libSBML Python API  5.11.0
convertCobraToFbc.py

Example of converting a COBRA-style SBML Level 2 model to SBML Level 3 using the Flux Balance Constraints package.

1 #!/usr/bin/env python
2 ##
3 ## @file convertCobraToFbc.py
4 ## @brief Convert COBRA L2 to L3 with FBC
5 ## @author Frank T. Bergmann
6 ##
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) 2013-2014 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,
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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
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39 ## written permission.
40 ## ------------------------------------------------------------------------ -->
41 
42 import sys
43 import os.path
44 import libsbml
45 
46 def main (args):
47  """usage: convertCobraToFbc.py input-filename output-filename
48  """
49  if len(args) != 3:
50  print(main.__doc__)
51  sys.exit(1)
52 
53  infile = args[1]
54  outfile = args[2]
55 
56  if not os.path.exists(infile):
57  print("[Error] %s : No such file." % (infile))
58  sys.exit(1)
59 
60  reader = libsbml.SBMLReader()
61  writer = libsbml.SBMLWriter()
62  sbmldoc = reader.readSBML(infile)
63 
64  if sbmldoc.getNumErrors() > 0:
65  if sbmldoc.getError(0).getErrorId() == libsbml.XMLFileUnreadable:
66  # Handle case of unreadable file here.
67  sbmldoc.printErrors()
68  elif sbmldoc.getError(0).getErrorId() == libsbml.XMLFileOperationError:
69  # Handle case of other file error here.
70  sbmldoc.printErrors()
71  else:
72  # Handle other error cases here.
73  sbmldoc.printErrors()
74 
75  sys.exit(1)
76 
78  props.addOption("convert cobra", True, "Convert Cobra model")
79  result = sbmldoc.convert(props)
80  if (result != libsbml.LIBSBML_OPERATION_SUCCESS):
81  print("[Error] Conversion failed... (%d)" %(result))
82  sys.exit(1)
83 
84  writer.writeSBML(sbmldoc, outfile)
85  print("[OK] converted file %s to %s" % (infile, outfile))
86 
87 if __name__ == '__main__':
88  main(sys.argv)