Mercurial > repos > tduigou > get_sbml_model

annotate get_infos.py @ 2:fa893f77dc22 draft

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planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 18fcec17fb6415ad5a59b9bcfa853e755c768e6f
author tduigou
date Mon, 24 Apr 2023 14:49:53 +0000
parents ceffb29b60c9
children 1482291aaa5c
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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 )
2
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5 from requests import get as r_get
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7
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8 def entry_point():
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9 parser = ArgumentParser('Returns cell informations')
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10 parser.add_argument(
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11 'infile',
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12 type=str,
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13 help='SBML input file (xml)'
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14 )
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15 parser.add_argument(
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16 '--comp',
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17 type=str,
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18 help='Path to store cell compartments'
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19 )
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20 parser.add_argument(
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21 '--biomass',
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22 type=str,
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23 help='Path to store biomass reaction ID'
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24 )
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25 parser.add_argument(
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26 '--hostid',
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27 type=str,
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28 help='Extended name of the host organism'
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29 )
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30 parser.add_argument(
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31 '--taxid',
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32 type=str,
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33 help='Path to store host taxonomy ID'
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34 )
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35 params = parser.parse_args()
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36
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37 sbml_doc = readSBMLFromFile(params.infile)
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38
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39 if params.comp:
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40 compartments = sbml_doc.getModel().getListOfCompartments()
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41 with open(params.comp, 'w') as f:
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42 f.write('#ID\tNAME\n')
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43 for comp in compartments:
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44 f.write(f'{comp.getId()}\t{comp.getName()}\n')
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45
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46 if params.biomass:
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47 reactions = sbml_doc.getModel().getListOfReactions()
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48 with open(params.biomass, 'w') as f:
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49 f.write('#ID\n')
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50 for rxn in reactions:
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51 if 'biomass' in rxn.getId().lower():
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52 f.write(f'{rxn.getId()}\n')
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53
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54 if params.taxid:
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55 # Extended Name
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56 server = 'http://bigg.ucsd.edu/api/v2/models/'
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57 ext = params.hostid
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58 r = r_get(server+ext, headers={ "Content-Type" : "application/json"})
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59 if not r.ok:
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60 print(f"Warning: unable to retrieve host name for id {params.hostid}")
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61 else:
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62 try:
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63 hostname = r.json()["organism"]
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64 except KeyError:
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65 print(f"*** Error: unable to retrieve host name for id {params.hostid}")
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66 return -1
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67 # TAXON ID
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68 server = 'https://rest.ensembl.org'
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69 ext = f'/taxonomy/id/{hostname}?'
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70 r = r_get(server+ext, headers={ "Content-Type" : "application/json"})
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71 if not r.ok:
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72 print(f"Warning: unable to retrieve taxonomy ID for host organism {hostname}")
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73 else:
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74 try:
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75 taxid = r.json()["parent"]["id"]
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76 except KeyError:
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77 print(f"Warning: unable to retrieve taxonomy ID for host organism {hostname}")
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78 with open(params.taxid, 'w') as f:
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79 f.write('#ID\n')
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80 f.write(f'{taxid}\n')
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81
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82
1
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83 if __name__ == "__main__":
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84 entry_point()