Mercurial > repos > tduigou > get_sbml_model

comparison get_infos.py @ 1:ceffb29b60c9 draft

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planemo upload commit 9c19f737cd6e2152151c8bf97a53ab1afe51a4a0
author tduigou
date Mon, 03 Apr 2023 09:18:22 +0000
parents
children fa893f77dc22
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0:4797d0b36ff3 1:ceffb29b60c9
1 from argparse import ArgumentParser
2 from libsbml import (
3 readSBMLFromFile
4 )
5
6
7 def entry_point():
8 parser = ArgumentParser('Returns cell informations')
9 parser.add_argument(
10 'infile',
11 type=str,
12 help='SBML input file (xml)'
13 )
14 parser.add_argument(
15 '--comp',
16 type=str,
17 help='Path to store cell compartments'
18 )
19 parser.add_argument(
20 '--biomass',
21 type=str,
22 help='Path to store biomass reaction ID'
23 )
24 params = parser.parse_args()
25
26 sbml_doc = readSBMLFromFile(params.infile)
27
28 if params.comp:
29 compartments = sbml_doc.getModel().getListOfCompartments()
30 with open(params.comp, 'w') as f:
31 f.write('#ID\tNAME\n')
32 for comp in compartments:
33 f.write(f'{comp.getId()}\t{comp.getName()}\n')
34
35 if params.biomass:
36 reactions = sbml_doc.getModel().getListOfReactions()
37 with open(params.biomass, 'w') as f:
38 f.write('#ID\n')
39 for rxn in reactions:
40 if 'biomass' in rxn.getId().lower():
41 f.write(f'{rxn.getId()}\n')
42
43 if __name__ == "__main__":
44 entry_point()