PhyloSoC:phyexport

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NAME

phyexport.pl - Export PhyloDB data to common tree file formats.

VERSION

This documentation refers to phyexport version 1.0.

SYNOPSIS

 USAGE: phyexport.pl
   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
       --outfile     # Full path to output file that will be created.
   ALTERNATIVE TO --dsn:
       --driver     # DB Driver "mysql", "Pg" "Oracle" 
       --dbname     # Name of database to use
       --host       # Host to connect with (ie. localhost)
   ADDITIONAL OPTIONS:
       --format      # "newick", "nexus" (default "newick")
       --tree        # Name of the tree to export
       --parent-node # Node to serve as root for a subtree export
       --help        # Print this help message
       --quiet       # Run the program in quiet mode.
       --db-node-id  # Preserve DB node names in export

DESCRIPTION

Export a tree stored in a PhyloDB database to a specified output format. Currently nexus, newick, lintree and New Hampshire Extended formats are supported. However; only the basic tree is currently supported. Branch data are not exported.

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.
-o, --outfile 
The full path of the output file that will be created.

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

-f, --format 
Format of the export 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

--parent-node 
Node id to serve as the root for a subtree export. Currenly not supported
--db-node-id 
Preserve database node ids when exporting the tree. For nodes that have existing labels in the label field, the node_id from the database will be indicated in parentesis.
-h, --help 
Print the help message.
-q, --quiet 
Print the program in quiet mode. No output will be printed to STDOUT and the user will not be prompted for intput.

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

Export a single tree

The following example would export the single tree named Cornus in the biosql database to the nexus formatted outfile cornus.nex.


   phyexport.pl -d 'DBI:mysql:database=biosql;host=localhost'
                -u UserName -p password -t cornus -o cornus.nex
                -f nex

If you have identified the dsn, username, and password in your environment this is simplified to.


   phyexport.pl -t cornus -o cornus.nex -f nex

Exporting the same tree in newick format would be


   phyexport.pl -t cornus -o cornus.newick -f new

Exporting in the New Hampshire extended foramt


   phyexport.pl -t cornus -o cornus.nhx -f nhx

DIAGNOSTICS

The known error messages below are followed by possible 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'

DEPENDENCIES

The phyinit 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.

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.
phyimport.pl 
Import common phylogenetic 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: 06/18/2007

Updated: 08/19/2007