/ 
onto-perl-0.30
/ CCO::Parser::InteractionManager

work

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.

NAME

CCO::Core::InteractionManager  - An IntAct to OBO parser/filter.

SYNOPSIS

use CCO::Core::InteractionManager; use strict;

my $A_t_intact_files_dir = "/home/pik/Bioinformatics/Erick_two/IntactFiles/At/"; my @A_t_intact_files = @{&get_intact_files ($A_t_intact_files_dir)};

my $A_t_interactionmanager = InteractionManager->new; $A_t_interactionmanager->work( "/home/pik/Bioinformatics/Erick_two/onto-perl-Intact-Optimized/DATA/pre_cco/pre_cco_A_thaliana.obo", "/home/pik/Bioinformatics/Erick_two/onto-perl-Intact-Optimized/DATA/pre_cco/cco_I_A_thaliana.obo", "3702", "/home/pik/Bioinformatics/Erick_two/onto-perl-Intact-Optimized/DATA/cco_ids/cco_i_A_thaliana.ids", "/home/pik/Bioinformatics/Erick_two/onto-perl-Intact-Optimized/DATA/cco_ids/cco_b_A_thaliana.ids", "/home/pik/Bioinformatics/Erick_two/onto-perl-Intact-Optimized/DATA/cco_ids/cco_i.ids", "/home/pik/Bioinformatics/Erick_two/onto-perl-Intact-Optimized/DATA/cco_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 "..")){ # print $intact_files_dir.$file,"\n"; push (@intact_files,$intact_files_dir.$file); } } closedir DIR; return \@intact_files; }

DESCRIPTION

A parser for IntAct to OBO conversion. The conversion is filtered according to the proteins already existing in the OBO file.

AUTHOR

Mikel Egana Aranguren, mikel.eganaaranguren@cs.man.ac.uk

COPYRIGHT AND LICENSE

Copyright (C) 2007 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.