1#!/usr/bin/env perl
2# -*-Perl-*-
3##
4## \file    addCVTerms.pl
5## \brief   adds controlled vocabulary terms to a species in a model
6## \author  Sarah Keating
7##
8## <!--------------------------------------------------------------------------
9## This sample program is distributed under a different license than the rest
10## of libSBML.  This program uses the open-source MIT license, as follows:
11##
12## Copyright (c) 2013-2018 by the California Institute of Technology
13## (California, USA), the European Bioinformatics Institute (EMBL-EBI, UK)
14## and the University of Heidelberg (Germany), with support from the National
15## Institutes of Health (USA) under grant R01GM070923.  All rights reserved.
16##
17## Permission is hereby granted, free of charge, to any person obtaining a
18## copy of this software and associated documentation files (the "Software"),
19## to deal in the Software without restriction, including without limitation
20## the rights to use, copy, modify, merge, publish, distribute, sublicense,
21## and/or sell copies of the Software, and to permit persons to whom the
22## Software is furnished to do so, subject to the following conditions:
23##
24## The above copyright notice and this permission notice shall be included in
25## all copies or substantial portions of the Software.
26##
27## THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
28## IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
29## FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
30## THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
31## LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
32## FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
33## DEALINGS IN THE SOFTWARE.
34##
35## Neither the name of the California Institute of Technology (Caltech), nor
36## of the European Bioinformatics Institute (EMBL-EBI), nor of the University
37## of Heidelberg, nor the names of any contributors, may be used to endorse
38## or promote products derived from this software without specific prior
39## written permission.
40## ------------------------------------------------------------------------ -->
41##
42
43use LibSBML;
44no strict;
45
46if ($#ARGV != 1) {
47  print "usage: addCVTerms <input-filename> <output-filename>\n";
48  print "       Adds controlled vocabulary term to a species\n";
49  exit 2;
50}
51
52$d = LibSBML::readSBML($ARGV[0]);
53$errors = $d->getNumErrors();
54
55if ($errors > 0) {
56    print("Read Error(s):");
57    $d->printErrors();
58    print("Correct the above and re-run.");
59    exit $errors;
60}
61
62$n = $d->getModel()->getNumSpecies();
63
64if ($n <= 0) {
65    print("Model has no species.\n Cannot add CV terms\n");
66    exit 0;
67}
68
69$s = $d->getModel()->getSpecies(0);
70if ( not $s->isSetMetaId()) {
71  $s->setMetaId("metaid_s0000052");
72}
73
74$cv = new LibSBML::CVTerm();
75$cv->setQualifierType($LibSBML::BIOLOGICAL_QUALIFIER);
76$cv->setBiologicalQualifierType($LibSBML::BQB_IS_VERSION_OF);
77$cv->addResource("http://www.geneontology.org/#GO:0005892");
78
79$cv2 = new LibSBML::CVTerm();
80$cv2->setQualifierType($LibSBML::BIOLOGICAL_QUALIFIER);
81$cv2->setBiologicalQualifierType($LibSBML::BQB_IS);
82$cv2->addResource("http://www.geneontology.org/#GO:0005895");
83
84$cv1 = new LibSBML::CVTerm();
85$cv1->setQualifierType($LibSBML::BIOLOGICAL_QUALIFIER);
86$cv1->setBiologicalQualifierType($LibSBML::BQB_IS_VERSION_OF);
87$cv1->addResource("http://www.ebi.ac.uk/interpro/#IPR002394");
88
89$s->addCVTerm($cv);
90$s->addCVTerm($cv2);
91$s->addCVTerm($cv1);
92
93LibSBML::writeSBML($d, $ARGV[1]);
94
95exit $errors;
96
97