NAME

OBO::CCO::OrthoMCLParser - An orthoMCL data to OBO translator

DESCRIPTION

Includes methods for adding information from orthoMCL data files to ontologies

orthoMCL can be obtained from http://orthomcl.cbil.upenn.edu/cgi-bin/OrthoMclWeb.cgi

The method 'parse()' parses an orthoMCL output data file into a data structure (hash of arrays) The method 'work()' incorporates data from an orthoMCL data file into an ontology, writes the ontology into an OBO file, writes map files.

AUTHOR

Vladimir Mironov vlmir@psb.ugent.be

COPYRIGHT AND LICENSE

Copyright (C) 2006, 2007, 2008 by Vladimir Mironov

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself, either Perl version 5.8.7 or, at your option, any later version of Perl 5 you may have available.

parse

Usage    - $OrthoMCLParser->parse()
Returns  - a reference to a data structure (hash of hashes) containing orthoMCL output data
Args     - orthoMCL output data file
Function - parses an orthoMCL output data file  into a data structure

work

Usage    - $OrthoMCLParser->work($omcl_data_ref, $file_names_ref, $taxa_ref)
Returns  - OBO::Core::Ontology object 
Args     - 1. reference to an orthoMCL data structure (output of parse()), 2. reference to a list of filenames (output OBO file, 4 map files (U,T,O,B, see the test file), 3. reference to a with taxons and taxon specific maps (see the test file)
Function - converts orthoMCL data into an ontology, writes OBO and map files