OBO::CCO::IntActParser - An IntAct to OBO parser/filter.
use OBO::CCO::IntActParser; 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( "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.$file); } } closedir DIR; return \@intact_files; }
A parser for IntAct to OBO conversion. The conversion is filtered according to the proteins already existing in the OBO file and the roles this proteins have in the interactions (prey, bait, neutral component). It deletes any interaction in OBO that it is not present in IntAct, for sync.
Mikel Egana Aranguren, mikel.eganaaranguren@cs.man.ac.uk
Copyright (C) 2007, 2008 by Mikel Egana Aranguren
This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself, either Perl version 5.8.7 or, at your option, any later version of Perl 5 you may have available.
Usage - IntActParser->work() Returns - A new OBO ontology with new proteins and interactions from IntAct Args - old OBO file, new OBO file, taxon (e.g. 3702), cco_i_taxon_ids file, cco_b_taxon_ids file, cco_i_ids file, cco_b_ids file, XML file 1, XML file 2, ... Function - Adds or deletes interactions to/from an OBO file, filtering the interactions from Intact XML files according to proteins already existing in CCO and their roles in IntAct (bait, prey, neutral component). It also includes any new proteins needed. It should be used for each taxon.
Usage - get_xref_acc($db, $term) Returns - the name of the external database and the ID (strings) Args - the database name and the term (OBO::Core::Term) Function - Given a term, get the xref of a given db. Otherwise, undef
Usage - add_term ($term_name,$term_id,$ontology) Returns - the added term object Args - the term name, term name id, ontology Function - add a term to the ontology, with an ID and name
Usage - add_xref ($term,$db,$acc) Returns - the provided term object Args - the term object, database name, accesion id Function - add an xref (database and accesion id) to a given term
Usage - add_def ($term,$db,$acc,$def_text) Returns - the provided term object Args - the term object, database name, accesion id, definition text Function - add an definition (definition text, database and accesion id) to a given term
Usage - add_synonym ($term,$db,$acc,$syn_text) Returns - the provided term object Args - the term object, database name, accesion id, synonym text Function - add an exact synonym (synonym text, database and accesion id) to a given term
Usage - add_comment ($term,$text) Returns - the provided term object Args - the term object, comment text Function - add a comment to a given term
Usage - retrieve_interactions ($interactor,@interactions) Returns - an array of interactions Args - an interactor object and the array of interaction objects extracted from an IntAct XML file Function - given an interactor, retrieve all the interactions that have the interactor as participant
Usage - get_role ($interactor_id,$interaction) Returns - role (string) Args - interactor id and interaction object Function - given and interactor id (e.g. 498), get its role in the interaction
Usage - get_interactor ($interactor_id,@interactors) Returns - interactor object Args - interactor id and arrayc of interactors extracted from an IntAct XML file Function - given an interactor id get the interactor object
Usage - add_interaction ($interaction, $ontology, $cco_i_taxon_ids_map, $cco_i_ids_map,$is_a) Returns - added interaction OBO term Args - interaction object, ontology, interaction id map (taxon), interaction id map (general), is_a relationship type id Function - add an interaction to CCO
Usage - add_interactor ($interactor,$ontology,$cco_b_taxon_ids_map,$cco_b_ids_map,$is_a,$has_source,$taxon) Returns - added interactor OBO term Args - interactor object, ontology, protein id map (taxon), protein id map (general), is_a relationship type id, has_source relationship type id, taxon id (e.g. 3702) Function - add an interactor to CCO
Usage - lookup ($item,@array) Returns - found result or undefined if not found Args - string to find, array Function - find and string in an array of strings
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.