PhyloSoC:phyimport

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NAME

phyimport.pl - Import phylogenetic trees from common file formats

VERSION

This documentation refers to phyimport version 1.0.

SYNOPSIS

 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

DESCRIPTION

Import tree files files from text common text files into the PhyloDB.

COMMAND LINE ARGUMENTS

Required Arguments

-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.
-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

Alternative to --dsn

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.

Additional Options

--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.

Additional Information

--version 
Show the program version.
--usage 
Show program usage statement.
--help 
Show a short help message.
--man 
Show the full program manual.

EXAMPLES

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

DIAGNOSTICS

The error messages below are followed by descriptions of the error and possible solutions.

CONFIGURATION AND ENVIRONMENT

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.

For example in the bash shell this would be done be editing your .bashrc file to contain:

   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.

DEPENDENCIES

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.

A RDBMS is also required. This can be one of:

MySQL - http://www.mysql.com 
PostgreSQL - http://www.postgresql.org 

BUGS AND LIMITATIONS

Known limitations:

  • Currently only stable with the MySQL Database driver.
  • DSN string must currently be in the form: DBI:mysql:database=biosql;host=localhost

Please report additional problems to James Estill <JamesEstill at gmail.com>

SEE ALSO

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.

LICENSE

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.

AUTHORS

James C. Estill <JamesEstill at gmail.com>

Hilmar Lapp <hlapp at gmx.net>

William Piel <william.piel at yale.edu>

HISTORY

Started: 05/30/2007

Updated: 08/17/2007