-
Notifications
You must be signed in to change notification settings - Fork 0
PhyloSoC:phyopt
phyopt.pl - Optimize trees in a PhyloDB database
This documentation refers to phyopt.pl version 1.0.
USAGE: phyopt.pl -d 'DBI:mysql:database=biosql;host=localhost'
-u UserName -p dbPass -t MyTree
REQUIRED ARGUMENTS:
--dsn # The DSN string the database to connect to
# Must conform to:
# 'DBI:mysql:database=biosql;host=localhost'
--dbuser # User name to connect with
--dbpass # Password to connect with
ALTERNATIVE TO --dsn:
--driver # "mysql", "Pg", "Oracle" (default "mysql")
--dbname # Name of database to use
--host # optional: host to connect with
ADDITIONAL OPTIONS:
--tree # Name of the tree to optimize.
# Otherwise the entire db is optimized.
--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
The phyopt program will optimize trees in a PhyloDB database by computing transitive closure paths as well as the left and right index values for the nested set indexes.
- -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
DSN must be in the form:
DBI:mysql:database=biosql;host=localhost - -u, --dbuser : The user name to connect with; default is the value in the environment variable DBI_USER.This user must have permission to create databases.
- -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.
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.
- -t, --tree : Name of the tree that will be optimized. Otherwise all trees in the database will be optimized.
- -q, --quiet : Run the program in quiet mode.
- --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.
Optimize a single tree
The following command options would optimize the tree named MyTree in the biosql database.
phyopt.pl -d 'DBI:mysql:database=biosql;host=localhost'
-u name -p password -t MyTree
Optimize entire database
The following commmand options would optimize all of the individual trees in the database named Angio.
phyopt.pl -d 'DBI:mysql:database=Angio;host=localhost'
-u name -p password
This could also be done by passing the individual components for connecting to the database.
phyopt.pl --driver mysql --database Angio --host localhost
-u name -p password
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'
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.
- phyimport.pl : Import common phylogenetic file formats.
- phyexport.pl : Export tree data in PhyloDB to common file formats.
- phyreport.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: 07/04/2007
Updated: 08/19/2007