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PhyloSoC:phyimport
phyimport.pl - Import phylogenetic trees from common file formats
This documentation refers to phyimport version 1.0.
USAGE: phyimport.pl -d 'DBI:mysql:database=biosql;host=localhost'
-u UserName -p dbPass -i InFilePath -f InFileFormat
REQUIRED ARGUMENTS:
--dsn # The DSN string for the DB connection
--dbuser # User name to connect with
--dbpass # User password to connect with
--infile # Full path to the tree file to import to the db
--format # "newick", "nexus" (default "newick")
ALTERNATIVE TO --dsn:
--driver # DB Driver "mysql", "Pg", "Oracle"
--dbname # Name of database to use
--host # Host to connect with (ie. localhost)
ADDITIONAL OPTIONS:
--tree # Tree name to use
--quiet # Run the program in quiet mode.
--verbose # Run the program in verbose mode.
ADDITIONAL INFORMATION:
--version # Show the program version
--usage # Show program usage
--help # Print short help message
--man # Open full program manual
Import tree files files from text common text files into the PhyloDB.
- -d, --dsn : The DSN of the database to connect to; default is the value in the environment variable DBI_DSN. If DBI_DSN has not been defined and the string is not passed to the command line, the dsn will be constructed from --driver, --dbname, --host
- -u, --dbuser : The user name to connect with; default is the value in the environment variable DBI_USER.
- -p, --dbpass : The password to connect with; default is the value in the environment variable DBI_PASSWORD. If this is not provided at the command line the user is prompted.
- -i, --infile : Path to the infile to import to the database
- -f, --format : Format of the input file. Accepted file format options are:
-nexus (-f nex) - http://www.bioperl.org/wiki/NEXUS_tree_format
-newick (-f newick) - http://www.bioperl.org/wiki/Newick_tree_format
-nhx (-f nhx) - http://www.bioperl.org/wiki/New_Hampshire_extended_tree_format
-lintree (-f lintree) -http://www.bioperl.org/wiki/Lintree_tree_format
An alternative to passing the full dsn at the command line is to provide the components separately.
- --host : The database host to connect to; default is localhost.
- --dbname : The database name to connect to; default is biosql.
- --driver : The database driver to connect with; default is mysql. Options other then mysql are currently not supported.
- --tree : The name of the tree that will be imported.
- -q, --quiet : Run the program in quiet mode. No output will be printed to STDOUT and the user will not be prompted for intput. CURRENTLY NOT IMPLEMENTED.
- --verbose : Execute the program in verbose mode.
- --version : Show the program version.
- --usage : Show program usage statement.
- --help : Show a short help message.
- --man : Show the full program manual.
Import single tree nexus format
The following example would import the tree stored as MyTree.nex with the name BigTree.
phyimport -d 'DBI:mysql:database=biosql;host=localhost'
-u name -p password -t BigTree -i MyTree.nex
-f nex
The error messages below are followed by descriptions of the error and possible solutions.
Many of the options passed at the command line can be set as options in the user's environment.
- DBI_USER : User name to connect to the database.
- DBI_PASSWORD : Password for the database connection
- DBI_DSN : DSN for database connection.
export DBI_USER=yourname
export DBI_PASS=yourpassword
export DBI_DSN='DBI:mysql:database=biosql;host-localhost'
When these are present in the environment, you can initialize a database with the above variables by simply typing phyinit.pl at the command line.
The phyimport.pl program is dependent on the following PERL modules:
- DBI - http://dbi.perl.org : The PERL Database Interface (DBI) module allows for connections to multiple databases.
- DBD::MySQL - http://search.cpan.org/~capttofu/DBD-mysql-4.005/lib/DBD/mysql.pm : MySQL database driver for DBI module.
- DBD::Pg - http://search.cpan.org/~rudy/DBD-Pg-1.32/Pg.pm : PostgreSQL database driver for the DBI module.
- Getopt::Long - http://perldoc.perl.org/Getopt/Long.html : The Getopt module allows for the passing of command line options to perl scripts.
- Bio::Tree - http://www.bioperl.org : The Bio::Tree module is part of the bioperl package.
- MySQL - http://www.mysql.com :
- PostgreSQL - http://www.postgresql.org :
Known limitations:
- Currently only stable with the MySQL Database driver.
- DSN string must currently be in the form: DBI:mysql:database=biosql;host=localhost
The program phyinit.pl is a component of a package of comand line programs for PhyloDB management. Additional programs include:
- phyinit.pl : Initialize a PhyloDB database.
- phyexport.pl : Export tree data in PhyloDB to common file formats.
- phyopt.pl : Compute optimization values for a PhyloDB database.
- phyqry.pl : Return a standard report of information for a given tree.
- phymod.pl : Modify an existing phylogenetic database by deleting, adding or copying branches.
This program may be used, distributed or modified under the same terms as Perl itself. Please consult the Perl Artistic License (http://www.perl.com/pub/a/language/misc/Artistic.html) for the terms under which you may use, modify, or distribute this script.
THIS SOFTWARE COMES AS IS, WITHOUT ANY EXPRESS OR IMPLIED WARRANTY. USE AT YOUR OWN RISK.
James C. Estill
Hilmar Lapp <hlapp></hlapp>
William Piel <william.piel></william.piel>
Started: 05/30/2007
Updated: 08/17/2007