#!/usr/bin/env perl
# $Id: get_term_id_vs_term_name.pl 2013-09-29 erick.antezana $
#
# Script : get_term_id_vs_term_name.pl
# Purpose : Generates a flat file with two columns (TAB separated) with the
# get_term_id and term_definition from the elements of the given OBO ontology.
# Usage : get_term_id_vs_term_name.pl my_ontology.obo > get_term_id_vs_term_name.txt
# License : Copyright (c) 2006-2014 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 $onto_file = shift(@ARGV);
die "The input OBO file was not found." if (!$onto_file);
my $ontology = $my_parser->work($onto_file);
foreach my $term (sort {$a->id() cmp $b->id()} @{$ontology->get_terms()}) {
print $term->id(), "\t", $term->name(), "\n" if (defined $term->id() && $term->name());
}
exit 0;
__END__
=head1 NAME
get_term_id_vs_term_name.pl - Gets the term IDs and term names of a given ontology.
=head1 DESCRIPTION
Generates a flat file with two columns (TAB separated) with the
get_term_id and term_definition from the elements of the given OBO ontology.
=head1 AUTHOR
Erick Antezana, E<lt>erick.antezana -@- gmail.comE<gt>
=head1 COPYRIGHT AND LICENSE
Copyright (c) 2006-2014 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