#!/usr/bin/env perl
# $Id: get_terms.pl 2015-10-29 erick.antezana $
#
# Script : get_terms.pl
# Purpose : Gets all the terms in a given ontology.
# Usage : get_terms.pl my_ontology.obo > terms.txt
# License : Copyright (c) 2006-2015 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 OBO::Parser::OBOParser;
use Getopt::Long;
my %opts = ();
GetOptions (\%opts,
'f=s{1,1}',
'help|h')
or die("Error in command line arguments, ask for help: -h\n");
my $file = $opts{f};
unless ($file) {print_help()};
sub print_help {
print "\n";
print "\tdescription: This script retrieves all the names of the terms (and their IDs).\n";
print "\tusage : get_terms.pl [options]\n";
print "\toptions :\n";
print "\t\t-f OBO input file\n";
print "\texample:\n";
print "\t\tperl get_terms.pl -f go.obo\n";
exit;
}
my $my_parser = OBO::Parser::OBOParser->new();
my $ontology = $my_parser->work($file);
my @sorted_terms = map { $_->[0] } # restore original values
sort { $a->[1] cmp $b->[1] } # sort
map { [$_, $_->id()] } # transform: value, sortkey
@{$ontology->get_terms()};
foreach my $t (@sorted_terms) {
my $t_name = $t->name();
if (defined $t_name) {
print $t->id(), "\t", $t->name(), "\n";
} else {
print $t->id(), "\n";
}
}
exit 0;
__END__
=head1 NAME
get_terms.pl - Gets all the terms in a given ontology.
=head1 DESCRIPTION
This script retrieves all the names of the terms (and their IDs)
in a given OBO-formatted ontology.
=head1 AUTHOR
Erick Antezana, E<lt>erick.antezana -@- gmail.comE<gt>
=head1 COPYRIGHT AND LICENSE
Copyright (c) 2006-2015 by Erick Antezana. All rights reserved.
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