#!/usr/bin/env perl
# $Id: obo_trimming.pl 2013-09-29 erick.antezana $
#
# Script : obo_trimming.pl
# Purpose : This script trims a given branch of an OBO ontology.
# Usage : obo_trimming.pl my_ontology.obo term_ids.txt> my_ontology_trimmed.obo
# License : Copyright (c) 2006-2013 by Erick Antezana. All rights reserved.
# This program is free software; you can redistribute it and/or
# modify it under the same terms as Perl itself.
# Contact : Erick Antezana <erick.antezana -@- gmail.com>
#
################################################################################
use Carp;
use strict;
use warnings;
use OBO::Parser::OBOParser;
my $my_parser = OBO::Parser::OBOParser->new();
my $ontology_file = shift(@ARGV);
my $ontology = $my_parser->work($ontology_file);
my $term_ids_file = shift(@ARGV);
open TERM_IDS, $term_ids_file || die "Cannot open term IDs file";
chomp(my @term_ids = <TERM_IDS>);
close TERM_IDS;
foreach my $term_id (@term_ids) {
my $node = $ontology->get_term_by_id($term_id);
foreach my $term (@{$ontology->get_descendent_terms($node)}) {
$ontology->delete_term($term);
}
$ontology->delete_term($node);
}
# export the new trimmed ontology
$ontology->export('obo', \*STDOUT);
exit 0;
__END__
=head1 NAME
obo_trimming.pl - This script trims a given branch of an OBO ontology.
=head1 USAGE
obo_trimming.pl my_ontology.obo term_ids.txt > my_ontology_trimmed.obo
=head1 DESCRIPTION
Trims an OBO-formatted ontology. The name of the term is used to filter out
the branches that need be trimmed out.
=head1 AUTHOR
Erick Antezana, E<lt>erick.antezana -@- gmail.comE<gt>
=head1 COPYRIGHT AND LICENSE
Copyright (c) 2006-2013 by Erick Antezana
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.
=cut