Mercurial > repos > tduigou > get_sbml_model

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