OBO::CCO::GoaParser - A GOA associations to OBO translator.
Includes methods for adding information from GOA association files to ontologies GOA associations files can be obtained from http://www.ebi.ac.uk/GOA/proteomes.html
The method 'parse' parses the GOA association file and returns a OBO::CCO::GoaAssociationSet object
The method 'work' incorporates OBJ_SRC, OBJ_ID, OBJ_SYMB, SYNONYM, DESCRIPTION into the input ontology, writes the ontology into an OBO file, writes map files. This method assumes: 1. the ontology contains already the term 'protein' 2. the ontology already contains all and only the necessary GO terms. 3. the ontology already contains the relationship types 'is_a', 'participates_in', 'has_participant' 4. the input GOA association file contains entries for one species only and for GO terms present in the input ontology only
Vladimir Mironov <vladimir.mironov@bio.ntnu.no>
Copyright (C) 2006, 2007, 2008, 2009, 2010 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.
Usage - $GoaParser->parse(GOA_association_file) Returns - An OBO::CCO::GoaAssociationSet object Args - GOA associations file Function - converts a GOA associations file into a OBO::CCO::GoaAssociationSet object
Usage - $GoaParser->work($ref_file_names) Returns - updated OBO::Core::Ontology object Args - reference to a list of filenames(input OBO file, output OBO file, GOA associations file, CCO_id/Uniprot_id map file one taxon only, CCO_id/Uniprot_id map file all taxa) Function - parses a GOA associations file, adds relevant information to the input ontology, writes OBO and map files
Usage - $GoaParser->add_goa_assocs($ref_file_names) Returns - updated OBO::Core::Ontology object Args - reference to a list of filenames(input OBO file, output OBO file, GOA associations file, UniProt map file 'AC'\t'ID', 'go_id'\t'cco_id' map file) Function - parses a GOA associations file, adds new associations to the input ontology, writes OBO
To install OBO::Util::Set, copy and paste the appropriate command in to your terminal.
cpanm
cpanm OBO::Util::Set
CPAN shell
perl -MCPAN -e shell install OBO::Util::Set
For more information on module installation, please visit the detailed CPAN module installation guide.