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#!/usr/bin/python3
##
## \file addCVTerms.py
## \brief adds controlled vocabulary terms to a species in a model
## \author Sarah Keating
##
## <!--------------------------------------------------------------------------
## This sample program is distributed under a different license than the rest
## of libSBML. This program uses the open-source MIT license, as follows:
##
## Copyright (c) 2013-2018 by the California Institute of Technology
## (California, USA), the European Bioinformatics Institute (EMBL-EBI, UK)
## and the University of Heidelberg (Germany), with support from the National
## Institutes of Health (USA) under grant R01GM070923. All rights reserved.
##
## Permission is hereby granted, free of charge, to any person obtaining a
## copy of this software and associated documentation files (the "Software"),
## to deal in the Software without restriction, including without limitation
## the rights to use, copy, modify, merge, publish, distribute, sublicense,
## and/or sell copies of the Software, and to permit persons to whom the
## Software is furnished to do so, subject to the following conditions:
##
## The above copyright notice and this permission notice shall be included in
## all copies or substantial portions of the Software.
##
## THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
## IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
## FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
## THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
## LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
## FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
## DEALINGS IN THE SOFTWARE.
##
## Neither the name of the California Institute of Technology (Caltech), nor
## of the European Bioinformatics Institute (EMBL-EBI), nor of the University
## of Heidelberg, nor the names of any contributors, may be used to endorse
## or promote products derived from this software without specific prior
## written permission.
## ------------------------------------------------------------------------ -->
import sys
import os.path
from libsbml import *
def main (args):
"""usage: addCVTerms <input-filename> <output-filename>
Adds controlled vocabulary term to a species
"""
if len(args) != 3:
print(main.__doc__)
sys.exit(2)
d = readSBML(args[1])
errors = d.getNumErrors()
if errors > 0:
print("Read Error(s):")
d.printErrors()
print("Correct the above and re-run.")
else:
n = d.getModel().getNumSpecies()
if n <= 0:
print("Model has no species.\n Cannot add CV terms\n")
else:
s = d.getModel().getSpecies(0)
if not s.isSetMetaId():
s.setMetaId('unique_id_1')
cv = CVTerm()
cv.setQualifierType(BIOLOGICAL_QUALIFIER)
cv.setBiologicalQualifierType(BQB_IS_VERSION_OF)
cv.addResource("http://www.geneontology.org/#GO:0005892")
cv2 = CVTerm()
cv2.setQualifierType(BIOLOGICAL_QUALIFIER)
cv2.setBiologicalQualifierType(BQB_IS)
cv2.addResource("http://www.geneontology.org/#GO:0005895")
cv1 = CVTerm()
cv1.setQualifierType(BIOLOGICAL_QUALIFIER)
cv1.setBiologicalQualifierType(BQB_IS_VERSION_OF)
cv1.addResource("http://www.ebi.ac.uk/interpro/#IPR002394")
s.addCVTerm(cv)
s.addCVTerm(cv2)
s.addCVTerm(cv1)
writeSBML(d, args[2])
return errors
if __name__ == '__main__':
main(sys.argv)
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