Mercurial > repos > tduigou > get_sbml_model

annotate get_infos.py @ 7:8dc4d3964ab5 draft

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planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 09fcdb371be214b222a2e1c540d7c6e7489ca258
author tduigou
date Mon, 04 Sep 2023 14:19:43 +0000
parents 1482291aaa5c
children 768ed7cc0978
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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 from requests import get as r_get
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6
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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 # argument to tag file from BiGG
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16 parser.add_argument(
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17 '--bigg',
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18 action='store_true',
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19 help='Tag file from BiGG'
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20 )
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21 parser.add_argument(
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22 '--comp',
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23 type=str,
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24 help='Path to store cell compartments'
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25 )
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26 parser.add_argument(
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27 '--biomass',
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28 type=str,
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29 help='Path to store biomass reaction ID'
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30 )
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31 parser.add_argument(
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32 '--hostid',
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33 type=str,
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34 help='Extended name of the host organism'
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35 )
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36 parser.add_argument(
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37 '--taxid',
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38 type=str,
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39 help='Path to store host taxonomy ID'
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40 )
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41 params = parser.parse_args()
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42
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43 sbml_doc = readSBMLFromFile(params.infile)
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44
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45 if params.comp:
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46 compartments = sbml_doc.getModel().getListOfCompartments()
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47 with open(params.comp, 'w') as f:
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48 f.write('#ID\tNAME\n')
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49 for comp in compartments:
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50 f.write(f'{comp.getId()}\t{comp.getName()}\n')
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51
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52 if params.biomass:
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53 reactions = sbml_doc.getModel().getListOfReactions()
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54 with open(params.biomass, 'w') as f:
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55 f.write('#ID\n')
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56 for rxn in reactions:
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57 if 'biomass' in rxn.getId().lower():
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58 f.write(f'{rxn.getId()}\n')
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59
2
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60 if params.taxid:
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61 hostname = ''
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62
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63 # Model from BiGG
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64 if params.bigg:
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65 # Extended Name
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66 server = 'http://bigg.ucsd.edu/api/v2/models/'
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67 ext = params.hostid
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68 r = r_get(server+ext, headers={ "Content-Type" : "application/json"})
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69 if not r.ok:
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70 print(f"Warning: unable to retrieve host name for id {params.hostid}")
4
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71 else:
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72 try:
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73 hostname = r.json()["organism"]
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74 except KeyError:
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75 print(f"Warning: unable to retrieve host name for id {params.hostid}")
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76 if not hostname:
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77 taxid = ''
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78 else:
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79 # TAXON ID
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80 server = 'https://rest.ensembl.org'
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81 ext = f'/taxonomy/id/{hostname}?'
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82 r = r_get(server+ext, headers={ "Content-Type" : "application/json"})
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83 if not r.ok:
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84 print(f"Warning: unable to retrieve taxonomy ID for host organism {hostname}")
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85 else:
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86 try:
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87 taxid = r.json()["id"]
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88 except KeyError:
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89 print(f"Warning: unable to retrieve taxonomy ID for host organism {hostname}")
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90 taxid = ''
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91
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92 # Model from user
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93 else:
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94 taxid = params.hostid
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95
4
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96 with open(params.taxid, 'w') as f:
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97 f.write('#ID\n')
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98 f.write(f'{taxid}\n')
2
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99
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100
1
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101 if __name__ == "__main__":
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102 entry_point()