGCCACACUGGGACUGAGAUACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUUUUCCGCAAUGGGCGAAAGCCUGACGGAGCAAUACCGCGUGAGGGAAGACGGCCUGUGGGUUGUAAACCUCUUUUCUUAGGGAAGAAUCAAUGACGGUACCUAAGGAAUAAGCAUCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGAUGCAAGCGUUAUCCGGAAUCAUUGGGCGUAAAGAGUUCGUAGGUGGCUAAGCAAGUCUGUUGUUAAAGGCUGGGGCUUAACCCCAAAAAGGCAAUGGAAACUGUUUGGCUUGAGUACGGUAGGGGCAGAGGGAAUUCCUGGUGUAGCGGUGAAAUGCGUAGAUAUCAGGAAGAACACCGAUGGCGAAAGCACUCUGCUGGGCCGUUACUGACACUGAGGAACGAAAGCUAGGGUAGCAAAUGGGAUUAGAUACCCCAGUAGUCCUAGCCGUAAACUAUGGAUACUAGGUGUUGUGCGUAUCGACCCGUACAGUACCGUAGCUAACGCGUUAAGUAUCCCGCCUGGGGAGUACGCUCGCAAGAGUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGUAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCAGGGUUUGACAUGUCGCGAAUUUUCUUGAAAGAGAAAAGUGCCUUCGGGAACGCGAACACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUCGUUUUUAGUUGCCAUCAUUCAGUUGGGCACUCUAAAGAGACUGCCGGUGACAAGCCGGAGGAAGGUGGGGAUGACGUCAAGUCAGCAUGCCCCUUAUACCCUGGGCUACACACGUACUACAAUGGUCGGGACAAUAGGUUGCCAACUUGCGAAAGUGAGCUAAUCCGUUAAACCCGGCCUCAGUUCAGAUUGCAGGCUGCAACUCGCCUGCAUGAAGGUGGAAUCGCUAGUAAUCGCCGGUCAGCUAUACGGCGGUGAAUUCGUUCCCGGGCCUUGUACACACCGCCCGUCACACCACGGGAGUCGGCCAUGCCCGAAGUCGUUACCCUAACCAUUUCGGAGGGGGAUGCCUAAGGCAGGGCUGGUGACUGGGGUGAAGUCGUAACAAGGUAGCCGUACUGGAAGGUGCGGCUGGAUCACCUCCUUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.D.mobilis.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.D.mobilis.seq new file mode 100644 index 0000000..84b1c04 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.D.mobilis.seq @@ -0,0 +1,2 @@ +>d.5.a.D.mobilis +ACGGUGCCCGACCCGGCCAUAGUGGCCGGGCAACACCCGGUCUCGUUUCGAACCCGGAAGUUAAGCCGGCCACGUCAGAACGGCCGUGAGGUCCGAGAGGCCUCGCAGCCGUUCUGAGCUGGGAUCGGGCACC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.marismortui.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.marismortui.seq new file mode 100644 index 0000000..d202539 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.marismortui.seq @@ -0,0 +1,2 @@ +>d.5.a.H.marismortui +UUAGGCGGCCACAGCGGUGGGGUUGCCUCCCGUACCCAUCCCGAACACGGAAGAUAAGCCCACCAGCGUUCCGGGGAGUACUGGAGUGCGCGAGCCUCUGGGAAACCCGGUUCGCCGCCACC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.mediterranei.1.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.mediterranei.1.seq new file mode 100644 index 0000000..1bfbb69 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.mediterranei.1.seq @@ -0,0 +1,2 @@ +>d.5.a.H.mediterranei.1 +AUUAGGGCGGCCAGAGCGGUGAGGUUCCACCCGUACCCAUCCCGAACACGGAAGUUAAGCUCGCCUGCGUUCUGGUCAGUACUGGAGUGAGCGAUCCUCUGGGAAAUCCAGUUCGCCGCCCCU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.morrhuae.1.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.morrhuae.1.seq new file mode 100644 index 0000000..637ed19 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.morrhuae.1.seq @@ -0,0 +1,2 @@ +>d.5.a.H.morrhuae.1 +UUAAGGCGGCCACAGCGGCGGGGCGACUCCCGUACCCAUCCCGAACACGGCAGAUAAGCCCGCCAGCGUUCCAGCGAGUACUGGAGUGUGCGAACCUCUGGGAAAACUGGUUCGCCGCCUCCC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.morrhuae.2.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.morrhuae.2.seq new file mode 100644 index 0000000..1dd9dcf --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.morrhuae.2.seq @@ -0,0 +1,2 @@ +>d.5.a.H.morrhuae.2 +UUAAGGCGGCCACAGCGGCGGGGCGACUCCCGUACCCAUCCCGAACACGGCAGAUAAGCCCGCCAGCGUUCCAGCGAGUACUGGAGUGUGCGAACCUCUGGGAAAACUGGUUCGCCGCCU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.saccharovorum.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.saccharovorum.seq new file mode 100644 index 0000000..dba1e06 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.saccharovorum.seq @@ -0,0 +1,2 @@ +>d.5.a.H.saccharovorum +GGCAGCGGCCAUAGCGGUGGGGCGACACCCGUACCCAUUCCGAACACGGAAGUUAAGCCCACCAGCGUACCGGGAAGUACUGGAGUGAGCGAUCCUCUGGGAAGCGGGGUUCGCCGCCUGCCC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.salinarum.1.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.salinarum.1.seq new file mode 100644 index 0000000..13aca4b --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.salinarum.1.seq @@ -0,0 +1,2 @@ +>d.5.a.H.salinarum.1 +UUAAGGCGGCCAUAGCGGUGGGGUUACUCCCGUACCCAUCCCGAACACGGAAGAUAAGCCCGCCUGCGUUCCGGUCAGUACUGGAGUGCGAGCCUCUGGGAAAUCCGGUUCGCCGCCUACU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.salinarum.2.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.salinarum.2.seq new file mode 100644 index 0000000..cd1707d --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.salinarum.2.seq @@ -0,0 +1,2 @@ +>d.5.a.H.salinarum.2 +UUAAGGCGGCCAUAGCGGUGGGGUUACUCCCGUACCCAUCCCGAACACGGAAGAUAAGCCCGCCUGCGUUCCGGUCAGUACUGGAGUGCGCGAGCCUCUGGGAAAUCCGGUUCGCCGCCUACU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.volcanii.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.volcanii.seq new file mode 100644 index 0000000..149b7b4 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.volcanii.seq @@ -0,0 +1,2 @@ +>d.5.a.H.volcanii +UUAAGGCGGCCAGAGCGGUGAGGUUCCACCCGUACCCAUCCCGAACACGGAAGUUAAGCUCACCUGCGUUCUGGUCAGUACUGGAGUGAGCGAUCCUCUGGGAAAUCCAGUUCGCCGCCCCU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.barkeri.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.barkeri.seq new file mode 100644 index 0000000..aa89660 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.barkeri.seq @@ -0,0 +1,2 @@ +>d.5.a.M.barkeri +GGAGUUUGGCGCCAUAGCGGCAGUGUAACUCCUGUACCCAUCCCGAACACAGUAGAUAAGCCUGCCCGCGUUCCUUACUGUACUGAAGUGUGCGAGCCUUCGGGAACUCUGGAUCGCUGCCAUACUCACC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.fervidus.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.fervidus.seq new file mode 100644 index 0000000..014e2e9 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.fervidus.seq @@ -0,0 +1,2 @@ +>d.5.a.M.fervidus +GGGUACGGCGACCAUAGCGGGGGGGCCACACCUGAACCCGUUCCGAUCUCAGAAGUUAAGCCCCCCUGCGUUGGAGGUGGUACUGCAACGUUAGUUGCGGGAAGCCUCCAACGUCGCCGGCCCA diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.formicicum.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.formicicum.seq new file mode 100644 index 0000000..0d9789e --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.formicicum.seq @@ -0,0 +1,2 @@ +>d.5.a.M.formicicum +AGGUUGGCGGCCAUAGCGGAGGGGCCAUACCUGGUCUCGUUUCGAUCCCAGAAGUGAAGUCCUCCUGCGUUUUGUUGUUGUACUGUGGACGAGAGUCUAUGGGAAGCUCAUAACGCUGCCGGCCUC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.jannaschii.rrnA.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.jannaschii.rrnA.seq new file mode 100644 index 0000000..173a5b8 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.jannaschii.rrnA.seq @@ -0,0 +1,2 @@ +>d.5.a.M.jannaschii.rrnA +UGGUACGGCGGUCAUAGCGGGGGGGCCACACCCGAACCCAUCCCGAACUCGGAAGUUAAGCCCCCCAGCGAUGCCCCGAGUACUGCCAUCUGGCGGGAAAGGGGCGACGCCGCCGGCCAC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.jannaschii.rrnB.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.jannaschii.rrnB.seq new file mode 100644 index 0000000..8df9051 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.jannaschii.rrnB.seq @@ -0,0 +1,2 @@ +>d.5.a.M.jannaschii.rrnB +UGGUACGGCGGUCAUAGCGGGGGGGCCACACCCGAACCCAUCCCGAACUCGGAAGUUAAGCCCCCCAGCGAUGCCCCGAGUACUGCCAUCUGGCGGGAAAGGGGCGACACCGCCGGCCAC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.thermautotrophicus.1.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.thermautotrophicus.1.seq new file mode 100644 index 0000000..ac65026 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.thermautotrophicus.1.seq @@ -0,0 +1,2 @@ +>d.5.a.M.thermautotrophicus.1 +GGGGCAUGGCGGUCAUGGCGCAGGGGUUAUACCUGAUCUCGUUUCGAUCUCAGUAGUUAAGUCCUGCUGCGUUGUGGGUGUGUACUGCGGUUUUUUGCUGUGGGAAGCCCACUUCACUGCCAGCCACU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.thermolithotrophicus.2.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.thermolithotrophicus.2.seq new file mode 100644 index 0000000..2c27595 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.thermolithotrophicus.2.seq @@ -0,0 +1,2 @@ +>d.5.a.M.thermolithotrophicus.2 +UGAUAUAACGGUCAUAGCGGAGGAGCCACAUCCGAUCCCGUCCCGAUCUCGGAAAUUAAGCCCUCCAGCGAUACCCUAAGUACUGCCAUUUGGUGGGAACAGGGUGACGCUGUUGAUCAC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.tindarius.1.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.tindarius.1.seq new file mode 100644 index 0000000..bc9a31f --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.tindarius.1.seq @@ -0,0 +1,2 @@ +>d.5.a.M.tindarius.1 +GGAGUUUGGCGGCCAUAGCGGCGGGGCAAUUCCUGUACCCAUCCCGAACACAGAAGAUAAGCCCGCCUGCGUUCUAUACUGUACUAAAGUAUGAGAGUCUUUGGGAAAUAUGGAACGCUGCCAUCUCC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.vacuolata.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.vacuolata.seq new file mode 100644 index 0000000..2289727 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.vacuolata.seq @@ -0,0 +1,2 @@ +>d.5.a.M.vacuolata +GAUCUGGCAGCCAUAGCGGCAGGUGUAAUCCUGUACCCAUCCCGAACACAGUAGAUAAGCCUGCCCGCGUUCCUUGCCUGUACUGAAGUGUGCGAGCUUCGGGAACUCUGGAUCGUGCCAUAUCAGU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.N.magadii.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.N.magadii.seq new file mode 100644 index 0000000..1e9fb96 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.N.magadii.seq @@ -0,0 +1,2 @@ +>d.5.a.N.magadii +UUAAGGCGGCCAUCGCGGCGGGGUUCCUCCCGUACCCAUCCCGAACACGGAAGAUAAGCCUGCCUGCGUAUUGGUGAGUACUGGAGUGGGAGACCCUCUGGGAGAGCCGAUUCGCCGCCCCUACU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.P.aerophilum.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.P.aerophilum.seq new file mode 100644 index 0000000..35940f9 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.P.aerophilum.seq @@ -0,0 +1,2 @@ +>d.5.a.P.aerophilum +GCCCCUAACCCGGCCAUAGGCGCCGGUGAUACGCCCGGUCUCAUCAGAACCCGGAAGCUAAGGCCGGCGCCGCGCUCGGGAGUACUGGGCUCCGCGAGGGCCCGGGAAACCGGCGUGCUGGGAGGGGGCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.P.occultum.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.P.occultum.seq new file mode 100644 index 0000000..fe1e44d --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.P.occultum.seq @@ -0,0 +1,2 @@ +>d.5.a.P.occultum +UGGCCCGACCCGGCCAUAGCGGCCGGGCAACACCCGGACUCAUGUCGAACCCGGAAGUUAAGCCGGCCGCGUUGGGGGAUGCUGUGGGGUCCGCGAGGCCCCGCAGCGCCCCCAAGCCGGGAUCGGGCCG diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.P.woesei.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.P.woesei.seq new file mode 100644 index 0000000..0db6b35 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.P.woesei.seq @@ -0,0 +1,2 @@ +>d.5.a.P.woesei +GGUACGGCGGUCAUAGCGGGGGGGCCACACCCGGUCUCAUUUCGAACCCGGAAGUUAAGCCCCCCAGCGAUCCCGGCUGUACUGCCCUCCGAGAGGGGGCGGGAACCGGGGACGCCGCCGGCCA diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.S.solfataricus.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.S.solfataricus.seq new file mode 100644 index 0000000..5e79dbe --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.S.solfataricus.seq @@ -0,0 +1,2 @@ +>d.5.a.S.solfataricus +GCCCACCCGGUCACAGUGAGCGGGCAACACCCGGACUCAUUUCGAACCCGGAAGUUAAGCCGCUCACGUUAGUGGGGCCGUGGAUACCGUGAGGAUCCGCAGCCCCACUAAGCUGGGAUGGGUUUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.Sulfolobus.sp.B12.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.Sulfolobus.sp.B12.seq new file mode 100644 index 0000000..993246c --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.Sulfolobus.sp.B12.seq @@ -0,0 +1,2 @@ +>d.5.a.Sulfolobus.sp.B12 +GCCCACCCGGCCACAGUGAGCGGGCAACACCCGGACUCAUUUCGAACCCGGAAGUUAAGCCGCUCACGUUGGUGGGGCCGUGGAUACCGUGAGGAUCCGCAGCCCCACUAAGCUGGGAUGGGCUUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.T.acidophilum.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.T.acidophilum.seq new file mode 100644 index 0000000..a7dad6b --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.T.acidophilum.seq @@ -0,0 +1,2 @@ +>d.5.a.T.acidophilum +GGCAACGGUCAUAGCAGCAGGGAAACACCAGAUCCCAUUCCGAACUCGACGGUUAAGCCUGCUGCGUAUUGCGUUGUACUGUAUGCCGCGAGGGUACGGGAAGCGCAAUAUGCUGUUACCACU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.T.celer.1.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.T.celer.1.seq new file mode 100644 index 0000000..91d9b16 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.T.celer.1.seq @@ -0,0 +1,2 @@ +>d.5.a.T.celer.1 +GGUACGGCGGUCAUAGCGGCGGGGUCACACCCGGUCUCGUUUCGACCCCGGAAGUUAAGCCCGCCAGCGAUCCCGGUUGUACUGCCCUCCGGGAGGGGGCGGGAAGCCGGGGACGCCGCCGGCCACU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.b.A.tumefaciens.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.b.A.tumefaciens.seq new file mode 100644 index 0000000..758f2f3 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.b.A.tumefaciens.seq @@ -0,0 +1,2 @@ +>d.5.b.A.tumefaciens +CGACCUGGUGGUCAUCGCGGGGCGGCUGCACCCGUUCCCUUUCCGAACACGGCCGUGAAACGCCCCAGCGCCAAUGGUACUUCGUCUCAAGACGCGGGAGAGUAGGUCGCUGCCAGGUCU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.b.D.radiodurans.rrnB.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.b.D.radiodurans.rrnB.seq new file mode 100644 index 0000000..42aafa3 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.b.D.radiodurans.rrnB.seq @@ -0,0 +1,2 @@ +>d.5.b.D.radiodurans.rrnB +ACACCCCCGUGCCCAUAGCACUGUGGAACCACCCCACCCCAUGCCGAACUGGGUCGUGAAACACAGCAGCGCCAAUGAUACUCGGACCGCAGGGUCCCGGAAAAGUCGGUCAGCGCGGGGGUUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.b.E.coli.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.b.E.coli.seq new file mode 100644 index 0000000..c43add3 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.b.E.coli.seq @@ -0,0 +1,2 @@ +>d.5.b.E.coli +UGCCUGGCGGCCGUAGCGCGGUGGUCCCACCUGACCCCAUGCCGAACUCAGAAGUGAAACGCCGUAGCGCCGAUGGUAGUGUGGGGUCUCCCCAUGCGAGAGUAGGGAACUGCCAGGCAU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.b.G.stearothermophilus.2.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.b.G.stearothermophilus.2.seq new file mode 100644 index 0000000..215d002 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.b.G.stearothermophilus.2.seq @@ -0,0 +1,2 @@ +>d.5.b.G.stearothermophilus.2 +CCUAGUGGUGAUAGCGGAGGGGAAACACCCGUUCCCAUCCCGAACACGGAAGUUAAGCCCUCCAGCGCCGAUGGUAGUUGGGGCCAGCGCCCCUGCAAGAGUAGGUCGCUGCUAGGC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.b.G.stearothermophilus.3.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.b.G.stearothermophilus.3.seq new file mode 100644 index 0000000..c061b92 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.b.G.stearothermophilus.3.seq @@ -0,0 +1,2 @@ +>d.5.b.G.stearothermophilus.3 +CCUAGUGACAAUAGCGAGAGAGGAAACACCCGUCUCCAUCCCGAACACGAAGGUUAAGCUCUCCCAGCGCCGAUGGUAGUUGGGGCCAGCGCCCCUGCAAGAGUAGGUUGUCGCUAGGC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.b.G.stearothermophilus.4.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.b.G.stearothermophilus.4.seq new file mode 100644 index 0000000..c3fb93d --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.b.G.stearothermophilus.4.seq @@ -0,0 +1,2 @@ +>d.5.b.G.stearothermophilus.4 +CCUAGUGGUGAUAGCGGAGGGGAAACACCCGUUCCCAUCCCGAACACGGAAGUUAAGCCCUCCAGCGCCGAUGGUAGUUGGGGCCAGCGCCCCUGCAAGAGUAGGCCGCUGCUAGGC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.b.M.genitalium.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.b.M.genitalium.seq new file mode 100644 index 0000000..f3cf935 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.b.M.genitalium.seq @@ -0,0 +1,2 @@ +>d.5.b.M.genitalium +UUUUGUUUGGUGCUAAUAUCGCUGUGGAAACACCUGGAACCAUCCCGAACCCAGCAGUUAAGCACAGUGGAGCUAAAUGUAGGUAGUAAUACUGAGAAUAGGUAAGCACCAAGCAAAA diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.aquaticus.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.aquaticus.seq new file mode 100644 index 0000000..2eb8001 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.aquaticus.seq @@ -0,0 +1,2 @@ +>d.5.e.A.aquaticus +GUCAACGGCCAUACCACGUUGAAAGCACCGCUUCUCGUCCGAUCAGCAAAGUUAAGCAACGUUGGGUCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAACACCAGAUGCUGUUGACUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.aurita.2.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.aurita.2.seq new file mode 100644 index 0000000..4691f30 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.aurita.2.seq @@ -0,0 +1,2 @@ +>d.5.e.A.aurita.2 +GCCUACGACUAUACCACCAUGAAUACACCGGUUCUCGUCCGAUCACCGAAGUUAAGUAUGGUAGGGCCGGGUCAGUACCUGGAUGGGUGACCGCCUGGGAACACCCGGUGUUGUAGGCCU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.domesticus.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.domesticus.seq new file mode 100644 index 0000000..21ffcae --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.domesticus.seq @@ -0,0 +1,2 @@ +>d.5.e.A.domesticus +GCCAACGUCCAUACCACGUUGAAAGCACCGGUUCUCGUCCGAUCACCGAAGUUAAGCAGCGUCGGGCGCGGUUAGUACUUGGAUGGGUGACCGCCUGGGAACCCCGCGUGACGUUGGCAU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.equina.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.equina.seq new file mode 100644 index 0000000..e343cc3 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.equina.seq @@ -0,0 +1,2 @@ +>d.5.e.A.equina +GUCUACGGCCAUACCACCGGGAAAAUACCGGUUCUCGUCCGAUCACCGAAGUCAAGCCCGGUAGGGCCAGGUUAGUACUUGGAUGGGUGACCGCCUGGGAAUACCUGGUGCUGUAGACUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.immersus.1.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.immersus.1.seq new file mode 100644 index 0000000..0b3da01 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.immersus.1.seq @@ -0,0 +1,2 @@ +>d.5.e.A.immersus.1 +ACAUACGGCCAUAGAUUGAAGAAUAUACGGGAUCCCGUCCGCUCUCCCAUAGUCAAGCUUCUAAUCGCCAAGUUAGUACUGCGGUGGGUGACCACGCGGGAAUCCUUGGUGCUGUAUGU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.magnoliae.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.magnoliae.seq new file mode 100644 index 0000000..336539c --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.magnoliae.seq @@ -0,0 +1,2 @@ +>d.5.e.A.magnoliae +GGCAACGACCAUACCACGUUGAAUACACCAGUUCUCGUCCGAUCACUGAAGUUAAGCAACGUCGGGCGUAGUUAGUACUUGGAUGGGUGACCGCUUGGGAACACUACGUGCCGUUGGCAU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.pernyi.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.pernyi.seq new file mode 100644 index 0000000..8b924c3 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.pernyi.seq @@ -0,0 +1,2 @@ +>d.5.e.A.pernyi +GACAACGUCCAUACCACGUUGAAAACACCGGUUCUCGUCCGAUCACCGAAGUUAAGCAACGUCGGGCGCGGUCAGUACUUGGAUGGGUGACCGCCUGGGAACACCGCGUGACGUUGGCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.salina.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.salina.seq new file mode 100644 index 0000000..bd70eab --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.salina.seq @@ -0,0 +1,2 @@ +>d.5.e.A.salina +ACCAACGGCCAUACCACGUUGAAAGUACCCAGUCUCGUCAGAUCCUGGAAGUCACACAACGUCGGGCCCGGUCAGUACUUGGAUGGGUGACCGCCUGGGAACACCGGGUGCUGUUGGCAU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.tabira.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.tabira.seq new file mode 100644 index 0000000..311e3c2 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.tabira.seq @@ -0,0 +1,2 @@ +>d.5.e.A.tabira +GCUUACAGCCAUACUGUCCUGAGCACGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGGACAAGGCCUGGUUAGUACUUGGAUGGGAGACUGCCUGGGAAUACCAGGUGCUGUAAGCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.B.napus.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.B.napus.seq new file mode 100644 index 0000000..b3d1240 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.B.napus.seq @@ -0,0 +1,2 @@ +>d.5.e.B.napus +GGGUGCGAUCAUACCAGCACUAAUGCACCGGAUCCCAUCAGAACUCCGCAGUUAAGCGUGCUUGGGCGAGAGUAGUACUAGGAUGGGUGACCUCCUGGGAAGUCCUCGUGUUGCACCCCU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.B.neritina.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.B.neritina.seq new file mode 100644 index 0000000..c94dd69 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.B.neritina.seq @@ -0,0 +1,2 @@ +>d.5.e.B.neritina +GUUUACGGCCAUAUCACGUUGAAAACGCCAGUUCUCGUCCGAUCACUGAAGCUAAGCAACGUCGAGCCUGGUUAGUACUUGGAUGGGUGACCGCCUGGGAAUACCAGGUGCUGUAGACUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.B.taurus.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.B.taurus.seq new file mode 100644 index 0000000..0f615ff --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.B.taurus.seq @@ -0,0 +1,2 @@ +>d.5.e.B.taurus +GUCUACGGCCAUACCACCCUGAACGCGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGGGUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCGGGUGCUGUAGGCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.B.vorax.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.B.vorax.seq new file mode 100644 index 0000000..7d2da47 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.B.vorax.seq @@ -0,0 +1,2 @@ +>d.5.e.B.vorax +GUUAUCGGCCAUACUAAGCCAAAAGCACCGGAUCCCAUUCGAACUCCGAAGUUAAGCGGCUUAAGGCAUGGUUAGUACUAAGGUGGGGGACCGCUUGGGAAGCCCAUGUGCUGAUAGCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.B.vulgaris.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.B.vulgaris.seq new file mode 100644 index 0000000..a05bd88 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.B.vulgaris.seq @@ -0,0 +1,2 @@ +>d.5.e.B.vulgaris +GGGUGCGAUCAUACCAGCACUAAUGCACCGGAUCCCAUCAGAACUCCGCAGUUAAGCGUGCUUGGGCGAGAGUAGUACUAGGAUGGGUGACCUCCUGGGAAGUCCUCGUGUUGCACCCCU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.C.carpio.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.C.carpio.seq new file mode 100644 index 0000000..32ee26d --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.C.carpio.seq @@ -0,0 +1,2 @@ +>d.5.e.C.carpio +GCUUACGGCCAUACCACCCUGAGCACGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGGGUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCAGGUGCUGUAAGCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.C.elegans.1.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.C.elegans.1.seq new file mode 100644 index 0000000..91c3d86 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.C.elegans.1.seq @@ -0,0 +1,2 @@ +>d.5.e.C.elegans.1 +GCUUACGACCAUAUCACGUUGAAUGCACGCCAUCCCGUCCGAUCUGGCAAGUUAAGCAACGUUGAGUCCAGUUAGUACUUGGAUCGGAGACGGCCUGGGAAUCCUGGAUGUUGUAAGCU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.C.elegans.2.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.C.elegans.2.seq new file mode 100644 index 0000000..4a4584e --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.C.elegans.2.seq @@ -0,0 +1,2 @@ +>d.5.e.C.elegans.2 +GCUUACGACCAUAUCACGUUGAAUGCACGCCAUCCCGUCCGAUCUGGCAAGUUAAGCAACGUUGAGUCCAGUUAGUACUUGGAUCGGAGACGGCCUGGGAAUCCUGGAUGUUGUAAGCU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.C.quinquecirrha.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.C.quinquecirrha.seq new file mode 100644 index 0000000..4eef3e3 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.C.quinquecirrha.seq @@ -0,0 +1,2 @@ +>d.5.e.C.quinquecirrha +GCCUACGACCAUACCACCAUGAGUAUACCGGUUCUCGUCCGAUCACCGGAGUCAAGCAUGGUCGGGCCGGGUCAGUACCUGGAUGGGUGACCGCCUGGGAACACCUGGUGUUGUAGGCCU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.C.revoluta.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.C.revoluta.seq new file mode 100644 index 0000000..0a9db8c --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.C.revoluta.seq @@ -0,0 +1,2 @@ +>d.5.e.C.revoluta +GGGUGCGAUCAUACCAGCGUUAAUGCACCGGAUCCCAUCAGAACUCCGCAGUUAAGCGCGCUUGGGUUGGAGUAGUACUAGGAUGGGUGACCUCCUGGGAAGUCCUAAUAUUGCACCCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.C.vicina.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.C.vicina.seq new file mode 100644 index 0000000..b9bba74 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.C.vicina.seq @@ -0,0 +1,2 @@ +>d.5.e.C.vicina +GCCAACGACCAUACCACGCUGAAUACAUCGGUUCUCGUCCGAUCACCGAAAUUAAGCAGCGUCGGGCGCGGUUAGUACUUAGAUGGGGGACCGCUUGGGAACACCGCGUGUUGUUGGCAU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.D.mauritiana.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.D.mauritiana.seq new file mode 100644 index 0000000..fe798c7 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.D.mauritiana.seq @@ -0,0 +1,2 @@ +>d.5.e.D.mauritiana +GCCAACGACCAUACCACGCUGAAUACAUCGGUUCUCGUCCGAUCACCGAAAUUAAGCAGCGUCGGGCGCGGUUAGUACUUAGAUGGGGGACCGCUUGGGAACACCGCGUGUUGUUGGCCU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.D.melanogaster.1.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.D.melanogaster.1.seq new file mode 100644 index 0000000..2a8d663 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.D.melanogaster.1.seq @@ -0,0 +1,2 @@ +>d.5.e.D.melanogaster.1 +GCCAACGACCAUACCACGCUGAAUACAUCGGUUCUCGUCCGAUCACCGAAAUUAAGCAGCGUCGCGGGCGGUUAGUACUUAGAUGGGGGACCGCUUGGGAACACCGCGUGUUGUUGGCCU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.D.melanogaster.2.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.D.melanogaster.2.seq new file mode 100644 index 0000000..05ba8f8 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.D.melanogaster.2.seq @@ -0,0 +1,2 @@ +>d.5.e.D.melanogaster.2 +GCCAACGACCAUACCACGCUGAAUACAUCGGUUCUCGUCCGAUCACCGAAAUUAAGCAGCGUCGGGCGCGGUUAGUACUUAGAUGAGGGACCGCUUGGGAACACCGCGUGUUGUUGGCCUCGUCCACAACUUUUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.E.eurystomus.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.E.eurystomus.seq new file mode 100644 index 0000000..e715502 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.E.eurystomus.seq @@ -0,0 +1,2 @@ +>d.5.e.E.eurystomus +GCUAUCGGCCAUACUAAGCCAAAUGCACCGGAUCCCUUCCGAACUCCGAAGUUAAGCGGUUUAAGGCCUGUUAAGUACUGAGGUGGGGGACCACUCGGGAACUUCAGGUGCUGAUAGCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.E.gracilis.1.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.E.gracilis.1.seq new file mode 100644 index 0000000..c73a6b7 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.E.gracilis.1.seq @@ -0,0 +1,2 @@ +>d.5.e.E.gracilis.1 +GAGUACGGCCAUACUACCGGGAAUACACCUGAACCCGUUCGAUUUCAGAAGUUAAGCCGGGUUAGGCCCAGUUAGUACUGAGUGGGCGACCACUUGGGAACACUGGGUGCUGUACGCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.E.gracilis.2.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.E.gracilis.2.seq new file mode 100644 index 0000000..895e4e4 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.E.gracilis.2.seq @@ -0,0 +1,2 @@ +>d.5.e.E.gracilis.2 +GGCGUACGGCCAUACUACCGGGAAUACACCUGAACCCGUUCGAUUUCAGAAGUUAAGCCUGGUCAGGCCCAGUUAGUACUGAGGUGGGCGACCACUUGGGAACACUGGGUGCUGUACGCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.E.kokanica.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.E.kokanica.seq new file mode 100644 index 0000000..33c38fc --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.E.kokanica.seq @@ -0,0 +1,2 @@ +>d.5.e.E.kokanica +GGGUGCGAUCAUACCAGCGUUAAUGCACCGGAUCCCAUCAGAACUCCGCAGUUAAGCGCGCUUGGGCUAGAGUAGUACUGGGAUGGGUGACCUCCCGGGAAGUCCUAGUGUUGCACCCUC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.E.woodruffi.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.E.woodruffi.seq new file mode 100644 index 0000000..2b22082 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.E.woodruffi.seq @@ -0,0 +1,2 @@ +>d.5.e.E.woodruffi +GCUAUCGGCCAUACUAAGCCAAAUGCACCGGAUCCCAUCCGAACUCCGAAGUUAAGCGGUUUAAGGCCUGUUAAGUACUGAGGUGGGGGACCACUCGGGAACUUCAGGUGCUGAUAGCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.F.hygrometrica.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.F.hygrometrica.seq new file mode 100644 index 0000000..946b73c --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.F.hygrometrica.seq @@ -0,0 +1,2 @@ +>d.5.e.F.hygrometrica +UGAUGCGGUCAUACCAAGGCUACUACACCAGAUCCCAUCAGAACUCUGAAGUUAAGCGCCUUUGGGCCGGAAUAGUACUGGGAUGGGUGACCUCCCGGGAAGUCCCGGUGCUGCAUCCAC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.F.neoformans.1.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.F.neoformans.1.seq new file mode 100644 index 0000000..30eaebf --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.F.neoformans.1.seq @@ -0,0 +1,2 @@ +>d.5.e.F.neoformans.1 +AUCCACGGCCAUAGCCUUCAUAGAGCACCCUGCCCCGUCCGAUCCAGGAAGUUAAGCUGAACAGCGCUCGGUUAGUACCACGGUGGGGGACCACGUGGGAAUCCCGGGUGCCGUGGUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.G.arboreum.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.G.arboreum.seq new file mode 100644 index 0000000..7b952b0 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.G.arboreum.seq @@ -0,0 +1,2 @@ +>d.5.e.G.arboreum +GGGUGCGAUCAUACCAGCACUAAACCACCGGAUUCCAUCAGUGCUCCCCAGUUAAGCGUGCUUGGCCGAGAGUAGAACUAGGGUGGGUGACCUCCUGGGAAGUCCUCGUGUUGCACCCCU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.G.biloba.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.G.biloba.seq new file mode 100644 index 0000000..cb7eb79 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.G.biloba.seq @@ -0,0 +1,2 @@ +>d.5.e.G.biloba +GGGUGCGAUCAUACCAGCGUUAAUGCACCGGAUCCCAUCAGAACUCCGCAGUUAAGCACGCUUGGGCUGGAGUAGUACUAGGAUGGGUGACCUCCUGGGAAGUCCCAGUGUUGCACCCUC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.G.gnemon.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.G.gnemon.seq new file mode 100644 index 0000000..178c783 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.G.gnemon.seq @@ -0,0 +1,2 @@ +>d.5.e.G.gnemon +GGGUGCGAUAAUACCACCGCUAACGUAUCGGAUCCGAUCAGAACUCCGUAAUUAAGCGCGCUUGGGCUAGAGUAGUACUGGGAUGGGUGACCUCUCGGGAAGUCCUAGUGUUGCACCCAC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.G.riobambae.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.G.riobambae.seq new file mode 100644 index 0000000..1d478a3 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.G.riobambae.seq @@ -0,0 +1,2 @@ +>d.5.e.G.riobambae +GCCUACGGCCACACCACCCUGAACACGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGGGUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCAGGUGCUGUAGGCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.japonica.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.japonica.seq new file mode 100644 index 0000000..f67da34 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.japonica.seq @@ -0,0 +1,2 @@ +>d.5.e.H.japonica +GUCUACGACCAUACCACGUUGAAAACACCGGUUCUCGUCCGAUCACCGAAGUUAAGCAACGUAGGGCCUGCCCAGUACUUGGAUGGGUGACCGCCUGGGAACAGCAGGUGUUGUAGACUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.oculata.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.oculata.seq new file mode 100644 index 0000000..49bf2a1 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.oculata.seq @@ -0,0 +1,2 @@ +>d.5.e.H.oculata +GCCUGCGGCCAUACCACGUUGAAUGCACCGGUUCCCAUCUGAACACCGAAGUUAAGCAACGUCGGGCCAGCUUAGUACCUGGAUGGGUGACCGCCUGGGAAUCGCUGGUGCUGCAGGCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sanguinea.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sanguinea.seq new file mode 100644 index 0000000..55c19b9 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sanguinea.seq @@ -0,0 +1,2 @@ +>d.5.e.H.sanguinea +GUCUACGACCAUACCACGUUGAAAACACCGGUUCUCGUCCGAUCACCGAAGUUAAGCAACGUAGGGCCUGCCCAGUACUUGGAUGGGUGACCGCCUGGGAACAGCAGGUGUUGUAGACUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.1.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.1.seq new file mode 100644 index 0000000..517c965 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.1.seq @@ -0,0 +1,2 @@ +>d.5.e.H.sapiens.1 +AUCUAUGGCUGUACCGCUCUGAACGUGCACUAUCUCUUCUGAUCUCAAAAGCUAAGCAGGGUCAGGCCUGGUUAGUACUGGAAUGGGAGACCACAUGGGAAAACUGGGUGCUGUAGGCU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.2.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.2.seq new file mode 100644 index 0000000..1b449fa --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.2.seq @@ -0,0 +1,2 @@ +>d.5.e.H.sapiens.2 +GUCUACGGCCAUACCACCCUGAACGCGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGGGUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCGGGUGCUGUAGGCUUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.3.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.3.seq new file mode 100644 index 0000000..d82f578 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.3.seq @@ -0,0 +1,2 @@ +>d.5.e.H.sapiens.3 +GUCUACGGCCAUACCACCCUGAACGCGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGGGUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCGGGUGCUGUAGGCUUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.4.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.4.seq new file mode 100644 index 0000000..fdcdc80 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.4.seq @@ -0,0 +1,2 @@ +>d.5.e.H.sapiens.4 +GUCUACGGCCAUACCACCCUGAACGCGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGGGUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCGGGUGCUGUAGGCUUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.5.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.5.seq new file mode 100644 index 0000000..627f910 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.5.seq @@ -0,0 +1,2 @@ +>d.5.e.H.sapiens.5 +GUCUACGGCCAUACCACCCUGAACGCGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGGGUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCGGGUGCUGUAGGCUUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.6.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.6.seq new file mode 100644 index 0000000..01812e1 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.6.seq @@ -0,0 +1,2 @@ +>d.5.e.H.sapiens.6 +GUCUACGGCCAUACCACCCUGAACGCGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGGGUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCGGGUGCUGUAGGCUUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.Hemicentrotus.sp.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.Hemicentrotus.sp.seq new file mode 100644 index 0000000..a8577d9 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.Hemicentrotus.sp.seq @@ -0,0 +1,2 @@ +>d.5.e.Hemicentrotus.sp +GUUUACGACCAUACCAUGCUGAAUAUACCGGUUCUCGUCCGAUCACCGAAGUCAAGCAGCAUAGGGCCCGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCGGGUGUUGUAGGCAU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.I.iguana.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.I.iguana.seq new file mode 100644 index 0000000..fb02dc3 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.I.iguana.seq @@ -0,0 +1,2 @@ +>d.5.e.I.iguana +GCCUACGGCCAUACCACCCUGAACACGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGGGUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCGGGUGCUGUAGGCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.I.illecebrosus.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.I.illecebrosus.seq new file mode 100644 index 0000000..39aa1e2 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.I.illecebrosus.seq @@ -0,0 +1,2 @@ +>d.5.e.I.illecebrosus +GCUUACGGCCAUAUCACGCUGAAUACACCGGUUCUCGUCCGAUCACCGAAGUUAAGCAACGUAGAGCCUAGUCAGUACUUGGAUGGGUGACCGCCUGGGAAUACUAGGUGCUGUAAGCAU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.L.decidua.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.L.decidua.seq new file mode 100644 index 0000000..9a40744 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.L.decidua.seq @@ -0,0 +1,2 @@ +>d.5.e.L.decidua +GGGUGCGAUCAUACCAGCGUUAAUGCACCGGAUCCCAUCAGAACUCCGCAGUUAAGCACGCUUGGGCUAGAGUAGUGCUGGGAUGGGUGACCUCCCGGGAAGUCCUAGUGUUGCACCCUC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.L.edodes.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.L.edodes.seq new file mode 100644 index 0000000..2d9f606 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.L.edodes.seq @@ -0,0 +1,2 @@ +>d.5.e.L.edodes +AUCCACGGCCAUAGGACUCUGAAAGAACCGCAUCCCGUCUGAUCUGCGCAGUUAACCAGAGUGCCGCCUAGUUAGUACCACGGUGGGGGACCACGCGGGAAUCCUAGGUGCUGUAGUUUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.L.geniculatus.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.L.geniculatus.seq new file mode 100644 index 0000000..73c1db0 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.L.geniculatus.seq @@ -0,0 +1,2 @@ +>d.5.e.L.geniculatus +GUCUACGACCAUAUCACGUUGAAAACACCGGUUCUCGUCCGAUCACCGAAGUUAAGCAACGUCGAGCGUGGUUAGUACGUGGAUGGGUGACCGCCUCGGAAUACCACGUGUUGUAGGCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.L.japonicum.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.L.japonicum.seq new file mode 100644 index 0000000..83e9877 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.L.japonicum.seq @@ -0,0 +1,2 @@ +>d.5.e.L.japonicum +GCCUACGACCAUAUCACCCUGAAUACGCCCGAUCUCGUCCGAUCUCGGAAGCUAAGCAGGGUCGAGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCAGGUGUUGUAGGCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.L.luteus.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.L.luteus.seq new file mode 100644 index 0000000..9d33a3c --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.L.luteus.seq @@ -0,0 +1,2 @@ +>d.5.e.L.luteus +AGGUGCGAUCAUACCAGCACUAAUGCACCGGAUCCCAUCAGAACUCCGCAGUUAAGCGUGCUUGGGCGAGAGUAGUACUAGGAUGGGUGACCUCCUGGGAAGUCCUCGUGUUGCACCUCC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.L.usitatissimum.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.L.usitatissimum.seq new file mode 100644 index 0000000..2e8a669 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.L.usitatissimum.seq @@ -0,0 +1,2 @@ +>d.5.e.L.usitatissimum +GGGUGCGAUCAUACCAGCACUAAUGCACCGGAUCCCAUCAGAACUCCGAAGUUAAACGUGCUUGGGCGAGAGUAGUACUAAGAUGGGUGACCUCUUGGGAAGUCCUCGUGUUGCACCCCC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.M.auratus.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.M.auratus.seq new file mode 100644 index 0000000..dfa7faa --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.M.auratus.seq @@ -0,0 +1,2 @@ +>d.5.e.M.auratus +GUCUACGGCCAUACCACCCUGAACGCGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGGGUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCGGGUGCUGUAGGCUUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.M.fossilis.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.M.fossilis.seq new file mode 100644 index 0000000..046a55c --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.M.fossilis.seq @@ -0,0 +1,2 @@ +>d.5.e.M.fossilis +GCUUACGGCCAUACCACCCUGAGCACGCCCGAUCUCGUCCGAUCUCGGAAGCUAAGCAGGGUCGGGCCUGGUUAGUACUUGGAUGGGAGACUGCCUGGGAAUACCAGGUGUUGUAAGCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.M.glyptostroboides.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.M.glyptostroboides.seq new file mode 100644 index 0000000..1d4c204 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.M.glyptostroboides.seq @@ -0,0 +1,2 @@ +>d.5.e.M.glyptostroboides +GGGUGCGAUCAUACCAGCGUUAGUGCACCGGAUCCCAUCAGAACUCCGCAGUUAAGCGCGCUUGGGCCGGAGUAGUACUGGGAUGGGUGACCUCCCGGGAAGUCCCGGUAUUGCACCCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.M.musculus.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.M.musculus.seq new file mode 100644 index 0000000..fa29c33 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.M.musculus.seq @@ -0,0 +1,2 @@ +>d.5.e.M.musculus +GUCUACGGCCAUACCACCCUGAACGCGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGGGUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCGGGUGCUGUAGGCUUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.M.salmoides.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.M.salmoides.seq new file mode 100644 index 0000000..3101592 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.M.salmoides.seq @@ -0,0 +1,2 @@ +>d.5.e.M.salmoides +GCUUACGGCCACACCACCCUGAACACGCCCGAUCUCGUCCGAUCUCGGAAGCUAAGCAGGGUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCAGGUGUCGUAGGCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.N.dofleini.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.N.dofleini.seq new file mode 100644 index 0000000..df2ff9f --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.N.dofleini.seq @@ -0,0 +1,2 @@ +>d.5.e.N.dofleini +GUCUACGACCAUACCACAAUGAACACACCGGUUCUCGUCCGAUCACCGAAGUUAAGCAUUGUCGGGCCAGGAUAGUACCUGGAUGGGGGACCGCCUGGGAACGCCUGGUGUCGUAGACUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.N.viridescens.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.N.viridescens.seq new file mode 100644 index 0000000..a966f10 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.N.viridescens.seq @@ -0,0 +1,2 @@ +>d.5.e.N.viridescens +GCUUACGGCCAUACCACCCUGAAAGCACCUGAUCUCGUCUGAUCUCAGAAGUUAAGCAGGGUCGGGCCUGGUUAGUACCUGGAUGGGAGACCGCCUUGGAAUACCAGGUGCUGUAGGCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.O.mykiss.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.O.mykiss.seq new file mode 100644 index 0000000..0f05eee --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.O.mykiss.seq @@ -0,0 +1,2 @@ +>d.5.e.O.mykiss +GCUUACGGCCAUACCAGCCUGAAUACGCCCGAUCUCGUCCGAUCUCGGAAGCUAAGCAGGGUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCAGGUGCUGUAAGCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.O.sativa.1.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.O.sativa.1.seq new file mode 100644 index 0000000..614084f --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.O.sativa.1.seq @@ -0,0 +1,2 @@ +>d.5.e.O.sativa.1 +GGAUGCGAUCAUACCAGCACUAAAGCACCGGAUCCCAUCAGAACUCCGAAGUUAAGCGUGCUUGGGCGAGAGUAGUACUAGGAUGGGUGACCUCCUGGGAAGUCCUUGUGUUGCAUCCC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.O.sativa.2.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.O.sativa.2.seq new file mode 100644 index 0000000..bb31e0b --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.O.sativa.2.seq @@ -0,0 +1,2 @@ +>d.5.e.O.sativa.2 +GGAUGCGAUCAUACGAGGACGAAAGCACCGGAUCCCAUCAGAACUCCGAAGUUAAGCGUGCUUGGGCGAGAGUAGUACUAGGAUGGGUGACCUCCUGGGAAGUCCUUGUGUUGCAUCCC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.brevicirris.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.brevicirris.seq new file mode 100644 index 0000000..9c4e025 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.brevicirris.seq @@ -0,0 +1,2 @@ +>d.5.e.P.brevicirris +GCCUACGGCCAUACUACGUUGAAAACACCGGUUCUCGUCUGAUCACCGAAGUUAAGCAACGUCGGGCCUGGUUAGUACUUGGAUGGGUGACCGCCUGGGAAUACCAGGUGCUGUAGGUUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.coxalis.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.coxalis.seq new file mode 100644 index 0000000..035e1ec --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.coxalis.seq @@ -0,0 +1,2 @@ +>d.5.e.P.coxalis +GUCAACGGCCAUACCACGUUGAAAGCACCACUUCUCGUCCGAUCAGCGAAGUUAAGCAACGUUGGGUCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAACACCAGAUGCUGUUGGCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.gouldii.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.gouldii.seq new file mode 100644 index 0000000..bb21939 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.gouldii.seq @@ -0,0 +1,2 @@ +>d.5.e.P.gouldii +GCCUACGACCAUACCACGUUGAAAACACCAGUUCUCGUCCGAUCACUGAAGUUAAGCAACGUCGGGCCAGGUUAGUACUUGGAUGGGUGACCGCCUGGGAAUACCUGGUGUUGUAGGCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.hybrida.1.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.hybrida.1.seq new file mode 100644 index 0000000..cee3f47 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.hybrida.1.seq @@ -0,0 +1,2 @@ +>d.5.e.P.hybrida.1 +GGAUGCGAUCAUACCAGCACUAACGCACCGGAUCCCAUCAGAACUCCGAAGUUAAGCGUGCUUGGGCGAGAGUAGUACUGGAAUGGGUGACCCUCCGGGAAGUCCUCGUGUUGCAUCCCU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.hybrida.2.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.hybrida.2.seq new file mode 100644 index 0000000..4b4969f --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.hybrida.2.seq @@ -0,0 +1,2 @@ +>d.5.e.P.hybrida.2 +AGAUGCGAUCAUACCAGCACUAACGCACCGGAUCCCAUCAGAACUCCGAAGCUAAGCGUGCUUGGGCGAGAGUAGUACUGGAAUGGGUGACCCUCCGGGAAGUCCUCGUGUUGCAUCCCG diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.radiata.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.radiata.seq new file mode 100644 index 0000000..0fe2e5f --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.radiata.seq @@ -0,0 +1,2 @@ +>d.5.e.P.radiata +GGGUGCGAUCAUACCAGCGUUAAUGCACCGAAUCCCAUCAGAACUCCGCAGUUUAGCGCGCUUGGGCUAGAGUAGUACUGGGAUGGGUGACCUCCCGGGAAGUCCUAGUGUUGCACCCUC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.reticulata.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.reticulata.seq new file mode 100644 index 0000000..48aafa5 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.reticulata.seq @@ -0,0 +1,2 @@ +>d.5.e.P.reticulata +GAUAGCGUCCAUACCACACUGAAAACACCGGUUCUCGUCCGAUCACCGCAGUUAAGCAGUGUCGGGCCCAGUUAGUACUUGGAUGGGUGACCGCCUGGGAAUACUGGGUGUCGCUACCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.tetraurelia.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.tetraurelia.seq new file mode 100644 index 0000000..ac85b0c --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.tetraurelia.seq @@ -0,0 +1,2 @@ +>d.5.e.P.tetraurelia +GUUGGUGGCCAUACUAAGCCUAAAGCACCGGAUCCCAUUCGAACUCCGAAGUUAAGCGGCUUAAGGCGAGGUUAGUACUAAGGUGGGGGACCGCUUGGGAAGUCCUCGUGUUGACAACCC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.waltl.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.waltl.seq new file mode 100644 index 0000000..686043c --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.waltl.seq @@ -0,0 +1,2 @@ +>d.5.e.P.waltl +GCCUACGGCCAUACCACCCUGAAUGCGCCCGAUCUCGUCCGAUCUCGGAAGCUAAGCAGGGUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCAGGUGCUGUAGGCAU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.Phytomonas.sp.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.Phytomonas.sp.seq new file mode 100644 index 0000000..7356089 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.Phytomonas.sp.seq @@ -0,0 +1,2 @@ +>d.5.e.Phytomonas.sp +GGGUACGACCAUACUUGGCUGAAAGCACCACAUCCCGUCCGAUUUGUGAAGUUAAGCAGCCACAGGCUUAGUUAGUACUGAGGUCAGUGAUGACUCGGGAACCCUGAGUGCCGUACCCUCCACAACACUC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.Q.petraea.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.Q.petraea.seq new file mode 100644 index 0000000..4611843 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.Q.petraea.seq @@ -0,0 +1,2 @@ +>d.5.e.Q.petraea +GGGUGCGAUCAUACCAACACUAAUGCACCGGAUCCCAUCAGAACUCCGCAGUUAAGCGUGUUUGGGCGAGAGUAGUACUAGGAUGGGUGACCUCCUGGGAAGUCCUCGUGUUGCACCCCU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.R.norvegicus.1.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.R.norvegicus.1.seq new file mode 100644 index 0000000..b317aac --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.R.norvegicus.1.seq @@ -0,0 +1,2 @@ +>d.5.e.R.norvegicus.1 +GUCUACGGCCAUACCACCCUGAACGCGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGGGUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCGGGUGCUGUAGGCUUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.R.norvegicus.2.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.R.norvegicus.2.seq new file mode 100644 index 0000000..9bfefd4 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.R.norvegicus.2.seq @@ -0,0 +1,2 @@ +>d.5.e.R.norvegicus.2 +GUCUACGGCCAUACCACCCUGAACGCGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGGGUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCGGGUGCUGUAGGCUUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.R.norvegicus.3.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.R.norvegicus.3.seq new file mode 100644 index 0000000..97d8ffd --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.R.norvegicus.3.seq @@ -0,0 +1,2 @@ +>d.5.e.R.norvegicus.3 +GUCUACGGCCAUACCACCCUGAACGCGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGGGUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCGGGUGCUGUAGGCUUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.aggregatum.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.aggregatum.seq new file mode 100644 index 0000000..91ab62d --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.aggregatum.seq @@ -0,0 +1,2 @@ +>d.5.e.S.aggregatum +ACAGCCGUUCAUACCACACGGAGAAUACCGGAUCUCGUUCGAACUCCGCAGUCAAGCCGUGUCGGGCGUGCUCAGUACUACCAUAGGGGACUGGGUGGGAAGCGUGCGUGACGGCUGUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.canicula.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.canicula.seq new file mode 100644 index 0000000..f821f70 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.canicula.seq @@ -0,0 +1,2 @@ +>d.5.e.S.canicula +GCCUACGGCCAUACUAGUCUGAAAACGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGAUUCAGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCAGGUGCAGUAGGCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.cerevisiae.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.cerevisiae.seq new file mode 100644 index 0000000..99153a7 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.cerevisiae.seq @@ -0,0 +1,2 @@ +>d.5.e.S.cerevisiae +GGUUGCGGCCAUAUCUACCAGAAAGCACCGUUUCCCGUCCGAUCAACUGUGUUAAGCUGGUAGAGCCUGACCGAGUAGUGUAUGGGUGACCAUACGCGAAACUCAGGUGCUGCAAUCU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.cynthia.XBM.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.cynthia.XBM.seq new file mode 100644 index 0000000..7301bd3 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.cynthia.XBM.seq @@ -0,0 +1,2 @@ +>d.5.e.S.cynthia.XBM +GCCAACGUCCAUACCAUGUUGAAUACACCGGUUCUCGUCCGAUCACCGAAGUCAAGCAACAUCGGGCGUAGUCAGUACUUGGAUGGGUGACCGCCUGGGAACACUACGUGAUGUUGGCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.kowalevskii.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.kowalevskii.seq new file mode 100644 index 0000000..c309c20 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.kowalevskii.seq @@ -0,0 +1,2 @@ +>d.5.e.S.kowalevskii +GCCUACGGCCAUACCACGUAGAAUGCACCGGUUCUCGUCCGAUCACCGAAGUUAAGCUGCGUCGGGCGUGGUUAGUACUUGCAUGGGAGACCGGCUGGGAAUACCACGUGCUGUAGGCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.officinalis.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.officinalis.seq new file mode 100644 index 0000000..fbcd514 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.officinalis.seq @@ -0,0 +1,2 @@ +>d.5.e.S.officinalis +GCUUACGGCCAUAUCACGCUGAAAACACCGGUUCUCGUCCGAACACCGAAGUUAAGCAACGUAGAGCCUGGUGAGUACUUGGAUGGGUGACCGCUUGGGAAUACCAGGUGCUGUAAGCAU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.pombe.1.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.pombe.1.seq new file mode 100644 index 0000000..45e16c8 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.pombe.1.seq @@ -0,0 +1,2 @@ +>d.5.e.S.pombe.1 +GUCUACGGCCAUACCUAGGCGAAAACACCAGUUCCCGUCCGAUCACUGCAGUUAAGCGUCUGAGGGCCUCGUUAGUACUAUGGUUGGAGACAACAUGGGAAUCCGGGGUGCUGUAGGCU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.T.aestivum.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.T.aestivum.seq new file mode 100644 index 0000000..dacd0d4 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.T.aestivum.seq @@ -0,0 +1,2 @@ +>d.5.e.T.aestivum +GGAUGCGAUCAUACCAGCACUAAGGCAUCGGAUCCCGUCAGAACUCCGAAGUUAAGCGUGCUUGGGCGAGAGUAGUACAAGGAUGGGUGACCUCUUGGGAAGUCCUCGUGUUGCAUUCCC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.T.borreli.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.T.borreli.seq new file mode 100644 index 0000000..91d76b6 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.T.borreli.seq @@ -0,0 +1,2 @@ +>d.5.e.T.borreli +GGGUACGUCCAUACUUGGCUGAAAGCACCAUAUCCCGUCCGAUUUGUGAAGUUAAGCAGCCACAGGCUUAGUUAGUACUGAGGUCAGUGAUGACUUGGGAACCCUAAGUGUCGUACUCCC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.T.cruzi.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.T.cruzi.seq new file mode 100644 index 0000000..b4fe443 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.T.cruzi.seq @@ -0,0 +1,2 @@ +>d.5.e.T.cruzi +GGGUACGACCAUACUUGGCCGAGUGCACCACAUCCCGUCCGAUUUGUGAAGUUAAGCGGCCACAGGCCUCGUUAGUACGGCGAUCAGUGAUGGCGCUGGAACCCGGGGUGCCGUACCCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.T.monococcum.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.T.monococcum.seq new file mode 100644 index 0000000..0d095ee --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.T.monococcum.seq @@ -0,0 +1,2 @@ +>d.5.e.T.monococcum +GGAUGCGAUCAUACCAGCACUAAAGCACCGGAUCCCAUCAGAACUCUGAAGUUAAGCGUGCUUGGGCGAGAGUAGUACUAGGAUGGGUGACCUCCUCGGAAGUCCUCGUGUUGCAUUCCC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.T.thermophila.2.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.T.thermophila.2.seq new file mode 100644 index 0000000..2846ec9 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.T.thermophila.2.seq @@ -0,0 +1,2 @@ +>d.5.e.T.thermophila.2 +GUUGUCGGCCAUACUAAGGUGAAAACACCGGAUCCCAUUCGAACUCCGAAGUUAAGCGCCUUAAGGCUGGGUUAGUACUAAGGUGGGGGACCGCUUGGGAAGUCCCAGUGUCGAUAGCCU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.U.unicinctus.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.U.unicinctus.seq new file mode 100644 index 0000000..5b30dba --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.U.unicinctus.seq @@ -0,0 +1,2 @@ +>d.5.e.U.unicinctus +GUCUACGGCCAUACCACGUUGAAAACACCAGUUCUCGUCCGAUCACUGAAGUUAAGCAACGUCGGGCCCGGUUAGUACUUGGAUGGGUGACCGCCUGGGAAUACCGGGUGCUGUAGACUU diff --git a/gtfold-mfe/tests/data/constraints_sequences/combseq3.seq b/gtfold-mfe/tests/data/constraints_sequences/combseq3.seq new file mode 100644 index 0000000..2b55c97 --- /dev/null +++ b/gtfold-mfe/tests/data/constraints_sequences/combseq3.seq @@ -0,0 +1 @@ +CCCCAAAAGGGGAAAACCCCAAAAGGGGAAAACCCCAAAAGGGG diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/base_pair_distance1.constraint b/gtfold-mfe/tests/data/exitcodes_sequences/base_pair_distance1.constraint new file mode 100644 index 0000000..7029d7d --- /dev/null +++ b/gtfold-mfe/tests/data/exitcodes_sequences/base_pair_distance1.constraint @@ -0,0 +1 @@ +F 1 8 8 diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/base_pair_distance1.expectedresult b/gtfold-mfe/tests/data/exitcodes_sequences/base_pair_distance1.expectedresult new file mode 100644 index 0000000..d00491f --- /dev/null +++ b/gtfold-mfe/tests/data/exitcodes_sequences/base_pair_distance1.expectedresult @@ -0,0 +1 @@ +1 diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/base_pair_distance1.seq b/gtfold-mfe/tests/data/exitcodes_sequences/base_pair_distance1.seq new file mode 100644 index 0000000..0984ecd --- /dev/null +++ b/gtfold-mfe/tests/data/exitcodes_sequences/base_pair_distance1.seq @@ -0,0 +1 @@ +CCCCCGGGGGGAAAGGG diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/base_pair_distance2.constraint b/gtfold-mfe/tests/data/exitcodes_sequences/base_pair_distance2.constraint new file mode 100644 index 0000000..adb4fdb --- /dev/null +++ b/gtfold-mfe/tests/data/exitcodes_sequences/base_pair_distance2.constraint @@ -0,0 +1,5 @@ +F 1 19 2 +F 3 10 1 +F 4 8 1 +F 11 15 1 +F 24 25 1 diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/base_pair_distance2.expectedresult b/gtfold-mfe/tests/data/exitcodes_sequences/base_pair_distance2.expectedresult new file mode 100644 index 0000000..d00491f --- /dev/null +++ b/gtfold-mfe/tests/data/exitcodes_sequences/base_pair_distance2.expectedresult @@ -0,0 +1 @@ +1 diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/base_pair_distance2.seq b/gtfold-mfe/tests/data/exitcodes_sequences/base_pair_distance2.seq new file mode 100644 index 0000000..9a1d7d8 --- /dev/null +++ b/gtfold-mfe/tests/data/exitcodes_sequences/base_pair_distance2.seq @@ -0,0 +1 @@ +CCCCAAGAAGCAAAGAAGGCCCACGAAAA diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/default.expectedresult b/gtfold-mfe/tests/data/exitcodes_sequences/default.expectedresult new file mode 100644 index 0000000..573541a --- /dev/null +++ b/gtfold-mfe/tests/data/exitcodes_sequences/default.expectedresult @@ -0,0 +1 @@ +0 diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/duplicate_base1.constraint b/gtfold-mfe/tests/data/exitcodes_sequences/duplicate_base1.constraint new file mode 100644 index 0000000..cece32a --- /dev/null +++ b/gtfold-mfe/tests/data/exitcodes_sequences/duplicate_base1.constraint @@ -0,0 +1,4 @@ +F 1 19 2 +F 3 18 1 +F 4 7 1 +F 11 15 1 diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/duplicate_base1.expectedresult b/gtfold-mfe/tests/data/exitcodes_sequences/duplicate_base1.expectedresult new file mode 100644 index 0000000..d00491f --- /dev/null +++ b/gtfold-mfe/tests/data/exitcodes_sequences/duplicate_base1.expectedresult @@ -0,0 +1 @@ +1 diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/duplicate_base1.seq b/gtfold-mfe/tests/data/exitcodes_sequences/duplicate_base1.seq new file mode 100644 index 0000000..0964dc3 --- /dev/null +++ b/gtfold-mfe/tests/data/exitcodes_sequences/duplicate_base1.seq @@ -0,0 +1 @@ +CCCCAAGAAGCAAAGAAGG diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/invalid_base_number1.constraint b/gtfold-mfe/tests/data/exitcodes_sequences/invalid_base_number1.constraint new file mode 100644 index 0000000..2ce893a --- /dev/null +++ b/gtfold-mfe/tests/data/exitcodes_sequences/invalid_base_number1.constraint @@ -0,0 +1,4 @@ +F 0 19 2 +F 3 10 1 +F 4 8 1 +F 11 15 1 diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/invalid_base_number1.expectedresult b/gtfold-mfe/tests/data/exitcodes_sequences/invalid_base_number1.expectedresult new file mode 100644 index 0000000..d00491f --- /dev/null +++ b/gtfold-mfe/tests/data/exitcodes_sequences/invalid_base_number1.expectedresult @@ -0,0 +1 @@ +1 diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/invalid_base_number1.seq b/gtfold-mfe/tests/data/exitcodes_sequences/invalid_base_number1.seq new file mode 100644 index 0000000..0964dc3 --- /dev/null +++ b/gtfold-mfe/tests/data/exitcodes_sequences/invalid_base_number1.seq @@ -0,0 +1 @@ +CCCCAAGAAGCAAAGAAGG diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/invalid_base_number2.constraint b/gtfold-mfe/tests/data/exitcodes_sequences/invalid_base_number2.constraint new file mode 100644 index 0000000..65ea20f --- /dev/null +++ b/gtfold-mfe/tests/data/exitcodes_sequences/invalid_base_number2.constraint @@ -0,0 +1,4 @@ +F 1 19 2 +F 3 10 1 +F 4 8 1 +F 11 24 1 diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/invalid_base_number2.expectedresult b/gtfold-mfe/tests/data/exitcodes_sequences/invalid_base_number2.expectedresult new file mode 100644 index 0000000..d00491f --- /dev/null +++ b/gtfold-mfe/tests/data/exitcodes_sequences/invalid_base_number2.expectedresult @@ -0,0 +1 @@ +1 diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/invalid_base_number2.seq b/gtfold-mfe/tests/data/exitcodes_sequences/invalid_base_number2.seq new file mode 100644 index 0000000..0964dc3 --- /dev/null +++ b/gtfold-mfe/tests/data/exitcodes_sequences/invalid_base_number2.seq @@ -0,0 +1 @@ +CCCCAAGAAGCAAAGAAGG diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/normal_struct1.constraint b/gtfold-mfe/tests/data/exitcodes_sequences/normal_struct1.constraint new file mode 100644 index 0000000..2a01386 --- /dev/null +++ b/gtfold-mfe/tests/data/exitcodes_sequences/normal_struct1.constraint @@ -0,0 +1,4 @@ +F 1 19 2 +F 3 10 1 +F 4 8 1 +F 11 15 1 diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/normal_struct1.expectedresult b/gtfold-mfe/tests/data/exitcodes_sequences/normal_struct1.expectedresult new file mode 100644 index 0000000..573541a --- /dev/null +++ b/gtfold-mfe/tests/data/exitcodes_sequences/normal_struct1.expectedresult @@ -0,0 +1 @@ +0 diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/normal_struct1.seq b/gtfold-mfe/tests/data/exitcodes_sequences/normal_struct1.seq new file mode 100644 index 0000000..0964dc3 --- /dev/null +++ b/gtfold-mfe/tests/data/exitcodes_sequences/normal_struct1.seq @@ -0,0 +1 @@ +CCCCAAGAAGCAAAGAAGG diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/pseudoknot1.constraint b/gtfold-mfe/tests/data/exitcodes_sequences/pseudoknot1.constraint new file mode 100644 index 0000000..2a8e728 --- /dev/null +++ b/gtfold-mfe/tests/data/exitcodes_sequences/pseudoknot1.constraint @@ -0,0 +1,2 @@ +F 1 19 2 +F 15 21 1 diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/pseudoknot1.expectedresult b/gtfold-mfe/tests/data/exitcodes_sequences/pseudoknot1.expectedresult new file mode 100644 index 0000000..d00491f --- /dev/null +++ b/gtfold-mfe/tests/data/exitcodes_sequences/pseudoknot1.expectedresult @@ -0,0 +1 @@ +1 diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/pseudoknot1.seq b/gtfold-mfe/tests/data/exitcodes_sequences/pseudoknot1.seq new file mode 100644 index 0000000..23023c5 --- /dev/null +++ b/gtfold-mfe/tests/data/exitcodes_sequences/pseudoknot1.seq @@ -0,0 +1 @@ +CCAAAAAAAAAAAACAAGGAG diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/pseudoknot2.constraint b/gtfold-mfe/tests/data/exitcodes_sequences/pseudoknot2.constraint new file mode 100644 index 0000000..bcbe409 --- /dev/null +++ b/gtfold-mfe/tests/data/exitcodes_sequences/pseudoknot2.constraint @@ -0,0 +1,3 @@ +F 1 19 2 +F 3 10 2 +F 15 23 1 diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/pseudoknot2.expectedresult b/gtfold-mfe/tests/data/exitcodes_sequences/pseudoknot2.expectedresult new file mode 100644 index 0000000..d00491f --- /dev/null +++ b/gtfold-mfe/tests/data/exitcodes_sequences/pseudoknot2.expectedresult @@ -0,0 +1 @@ +1 diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/pseudoknot2.seq b/gtfold-mfe/tests/data/exitcodes_sequences/pseudoknot2.seq new file mode 100644 index 0000000..6b590de --- /dev/null +++ b/gtfold-mfe/tests/data/exitcodes_sequences/pseudoknot2.seq @@ -0,0 +1 @@ +CCCCAAAAGGAAAACAAGGAAAG diff --git a/gtfold-mfe/tests/data/subopt_sequences/combseq.seq b/gtfold-mfe/tests/data/subopt_sequences/combseq.seq new file mode 100644 index 0000000..ac737d0 --- /dev/null +++ b/gtfold-mfe/tests/data/subopt_sequences/combseq.seq @@ -0,0 +1 @@ +CCCAAAAGGGAAAACCCAAAAGGG diff --git a/gtfold-mfe/tests/data/subopt_sequences/combseq3.seq b/gtfold-mfe/tests/data/subopt_sequences/combseq3.seq new file mode 100644 index 0000000..2b55c97 --- /dev/null +++ b/gtfold-mfe/tests/data/subopt_sequences/combseq3.seq @@ -0,0 +1 @@ +CCCCAAAAGGGGAAAACCCCAAAAGGGGAAAACCCCAAAAGGGG diff --git a/gtfold-mfe/tests/data/subopt_sequences/combseq4.seq b/gtfold-mfe/tests/data/subopt_sequences/combseq4.seq new file mode 100644 index 0000000..c2722ec --- /dev/null +++ b/gtfold-mfe/tests/data/subopt_sequences/combseq4.seq @@ -0,0 +1 @@ +CCCCAAAACCCCAAAAGGGGAAAAGGGG diff --git a/gtfold-mfe/tests/data/subopt_sequences/cs1.seq b/gtfold-mfe/tests/data/subopt_sequences/cs1.seq new file mode 100644 index 0000000..5e4009c --- /dev/null +++ b/gtfold-mfe/tests/data/subopt_sequences/cs1.seq @@ -0,0 +1 @@ +CAAAAGAAAACAAAAG diff --git a/gtfold-mfe/tests/scripts/CompareGTCTwithUNACT.pm b/gtfold-mfe/tests/scripts/CompareGTCTwithUNACT.pm new file mode 100755 index 0000000..ddabcdc --- /dev/null +++ b/gtfold-mfe/tests/scripts/CompareGTCTwithUNACT.pm @@ -0,0 +1,64 @@ +#!/usr/bin/perl +package CompareGTCTwithUNACT; +use strict; +use warnings; +use Error; +use File::Basename; +use Exception::Class; + +require "compare_ct.pl"; + +sub test() +{ + my(%Config) = %{$_[1]}; + my(%Sequences) = %{$_[2]}; + my $logger = $_[4]; + + my $epsilon = 0.001; + my $gtdir = $Config{"G_GTFOLD_DIR"}; + my $unadir = $Config{"G_UNAFOLD_DIR"}; + my $workdir = $Config{"G_WORK_DIR"}; + + my $key; + my $value; + + while (($key, $value) = each(%Sequences)) { + + my $seqname=$key; + my $path; + my $suffix; + + my $seqfile = $value; + my $gtout = "$workdir$seqname-gt"; + my $unaout = "$workdir$seqname-una"; + my $gtoutfilename = $workdir."$seqname-gt.ct"; + my $unaoutfilename = $workdir."$seqname-una.ct"; + + my $gtcmd = "$gtdir/gtfold -m $seqfile --unafold -o $gtout > /dev/null"; + my $unacmd = "$unadir/hybrid-ss-min -s DAT $seqfile -o $unaout > /dev/null"; + + system("$gtcmd"); + system("$unacmd"); + + my @result; + eval { + @result = compare_ct_structures($gtoutfilename, $unaoutfilename); + }; + my $exception; + if ($exception = Exception::Class->caught('CompareCTException')) { + $logger->error("Test Failed: $seqname: $exception\n"); + next; + } + + my $diff1 = abs(1 - $result[0]); + my $diff2 = abs(1 - $result[1]); + if ($diff1 < $epsilon || $diff2 < $epsilon) { + $logger->info("TEST PASSED: $seqname: Specificity = $result[0], Selectivity = $result[1]"); + } + else { + $logger->info("TEST FAILED: $seqname: Specificity = $result[0], Selectivity = $result[1]\n". + "More Information: $result[2] $result[3]"); + } + } +} +1; diff --git a/gtfold-mfe/tests/scripts/ConstraintsVerification.pm b/gtfold-mfe/tests/scripts/ConstraintsVerification.pm new file mode 100755 index 0000000..22617bb --- /dev/null +++ b/gtfold-mfe/tests/scripts/ConstraintsVerification.pm @@ -0,0 +1,162 @@ +#!/usr/bin/perl +package ConstraintsVerification; +use strict; +use warnings; +use File::Basename; + +require 'test_utils.pl'; + +sub test() +{ + my(%Config) = %{$_[1]}; + my(%Sequences) = %{$_[2]}; + my(%local_sequences) = %{$_[3]}; + my $logger = $_[4]; + + my $gtdir = $Config{"G_GTFOLD_DIR"}; + my $unadir = $Config{"G_UNAFOLD_DIR"}; + my $workdir = $Config{"G_WORK_DIR"}; + + my $key; + my $value; + my %new_hash = (%local_sequences, %Sequences); + + while (($key, $value) = each(%new_hash)) { + + my $seqname=$key; + my $path; + my $suffix; + + my $seqfile = $value; + my $dirname = dirname($seqfile); + my $constraint_file = "$workdir/$seqname.constraint"; + my $gtout = "$workdir$seqname-gt"; + my $gtoutfilename = $workdir."$seqname-gt.ct"; + + my $gtcmd; + $gtcmd = "$gtdir/gtfold $seqfile -o $gtout > /dev/null 2>&1"; + system("$gtcmd"); + my $len = get_seq_len_from_ctfile($gtoutfilename); + my $CONSFILE; + open($CONSFILE, '>', $constraint_file) or die "Couldn't open $_"; + generate_constraints(1, $len, $CONSFILE); + close $CONSFILE; + + my $gtout_constraints = $gtout."_constraints"; + my $gtout_constraints_filename = "$gtout_constraints.ct"; + $gtcmd = "$gtdir/gtfold -c $constraint_file $seqfile -o $gtout_constraints > /dev/null 2>&1"; + my $exitcode = system("$gtcmd") >> 8; + + if ($exitcode != 0) { + $logger->error("TEST FAILED: $seqname : Assertion Failed, Exit Code incorrect: $exitcode. Constraint File: $constraint_file"); + next; + } + + my @violated_constraints = verify_constraints($gtout_constraints_filename, $constraint_file); + if (@violated_constraints) { + my @vc = join(',', @violated_constraints); + print scalar(@violated_constraints); + $logger->error("TEST FAILED: $seqname : Constraints Violated: Input Constraint File $constraint_file. Violated Constraints:\n @vc"); + } + else { + $logger->info("TEST PASSED: $seqname : Input Constraint File $constraint_file"); + } + } +} + +sub generate_constraints +{ + my $i = shift; + my $j = shift; + my $CONSFILE = shift; + + return if ($j-$i< 4); + + my $r = rand(); + print $CONSFILE "F $i $j 1\n" if $r <0.4; + print $CONSFILE "P $i $j 1\n" if $r >0.4 && $r<0.8; + print $CONSFILE "P $i 0 1\n" if $r >0.8; + + my $range = $j-$i; + my $ii = int(rand($range)) + $i; + $range = $j-$ii; + my $jj = int(rand($range)) + $ii; + + generate_constraints($i+1,$ii-1, $CONSFILE); + generate_constraints($jj+1,$j-1, $CONSFILE); +} + +sub get_seq_len_from_ctfile +{ + my $filename = shift; + open(IN, "<$filename"); + my $header = ; # ignore first line + close IN; + my ($len, $dG) = split(' ', $header); + return $len; +} + +sub verify_constraints { + + my $ctfilename = shift; + my $cffilename = shift; + + open CT, $ctfilename; + open CF, $cffilename; + + my %ct_hash = (); + my @rna; + my $count=1; + + my $header = ; # ignore first line + while () + { + my @ff = split(' ', $_); + $ct_hash{$ff[0]} = $ff[4]; + $rna[$count] = $ff[1]; + ++$count; + } + + my @violated_constraints = (); + while() + { + chomp; + my @ff = split(' ', $_); + if ($ff[0] eq 'P' && $ff[2] == 0) { # case SS + if ($ct_hash{$ff[1]} != 0) { + print $_."\n"; + push(@violated_constraints, $_); + } + } + elsif ($ff[0] eq 'P' && $ct_hash{$ff[1]} == $ff[2] && $ct_hash{$ff[2]} == $ff[1]) { # case P + print $_."\n"; + print "$ct_hash{$ff[1]} $ct_hash{$ff[2]}\n"; + push(@violated_constraints, $_); + } + elsif ($ff[0] eq 'F' && $ff[2] == 0) { + my $b = canPair($rna[$ff[1]], $rna[$ff[2]]); + if ($b == 1) { + print $_."\n"; + push(@violated_constraints, $_); + } + } + } + + close CT; + close CF; + + return @violated_constraints; +} + +sub canPair { + my ( $i, $j) = @_; + # (A,U), (U,A), (C,G), (G,C), (G,U) and (U,G). + return 1 if ($i eq 'A' && $j eq 'U') ; + return 1 if ($i eq 'U' && $j eq 'A') ; + return 1 if ($i eq 'C' && $j eq 'G') ; + return 1 if ($i eq 'G' && $j eq 'C') ; + return 1 if ($i eq 'G' && $j eq 'U') ; + return 1 if ($i eq 'U' && $j eq 'G') ; + return 0; +} +1; diff --git a/gtfold-mfe/tests/scripts/ExitCodes.pm b/gtfold-mfe/tests/scripts/ExitCodes.pm new file mode 100755 index 0000000..fbe7079 --- /dev/null +++ b/gtfold-mfe/tests/scripts/ExitCodes.pm @@ -0,0 +1,62 @@ +#!/usr/bin/perl +package ExitCodes; +use strict; +use warnings; +use File::Basename; + +sub test() +{ + my(%Config) = %{$_[1]}; + my(%Sequences) = %{$_[2]}; + my(%local_sequences) = %{$_[3]}; + my $logger = $_[4]; + + my $gtdir = $Config{"G_GTFOLD_DIR"}; + my $unadir = $Config{"G_UNAFOLD_DIR"}; + my $workdir = $Config{"G_WORK_DIR"}; + + my $key; + my $value; + my %new_hash = (%local_sequences, %Sequences); + # For testing pseudoknot detection logic + # we may only test the sequences specified in local_sequences + while (($key, $value) = each(%new_hash)) { + + my $seqname=$key; + my $path; + my $suffix; + + my $seqfile = $value; + my $dirname = dirname($seqfile); + my $constraint_file = "$dirname/$seqname.constraint"; + my $gtout = "$workdir$seqname-gt"; + my $gtoutfilename = $workdir."$seqname-gt.ct"; + + my $gtcmd; + if (-e $constraint_file) { + $gtcmd = "$gtdir/gtfold -c $constraint_file -m $seqfile -o $gtout > /dev/null 2>&1"; + } + else { + $gtcmd = "$gtdir/gtfold -m $seqfile -o $gtout > /dev/null 2>&1"; + } + + my $x = system("$gtcmd") >> 8; + + my $expected_result_file = "$dirname/$seqname.expectedresult"; + my $expected_result; + if (-e $expected_result_file) { + $expected_result = `head -n 1 $expected_result_file`; + } + else { + $expected_result = 0; + } + + if ($expected_result =~ $x) { + $logger->info("TEST PASSED: $seqname: Return Value $x matched expected output $expected_result"); + } + else { + $logger->error("TEST FAILED: $seqname: Return Value $x did not match expected output $expected_result"); + } + } +} +1; diff --git a/gtfold-mfe/tests/scripts/SampleTest.pm b/gtfold-mfe/tests/scripts/SampleTest.pm new file mode 100755 index 0000000..9686997 --- /dev/null +++ b/gtfold-mfe/tests/scripts/SampleTest.pm @@ -0,0 +1,26 @@ +#!/usr/bin/perl +package SampleTest; +use strict; +use warnings; + +sub test() +{ + my(%Config) = %{$_[1]}; + my(%Sequences) = %{$_[2]}; + my(%local_sequences) = %{$_[3]}; + my $logger = $_[4]; + + my $gtdir = $Config{"G_GTFOLD_DIR"}; + my $unadir = $Config{"G_UNAFOLD_DIR"}; + my $workdir = $Config{"G_WORK_DIR"}; + + my $key; + my $value; + my %new_hash = (%local_sequences, %Sequences); + + while (($key, $value) = each(%new_hash)) { + + my $seqname=$key; + } +} +1; diff --git a/gtfold-mfe/tests/scripts/Scoregtwithunafold.pm b/gtfold-mfe/tests/scripts/Scoregtwithunafold.pm new file mode 100755 index 0000000..7cdfb82 --- /dev/null +++ b/gtfold-mfe/tests/scripts/Scoregtwithunafold.pm @@ -0,0 +1,60 @@ +#!/usr/bin/perl +package Scoregtwithunafold; +use strict; +use warnings; +use File::Basename; + +sub test() +{ + my(%Config) = %{$_[1]}; + my(%Sequences) = %{$_[2]}; + my $logger = $_[4]; + + my $gtdir = $Config{"G_GTFOLD_DIR"}; + my $unadir = $Config{"G_UNAFOLD_DIR"}; + my $workdir = $Config{"G_WORK_DIR"}; + + my $key; + my $value; + + while (($key, $value) = each(%Sequences)) { + + my $seqname=$key; + my $path; + my $suffix; + + my $seqfile = $value; + my $gtout = "$workdir$seqname-gt"; + my $unaout = "$workdir$seqname-una"; + my $gtoutfilename = $workdir."$seqname-gt.ct"; + my $unaoutfilename = $workdir."$seqname-una.ct"; + + my $gtcmd = "$gtdir/gtfold -m $seqfile --unafold -o $gtout > /dev/null"; + my $unacmd = "$unadir/hybrid-ss-min -s DAT $seqfile -o $unaout > /dev/null"; + + system("$gtcmd"); + system("$unacmd"); + my $gtfold_energy = `head -1 $gtoutfilename`; + my $unafold_energy = `head -1 $unaoutfilename`; + + if ($gtfold_energy =~ m/([0-9.-]+$)/) { + $gtfold_energy = $1; + } + if ($unafold_energy =~ m/dG = ([0-9.-]+)/) { + $unafold_energy = $1; + } + + if ($gtfold_energy eq $unafold_energy) { + $logger->info("TEST PASSED: $seqname: Energy Value matched for MFE -> $gtfold_energy"); + } + else { + $logger->error("TEST FAILED: $seqname: Energy Value Not Matched for MFE -> gtfold = $gtfold_energy, unafold = $unafold_energy"); + } + #my $ctcmd1 = "/usr/local/bin/ct-energy $gtoutfilename"; + #my $ctcmd2 = "/usr/local/bin/ct-energy -s DAT $unaoutfilename"; + #system("$ctcmd1"); + #print "ct-energy = "; + #system("$ctcmd2"); + } +} +1; diff --git a/gtfold-mfe/tests/scripts/SuboptMatchStructures.pm b/gtfold-mfe/tests/scripts/SuboptMatchStructures.pm new file mode 100755 index 0000000..fa9d7ed --- /dev/null +++ b/gtfold-mfe/tests/scripts/SuboptMatchStructures.pm @@ -0,0 +1,126 @@ +#!/usr/bin/perl +package SuboptMatchStructures; +use strict; +use warnings; +use File::Basename; + +sub test() +{ + my(%Config) = %{$_[1]}; + my(%Sequences) = %{$_[2]}; + my(%local_sequences) = %{$_[3]}; + my $logger = $_[4]; + + my $gtdir = $Config{"G_GTFOLD_DIR"}; + my $rnadir = $Config{"G_RNAFOLD_DIR"}; + my $workdir = $Config{"G_WORK_DIR"}; + my $min_energy = $Config{"L_SUBOPTMATCHSTRUCTURES_MIN_ENERGY"}; + my $max_energy = $Config{"L_SUBOPTMATCHSTRUCTURES_MAX_ENERGY"}; + my $energy_stride = $Config{"L_SUBOPTMATCHSTRUCTURES_ENERGY_STRIDE"}; + + if (not(defined($min_energy))) { + $min_energy = 0; + } + if (not(defined($max_energy))) { + $max_energy = 3; + } + if (not(defined($energy_stride))) { + $energy_stride = 1; + } + + my $key; + my $value; + my %new_hash = (%local_sequences); + + while (($key, $value) = each(%new_hash)) { + + my $seqname=$key; + my $path; + my $suffix; + + my $seqfile = $value; + my $dirname = dirname($seqfile); + my $gtout = "$workdir$seqname-gt"; + my $rnaout = "$workdir$seqname-rna"; + my $gtoutfilename = $workdir."$seqname-gt.ct"; + + my %gtstruct_hash; + my %rnastruct_hash; + + my $energy; + for ($energy=$min_energy; $energy<=$max_energy; $energy=$energy+$energy_stride) { + + my $gtfile = $gtout.$energy; + my $rnafile = $rnaout.$energy."_ss.txt"; + my $gtcmd; + my $rnacmd; + $gtcmd = "$gtdir/gtfold --subopt $energy $seqfile -o $gtfile > /dev/null 2>&1"; + $rnacmd = "$rnadir/RNAsubopt -s DAT -e $energy < $seqfile > $rnafile"; + + system("$gtcmd"); + system("$rnacmd"); + + my $gtsubopt_file = $gtfile."_ss.txt"; + my $rnasubopt_file = $rnafile; + + my $gtsorted = $gtsubopt_file."_sorted"; + my $rnasubopt_sorted = $rnafile."_sorted"; + my $gtstructs = `cat $gtsubopt_file | sed '/[A-Z]/d' | sed '/^\$/d'`; + my $rnastructs = `cat $rnasubopt_file | sed '/[A-Z]/d' | sed '/^\$/d'`; + + %gtstruct_hash = split('[ \n]',$gtstructs); + %rnastruct_hash = split('[ \n]',$rnastructs); + + my $diff_file_name = "$workdir$seqname\_$energy.diff"; + + open (DIFF_FILE, ">> $diff_file_name"); + + my $diff = 0; + foreach my $key ( keys %gtstruct_hash ) + { + my $change = $gtstruct_hash{$key} + unless ( (exists $rnastruct_hash{$key}) && $gtstruct_hash{$key} eq $rnastruct_hash{$key} ); + # gotta check for existence to quiet warnings. + if(defined($change) && $change ne "") { + print DIFF_FILE $key. "\nGTFOLD Energy: ". $gtstruct_hash{$key}; + if (exists $rnastruct_hash{$key}) { + print DIFF_FILE "\nRNASubopt Energy: ". $rnastruct_hash{$key}; + } + else { + print DIFF_FILE "\nRNASubopt Energy: No corresponding structure"; + } + print DIFF_FILE "\n"; + $diff = 1; + } + } + + foreach my $key ( keys %rnastruct_hash ) + { + my $change = $rnastruct_hash{$key} + unless ( (exists $gtstruct_hash{$key}) && $gtstruct_hash{$key} eq $rnastruct_hash{$key} ); + # gotta check for existence to quiet warnings. + if(defined($change) && $change ne "") { + print DIFF_FILE $key. "\nRNASubopt Energy: ". $rnastruct_hash{$key}; + if (exists $gtstruct_hash{$key}) { + print DIFF_FILE "\nGTFOLD Energy: ". $gtstruct_hash{$key}; + } + else { + print DIFF_FILE "\nGTFOLD Energy: No corresponding structure"; + } + print DIFF_FILE "\n"; + $diff = 1; + } + } + + close DIFF_FILE; + + if ($diff == 0) { + $logger->info("TEST PASSED: $seqname: energy delta = $energy: Suboptimal Structures matched"); + } + else { + $logger->error("TEST FAILED: $seqname: energy delta = $energy: Suboptimal Structures not matched. Difference Written to file $diff_file_name"); + } + } + } +} +1; diff --git a/gtfold-mfe/tests/scripts/compare_ct.pl b/gtfold-mfe/tests/scripts/compare_ct.pl new file mode 100755 index 0000000..7196ffe --- /dev/null +++ b/gtfold-mfe/tests/scripts/compare_ct.pl @@ -0,0 +1,339 @@ +#!/usr/bin/perl + +use paul_specials; +use Error; +use Exception::Class('CompareCTException'); + +sub compare_ct_structures() +{ +my $ref_filename=$_[0]; +my $filename=$_[1]; + +open(REF, "< $ref_filename"); +open(RNA, "< $filename"); + +#printf "opened files $ref_filename and $filename\n\n\n"; + +@ref_struct = read_struct_ct(*REF); +@struct = read_struct_ct(*RNA); + +my $rlen = length($ref_struct[0]); +my $slen = length($struct[0]); +my $ref_seq = $ref_struct[0]; +my $seq = $struct[0]; + +$ref_struct[0]=$rlen; +$struct[0]=$slen; + +my $ref_dotb = table_to_bracket(\@ref_struct); +my $dotb = table_to_bracket(\@struct); + +$dotb =~ s/\(/\{/g; +$dotb =~ s/\)/\}/g; + + $_ = $ref_seq; + my $ref_nogaps = tr/\-//; + $_ = $seq; + my $nogaps = tr/\-//; + + + if (($rlen-$ref_nogaps) != ($slen-$nogaps)){ + CompareCTException->throw(error => "seq lengths aren't equal (reference = $rlen, prediction = $slen)! +$rlen-$ref_nogaps ne $slen-$nogaps +ref_nogaps = $ref_nogaps +nogaps = $nogaps + +>ref +$ref_seq +$ref_dotb +>str +$seq\n\n\n"); + } + +#print ">ref1 +#$ref_seq +#$ref_dotb +#>str1 +#$seq +#$dotb\n\n\n"; + +#If different lengths, gap or delete as appropriate: +while ($rlen != $slen){ + + for (my $i = 0; $i < length($ref_seq); $i++){ + if ( substr($ref_seq,$i,1) =~ '\-'){ + + if (substr($ref_dotb,$i,1) =~ '\.' ){ + substr($ref_seq,$i,1) = ""; + substr($ref_dotb,$i,1) = ""; + $i--; + } + elsif ((substr($seq,$i,1) ne substr($ref_seq,$i,1)) && (substr($ref_dotb,$i,1) ne '\.') ) { + substr($seq,$i,0) = "."; + substr($dotb,$i,0) = "."; + + substr($ref_seq,$i,1) = "."; + + + } + } + } + + + for (my $i = 0; $i < length($seq); $i++){ + + if ( substr($seq,$i,1) =~ '\-'){ + + if (substr($dotb,$i,1) =~ '\.' ){ + substr($seq,$i,1) = ""; + substr($dotb,$i,1) = ""; + $i--; + } + elsif (substr($seq,$i,1) ne substr($ref_seq,$i,1) && (substr($dotb,$i,1) ne '\.')) { + substr($ref_seq,$i,0) = "."; + substr($ref_dotb,$i,0) = "."; + substr($seq,$i,1) = "."; + + } + } + + } +#print ">ref +#$ref_seq +#$ref_dotb +#>str +#$seq +#$dotb\n\n"; + @ref_struct = make_pair_table($ref_dotb); + @struct = make_pair_table($dotb); + + #Update lengths after gapping + $rlen = length($ref_seq); + $slen = length($seq); + +} + + + +#print ">ref +#$ref_seq +#$ref_dotb +#>str +#$seq\n"; + + + +my $rcount = 0; +my $scount = 0; +my $true_pos = 0; +my $true_neg = 0; +my $false_neg = 0; +my $false_pos = 0; +my $conflict = 0; +my $contradict = 0; +my $temp = 0; + +for (my $i=1; $i<=$rlen; $i++){ + + #printf "%6d %6d\n", $ref_struct[$i], $struct[$i]; + + if ($ref_struct[$i]>0 && $ref_struct[$i]>$i){ + $rcount++; + #print "$rcount: $i-$ref_struct[$i]\n"; + } + + if ($struct[$i]>0 && $struct[$i]>$i){ + $scount++; + } + + if (($ref_struct[$i]==$struct[$i]) && $ref_struct[$i]>0 && $ref_struct[$i]>$i){ + #printf "%6d %6d\n", $ref_struct[$i], $struct[$i]; + $true_pos++; + $temp = $struct[$i]; + substr($dotb,$i-1,1) = '('; + substr($dotb,$temp-1,1) = ')'; + } + elsif (($ref_struct[$i]!=$struct[$i]) && $struct[$i]>0 && $struct[$i]>$i){ + + #print "struct: $i . $struct[$i]\n"; + + $prime5 = $i; + $prime3 = $struct[$i]; + + if ($ref_struct[$prime3]>0 || $ref_struct[$prime5]>0){ + #print " ref: $ref_struct[$prime3] . $ref_struct[$ref_struct[$prime3]] : $ref_struct[$prime5] . $ref_struct[$ref_struct[$prime5]]\n"; + $contradict++; + + substr($dotb,$prime5-1,1) = '<'; + substr($dotb,$prime3-1,1) = '>'; + + + } + else { + #check nested! + $j=$prime5; + $b=1; + while ($b && $j<$prime3 ) { + + if ( ($ref_struct[$j]>0 && $ref_struct[$j]<$prime5) || $ref_struct[$j]>$prime3 ) { + $b=0; + $conflict++; + #print "conflict $ref_struct[$j] . $j\n"; + + substr($dotb,$prime5-1,1) = '['; + substr($dotb,$prime3-1,1) = ']'; + + } + $j++; + } + + } + + + } + + for (my $j=$i+4; $j<=$rlen; $j++){ + + my $x = substr($ref_seq,$i-1,1); + my $y = substr($ref_seq,$j-1,1); + + if (ispair($x,$y) ){ + $true_neg++; + #print "$x $i $y $j\n"; + } + + } + + +} + + +#$false_pos = $scount - $true_pos; +$false_pos = $conflict + $contradict; +$false_neg = $rcount - $true_pos; + +$true_neg=$true_neg-$true_pos-$false_pos; + +my $sensitivity = 0; +my $selectivity =0; +if ($rcount>0){ + $sensitivity = $true_pos/($false_neg + $true_pos); #$rcount; +} +if ($scount>0){ + $selectivity = $true_pos/($false_pos + $true_pos); #$scount; +} + +my $approx_corr = ($sensitivity + $selectivity)/2; +my $N = $true_pos + $false_pos + $false_neg + $true_neg; + +my $corr_coeff = 0; +if ($true_pos>0){ +$corr_coeff = ($N*$sensitivity*$selectivity - $true_pos)/sqrt(($N*$sensitivity - $true_pos)*($N*$selectivity - $true_pos)); +} + + +my $MCC = 0; +my $MCCquotient = (($true_pos+$false_pos)*($true_pos+$false_neg)*($true_neg+$false_pos)*($true_neg+$false_neg)); + +if ($MCCquotient>0){ +$MCC = ($true_pos*$true_neg - $false_pos*$false_neg)/sqrt( $MCCquotient ); +} + +$old_false_pos = $scount - $true_pos; +$compatable = $old_false_pos - $false_pos; + +#print ">ref +#$ref_seq +#$ref_dotb +#>str +#$seq\n"; +#print "$dotb\n"; + +my $comparison_result = " +seq length = %6d +num of bps in ref = %6d +num of bps in sub = %6d +Basepair distance = %6d +true positives = %6d +true negatives = %6d +false positive = %6d +\t contradict = $contradict +\t conflict = $conflict +\t compatable = $compatable +false negative = %6d +sensitivity = %1.3f +selectivity = %1.3f +Approximate correlation = %1.3f +Correlation Coefficient = %1.3f +Matthews Corr. Coeff. = %1.3f + +\n\n", $rlen, $rcount, $scount, $false_pos+$false_neg+$compatable, $true_pos, $true_neg, $false_pos, $false_neg, $sensitivity, $selectivity, $approx_corr, $corr_coeff, $MCC; + +my $latex_comparison_result = "LaTeX: +Subj. File & BPs in Ref. & BPs in Subj. & TPs (sens.)& FPs (select.) & Matthews Corr. Coeff. (approx. corr.) & \\\\ +$filename & %d & %d & %d (%2.1f) & %d (%2.1f) & %1.3f (%2.1f) \\\\ \n\n", +$rcount, $scount, $true_pos, $sensitivity*100, $false_pos, $selectivity*100, $MCC, $approx_corr*100; + +#printf "%1.4f\t%1.4f\n", +#$sensitivity, $selectivity; + + return ($sensitivity, $selectivity, $comparison_result, $latex_comparison_result); +} + +sub read_struct_ct{ + +$fileptr = $_[0]; +my $seq = ""; + +my $i=-1; +while ( <$fileptr> ){ + + @F = split; + + #if ((/ = /) && ($#F!=5)) { + # next; + #} + + if ($i>=0){ + + $seq .= $F[1]; + $table[$i] = $F[4]; +} + $i++; + + #if ($F[4]==0) {$s .= "."; next} + #$s .= "(" if ($F[0]<$F[4]); + #$s .= ")" if ($F[0]>$F[4]); +} + + + $seq =~ tr/a-z/A-Z/; +#print "2: $seq\n\n"; + +return ($seq, @table); + +} + +sub ispair{ + my ($x, $y) = @_; + + if ( ($x eq 'A' && $y eq 'U')||($x eq 'U' && $y eq 'A') ) { + + return 1; + } + elsif ( ($x eq 'G' && $y eq 'C')||($x eq 'C' && $y eq 'G') ) { + + return 1; + } + elsif ( ($x eq 'G' && $y eq 'U')||($x eq 'U' && $y eq 'G') ) { + + return 1; + } + + else { + return 0; + } +} + +# End of file +1; diff --git a/gtfold-mfe/tests/scripts/paul_specials.pm b/gtfold-mfe/tests/scripts/paul_specials.pm new file mode 100755 index 0000000..304260d --- /dev/null +++ b/gtfold-mfe/tests/scripts/paul_specials.pm @@ -0,0 +1,163 @@ +package paul_specials; + +use strict; +use warnings; + +require Exporter; +our @ISA = qw(Exporter); +our @EXPORT = qw( table_to_bracket table_to_bracket5 make_pair_table); + +#input is base-pair table, output is dot-bracket notation. NOte: $table[0]=seq_length. +#ADD PKNOTS SUPPORT! +sub table_to_bracket { + + my $ref = shift; + my $dotb = "."; + my $temp = 0; + + my @tbl = @$ref; # + my $len = $tbl[0]; + + for (my $j = 0; $j < $len; $j++ ) { + substr($dotb, $j, 1) = "."; + } + #print "\n$dotb\n\n"; + + for (my $j = 1; $j < $len+1; $j++ ) { + + if ($tbl[$j]>$j) { + substr($dotb, $j-1, 1) = "\("; + $temp = $tbl[$j] - 1; + substr($dotb, $temp, 1) = "\)"; + } + + } + + return $dotb; +} + +sub table_to_bracket5 { + + my $ref = shift; + my $dotb = "."; + my $temp = 0; + + my @tbl = @$ref; + my $len = $tbl[0]+1; + + #print "table_to_bracket: len = $len\n"; + + for (my $j = 0; $j < $len; $j++ ) { + substr($dotb, $j, 1) = "."; + } + + for (my $j = 0; $j < $len; $j++ ) { + + if ($tbl[$j+1]>$j+1) { + substr($dotb, $j, 1) = "\("; + $temp = $tbl[$j+1] - 2; + substr($dotb, $temp, 1) = "\)"; + } + #elsif ($tbl[$j+1]== 0) { + # substr($dotb, $j, 1) = "\."; + #} + } + + return $dotb; +} + + + +sub make_pair_table { + my $str = shift; + my $i; + my @bps = (); + my @bps_square = (); + my @bps_curly = (); + my @bps_angle = (); + my @pair_table; + my $prime5; + my $prime3; + my $count = 0; + + my $len = length($str); + + #print "make_pair_table: len = $len\n"; + + $pair_table[0] = $len; + + for (my $j = 0; $j < $len; $j++ ) { + $pair_table[$j+1] = 0; + if ( substr($str,$j,1) =~ '\(' ){ + push(@bps, $j); + ++$count; + } + elsif ( substr($str,$j,1) =~ '\)' ){ + $prime5 = pop(@bps); + $prime3 = $j; + $pair_table[$prime3+1] = $prime5+1; + $pair_table[$prime5+1] = $prime3+1; + --$count; + #print "base-pair: $pair_table[$i][$prime3] . $pair_table[$i][$prime5]\n" + } + elsif ( substr($str,$j,1) =~ '\[' ){ + push(@bps_square, $j); + ++$count; + } + elsif ( substr($str,$j,1) =~ '\]' ){ + $prime5 = pop(@bps_square); + $prime3 = $j; + $pair_table[$prime3+1] = $prime5+1; + $pair_table[$prime5+1] = $prime3+1; + --$count; + } + elsif ( substr($str,$j,1) =~ '\{' ){ + push(@bps_curly, $j); + ++$count; + } + elsif ( substr($str,$j,1) =~ '\}' ){ + $prime5 = pop(@bps_curly); + $prime3 = $j; + $pair_table[$prime3+1] = $prime5+1; + $pair_table[$prime5+1] = $prime3+1; + --$count; + } + elsif ( substr($str,$j,1) =~ '\<' ){ + push(@bps_angle, $j); + ++$count; + } + elsif ( substr($str,$j,1) =~ '\>' ){ + $prime5 = pop(@bps_angle); + $prime3 = $j; + $pair_table[$prime3+1] = $prime5+1; + $pair_table[$prime5+1] = $prime3+1; + --$count; + } + } + +#({[<.>]}) + +#print "pair table:\n"; +#for ($i = 1; $i < $len+1; $i++ ) { +# print "$pair_table[$i] "; +#} + +#print "\n"; +# +#print "pair_table = $#pair_table\n"; + +if ($count){ + print "Unbalanced brackets in: +$str\n"; + die; +} + + + return @pair_table; + +} + + + + +1; diff --git a/gtfold-mfe/tests/scripts/start_test.pm b/gtfold-mfe/tests/scripts/start_test.pm new file mode 100755 index 0000000..83fb8ee --- /dev/null +++ b/gtfold-mfe/tests/scripts/start_test.pm @@ -0,0 +1,130 @@ +#!/usr/bin/perl +use strict; +use warnings; +use Module::Load; + +use File::Basename; +use File::Path; +use Log::Log4perl qw(:easy); + +require 'test_utils.pl'; + +my $configdir="../config"; + +Log::Log4perl::init( "$configdir/root-logger.conf" ); +my $logger = Log::Log4perl->get_logger; + + +$logger->info("Starting Tests..."); + +# Read Parameter File +my $paramfile = "$configdir/test-params.conf"; + +# Create Work Directory +my $workdir = "../work"; +$logger->info("Deleting directory $workdir"); +rmtree($workdir, 0, 1); +$logger->info("Creating work directory $workdir"); +mkdir $workdir; + +my %Config; + +%Config = load_config_file($paramfile); + +###### Prepare a Hashmap of Sequences ###### + +my %Sequences; +my @seqdir_arr = @{$Config{"G_SEQUENCE_DIR"}}; + +my $seq_include_regex = $Config{"G_INCLUDE_SEQUENCES"}; +my $seq_exclude_regex = $Config{"G_EXCLUDE_SEQUENCES"}; + +%Sequences = find_sequences_from_dir( + seq_include_regex => $seq_include_regex, + seq_exclude_regex => $seq_exclude_regex, + seq_dirs => @seqdir_arr); + +my $test_include_regex = $Config{"G_INCLUDE_TESTS"}; +my $test_exclude_regex = $Config{"G_EXCLUDE_TESTS"}; + +my $test_list_file = $Config{"G_TEST_LIST_FILE"}; + +open(TESTLISTFILE, $test_list_file) || die("Could not open file: $test_list_file"); + + while () { + + my $testname = $_; + chomp($testname); + + $testname =~ s/^\s*//; # Remove spaces at the start of the line + $testname =~ s/\s*$//; # Remove spaces at the end of the line + if ( ($testname !~ /^#/) && ($testname ne "") ) { # Ignore lines starting with # and blank lines + + my $test_include = (not defined($test_include_regex)) || ($testname =~ /$seq_include_regex/); + my $test_exclude = (not defined($test_exclude_regex)) || ($testname !~ /$test_exclude_regex/); + + if ( $test_include && $test_exclude ) { + my $uppertestname = uc($testname); + my $local_sequence_dirname = "L_".$uppertestname."_SEQUENCE_DIR"; + my $local_sequence_include_regex = $Config{"L_".$uppertestname."_SEQUENCE_INCLUDE"}; + my $local_sequence_exclude_regex = $Config{"L_".$uppertestname."_SEQUENCE_EXCLUDE"}; + my @local_sequence_dir; + my %local_sequences; + + if (defined($Config{$local_sequence_dirname})) { + @local_sequence_dir = @{$Config{$local_sequence_dirname}}; + %local_sequences = find_sequences_from_dir( + seq_include_regex => $local_sequence_include_regex, + seq_exclude_regex => $local_sequence_exclude_regex, + seq_dirs => @local_sequence_dir); + } + + my $module = $testname; + load($module); + $module->test(\%Config, \%Sequences, \%local_sequences, $logger); + } + } + } + + +sub find_sequences_from_dir +{ + +my %args = @_; + +my %seq_hash; +my $include_regex = $args{seq_include_regex}; +my $exclude_regex = $args{seq_exclude_regex}; +my @seqdirs = $args{seq_dirs}; + +if (scalar(@seqdirs) eq 0) { + return %seq_hash; +} + +foreach (@seqdirs) { + + opendir(DIR, $_) || die $!; + while (my $seqfile = readdir(DIR)) { + + my $seqname; + my $path; + my $suffix; + ($seqname,$path,$suffix) = fileparse($seqfile, (".seq", ".constraint")); + + if ((-d $seqfile) || $suffix ne '.seq') { + next; + } + + $seqfile = "$_$seqname$suffix"; + my $seq_include = (not defined($include_regex)) || ($seqname =~ /$include_regex/); + my $seq_exclude = (not defined($exclude_regex)) || ($seqname !~ /$exclude_regex/); + + if ( $seq_include && $seq_exclude ) { + $seq_hash{$seqname} = $seqfile; + $logger->info("Selected Sequence ... $seqname"); + } + } + +} + return %seq_hash; +} diff --git a/gtfold-mfe/tests/scripts/test_utils.pl b/gtfold-mfe/tests/scripts/test_utils.pl new file mode 100755 index 0000000..2a62542 --- /dev/null +++ b/gtfold-mfe/tests/scripts/test_utils.pl @@ -0,0 +1,84 @@ +#!/usr/bin/perl +use strict; +use File::Path; + +sub load_config_file() +{ + my $paramfile = $_[0]; + my %Config; + my $Name; + my $Value; + my $line; + my $orig_value; + open(PARAMFILE, $paramfile) || die("Could not open file: $paramfile"); + + while () { + + my $line = $_; + chomp($line); + + $line =~ s/^\s*//; # Remove spaces at the start of the line + $line =~ s/\s*$//; # Remove spaces at the end of the line + if ( ($line !~ /^#/) && ($line ne "") ) { # Ignore lines starting with # and blank lines + ($Name, $Value) = split (/=/, $line); # Split each line into name value pairs + + if ($Name =~ /.*_INCLUDE_SEQUENCES|.*_EXCLUDE_SEQUENCES|G_INCLUDE_TESTS|G_EXCLUDE_TESTS/) { + $orig_value= %Config->{$Name}; + $Value =~ s/[.]/\\./g; + $Value =~ s/[*]/.\*/g; + if ($orig_value ne "") { + $Value = $orig_value."|".$Value; + } + } + + if ($Name =~ /.*_SEQUENCE_DIR/) { + my @seqdir_arr = %Config->{$Name}; + push (@{%Config->{$Name}}, $Value); + next; + } + + %Config->{$Name} = $Value; # Create a hash of the name value pairs + + } + } + + $Value = %Config->{"G_INCLUDE_SEQUENCES"}; + +# printf($Value."\n"); +# if ("rad" =~ /\G$Value/) { +# printf("matched1\n"); +# } +# printf($Value."\n"); +# if ("a.a.dvdsf" =~ /\G(rad|a\..*)/g) { +# printf("matched2\n"); +# } +# printf($Value."\n"); +# if ("daf" =~ /\G$Value/) { +# printf("matched3\n"); +# } +# printf($Value."\n"); +# if ("d.afdsf" =~ /\G$Value/) { +# printf("matched4\n"); +# } +# printf($Value."\n"); +# if ("acc1" =~ /\G$Value/) { +# printf("matched5\n"); +# } +# printf($Value."\n"); +# if ("acc11" =~ /\G$Value/) { +# printf("matched6\n"); +# } +# printf($Value."\n"); +# if ("a..afjlhfj" =~ /\G$Value/) { +# printf("matched7\n"); +# } +# printf($Value."\n"); +# if ("afdjs" =~ /\G$Value/) { +# printf("matched8\n"); +# } + +# printf ("@{%Config->{'G_SEQUENCE_DIR'}}\n"); + + return %Config; +} +1;