OBO::CCO::InteractionManager - An IntAct to OBO parser/filter manager.
use OBO::CCO::InteractionManager; use strict;
my $A_t_intact_files_dir = "/IntactFiles/At/"; my @A_t_intact_files = @{&get_intact_files ($A_t_intact_files_dir)};
my $A_t_interactionmanager = InteractionManager->new; $A_t_interactionmanager->work( "pre_cco_A_thaliana.obo", "cco_I_A_thaliana.obo", "3702", "cco_i_A_thaliana.ids", "cco_b_A_thaliana.ids", "cco_i.ids", "cco_b.ids", @A_t_intact_files );
sub get_intact_files{ my $intact_files_dir = shift; my @intact_files = (); opendir(DIR, $intact_files_dir) || die "can't opendir $intact_files_dir: $!"; my @files = readdir(DIR); for my $file (@files){ if (!($file eq ".") and !($file eq "..")) { push (@intact_files,$intact_files_dir.$file); } } closedir DIR; return \@intact_files; }
A parser for IntAct to OBO conversion. The conversion is filtered according to the proteins already existing in the OBO file.
Mikel Egana Aranguren, mikel.eganaaranguren@cs.man.ac.uk
Copyright (C) 2007, 2008 by Mikel Egana Aranguren
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 - InteractionManager->work() Returns - A new OBO ontology with new proteins and interactions from IntAct Args - old OBO file, new OBO file, taxon (e.g. 3702), cco_i_taxon_ids file, cco_b_taxon_ids file, cco_i_ids file, cco_b_ids file, XML file 1, XML file 2, ... Function - Adds or deletes interactions to/from an OBO file, filtering the interactions from Intact XML files according to proteins already existing in CCO. It also includes any new proteins needed. It should be used for each taxa.
