Mercurial > repos > tduigou > get_sbml_model

annotate get_infos.py @ 7:33be348bf9d6 draft

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planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 1a86e55d9e8c539de5fe8110ba85a2489473bde4
author tduigou
date Tue, 26 Sep 2023 12:59:14 +0000
parents 4c773948a490
children 06366f104f78
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e276119e73c8 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
tduigou
parents:
diff changeset
1 from argparse import ArgumentParser
e276119e73c8 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
tduigou
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2 from libsbml import (
e276119e73c8 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
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3 readSBMLFromFile
e276119e73c8 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
tduigou
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4 )
2
52649039cf3f planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit d1f5bac36c249e0767ed0bb968a1f4b5843256e3
tduigou
parents: 1
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5 from requests import get as r_get
1
e276119e73c8 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
tduigou
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6
e276119e73c8 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
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7
e276119e73c8 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
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8 def entry_point():
e276119e73c8 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
tduigou
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9 parser = ArgumentParser('Returns cell informations')
e276119e73c8 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
tduigou
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10 parser.add_argument(
e276119e73c8 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
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11 'infile',
e276119e73c8 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
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12 type=str,
e276119e73c8 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
tduigou
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13 help='SBML input file (xml)'
e276119e73c8 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
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14 )
7
33be348bf9d6 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 1a86e55d9e8c539de5fe8110ba85a2489473bde4
tduigou
parents: 4
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15 # argument to tag file from BiGG
33be348bf9d6 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 1a86e55d9e8c539de5fe8110ba85a2489473bde4
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16 parser.add_argument(
33be348bf9d6 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 1a86e55d9e8c539de5fe8110ba85a2489473bde4
tduigou
parents: 4
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17 '--bigg',
33be348bf9d6 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 1a86e55d9e8c539de5fe8110ba85a2489473bde4
tduigou
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18 action='store_true',
33be348bf9d6 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 1a86e55d9e8c539de5fe8110ba85a2489473bde4
tduigou
parents: 4
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19 help='Tag file from BiGG'
33be348bf9d6 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 1a86e55d9e8c539de5fe8110ba85a2489473bde4
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20 )
1
e276119e73c8 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
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21 parser.add_argument(
e276119e73c8 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
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22 '--comp',
e276119e73c8 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
tduigou
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23 type=str,
e276119e73c8 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
tduigou
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24 help='Path to store cell compartments'
e276119e73c8 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
tduigou
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25 )
e276119e73c8 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
tduigou
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26 parser.add_argument(
e276119e73c8 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
tduigou
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27 '--biomass',
e276119e73c8 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
tduigou
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28 type=str,
e276119e73c8 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
tduigou
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29 help='Path to store biomass reaction ID'
e276119e73c8 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
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30 )
2
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tduigou
parents: 1
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31 parser.add_argument(
52649039cf3f planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit d1f5bac36c249e0767ed0bb968a1f4b5843256e3
tduigou
parents: 1
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32 '--hostid',
52649039cf3f planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit d1f5bac36c249e0767ed0bb968a1f4b5843256e3
tduigou
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33 type=str,
52649039cf3f planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit d1f5bac36c249e0767ed0bb968a1f4b5843256e3
tduigou
parents: 1
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34 help='Extended name of the host organism'
52649039cf3f planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit d1f5bac36c249e0767ed0bb968a1f4b5843256e3
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parents: 1
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35 )
52649039cf3f planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit d1f5bac36c249e0767ed0bb968a1f4b5843256e3
tduigou
parents: 1
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36 parser.add_argument(
52649039cf3f planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit d1f5bac36c249e0767ed0bb968a1f4b5843256e3
tduigou
parents: 1
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37 '--taxid',
52649039cf3f planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit d1f5bac36c249e0767ed0bb968a1f4b5843256e3
tduigou
parents: 1
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38 type=str,
52649039cf3f planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit d1f5bac36c249e0767ed0bb968a1f4b5843256e3
tduigou
parents: 1
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39 help='Path to store host taxonomy ID'
52649039cf3f planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit d1f5bac36c249e0767ed0bb968a1f4b5843256e3
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parents: 1
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40 )
1
e276119e73c8 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
tduigou
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41 params = parser.parse_args()
e276119e73c8 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
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42
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43 sbml_doc = readSBMLFromFile(params.infile)
e276119e73c8 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
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44
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45 if params.comp:
e276119e73c8 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
tduigou
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46 compartments = sbml_doc.getModel().getListOfCompartments()
e276119e73c8 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
tduigou
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47 with open(params.comp, 'w') as f:
e276119e73c8 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
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48 f.write('#ID\tNAME\n')
e276119e73c8 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
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49 for comp in compartments:
e276119e73c8 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
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50 f.write(f'{comp.getId()}\t{comp.getName()}\n')
e276119e73c8 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
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51
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52 if params.biomass:
e276119e73c8 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
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53 reactions = sbml_doc.getModel().getListOfReactions()
e276119e73c8 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
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54 with open(params.biomass, 'w') as f:
e276119e73c8 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
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55 f.write('#ID\n')
e276119e73c8 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
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56 for rxn in reactions:
e276119e73c8 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
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57 if 'biomass' in rxn.getId().lower():
e276119e73c8 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
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58 f.write(f'{rxn.getId()}\n')
e276119e73c8 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
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59
2
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60 if params.taxid:
7
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61 hostname = ''
33be348bf9d6 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 1a86e55d9e8c539de5fe8110ba85a2489473bde4
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62
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63 # Model from BiGG
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64 if params.bigg:
33be348bf9d6 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 1a86e55d9e8c539de5fe8110ba85a2489473bde4
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65 # Extended Name
33be348bf9d6 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 1a86e55d9e8c539de5fe8110ba85a2489473bde4
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66 server = 'http://bigg.ucsd.edu/api/v2/models/'
33be348bf9d6 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 1a86e55d9e8c539de5fe8110ba85a2489473bde4
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67 ext = params.hostid
4
4c773948a490 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 4a0b08beb8cdf51ab295a1f5f8c586d6bbaf5586
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68 r = r_get(server+ext, headers={ "Content-Type" : "application/json"})
4c773948a490 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 4a0b08beb8cdf51ab295a1f5f8c586d6bbaf5586
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69 if not r.ok:
7
33be348bf9d6 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 1a86e55d9e8c539de5fe8110ba85a2489473bde4
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70 print(f"Warning: unable to retrieve host name for id {params.hostid}")
4
4c773948a490 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 4a0b08beb8cdf51ab295a1f5f8c586d6bbaf5586
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71 else:
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72 try:
7
33be348bf9d6 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 1a86e55d9e8c539de5fe8110ba85a2489473bde4
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73 hostname = r.json()["organism"]
4
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74 except KeyError:
7
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75 print(f"Warning: unable to retrieve host name for id {params.hostid}")
33be348bf9d6 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 1a86e55d9e8c539de5fe8110ba85a2489473bde4
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76 if not hostname:
33be348bf9d6 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 1a86e55d9e8c539de5fe8110ba85a2489473bde4
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77 taxid = ''
33be348bf9d6 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 1a86e55d9e8c539de5fe8110ba85a2489473bde4
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78 else:
33be348bf9d6 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 1a86e55d9e8c539de5fe8110ba85a2489473bde4
tduigou
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79 # TAXON ID
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80 server = 'https://rest.ensembl.org'
33be348bf9d6 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 1a86e55d9e8c539de5fe8110ba85a2489473bde4
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81 ext = f'/taxonomy/id/{hostname}?'
33be348bf9d6 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 1a86e55d9e8c539de5fe8110ba85a2489473bde4
tduigou
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82 r = r_get(server+ext, headers={ "Content-Type" : "application/json"})
33be348bf9d6 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 1a86e55d9e8c539de5fe8110ba85a2489473bde4
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83 if not r.ok:
4
4c773948a490 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 4a0b08beb8cdf51ab295a1f5f8c586d6bbaf5586
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84 print(f"Warning: unable to retrieve taxonomy ID for host organism {hostname}")
7
33be348bf9d6 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 1a86e55d9e8c539de5fe8110ba85a2489473bde4
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85 else:
33be348bf9d6 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 1a86e55d9e8c539de5fe8110ba85a2489473bde4
tduigou
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86 try:
33be348bf9d6 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 1a86e55d9e8c539de5fe8110ba85a2489473bde4
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87 taxid = r.json()["id"]
33be348bf9d6 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 1a86e55d9e8c539de5fe8110ba85a2489473bde4
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88 except KeyError:
33be348bf9d6 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 1a86e55d9e8c539de5fe8110ba85a2489473bde4
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89 print(f"Warning: unable to retrieve taxonomy ID for host organism {hostname}")
33be348bf9d6 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 1a86e55d9e8c539de5fe8110ba85a2489473bde4
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90 taxid = ''
33be348bf9d6 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 1a86e55d9e8c539de5fe8110ba85a2489473bde4
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91
33be348bf9d6 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 1a86e55d9e8c539de5fe8110ba85a2489473bde4
tduigou
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92 # Model from user
33be348bf9d6 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 1a86e55d9e8c539de5fe8110ba85a2489473bde4
tduigou
parents: 4
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93 else:
33be348bf9d6 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 1a86e55d9e8c539de5fe8110ba85a2489473bde4
tduigou
parents: 4
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94 taxid = params.hostid
33be348bf9d6 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 1a86e55d9e8c539de5fe8110ba85a2489473bde4
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parents: 4
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95
4
4c773948a490 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 4a0b08beb8cdf51ab295a1f5f8c586d6bbaf5586
tduigou
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96 with open(params.taxid, 'w') as f:
4c773948a490 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 4a0b08beb8cdf51ab295a1f5f8c586d6bbaf5586
tduigou
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97 f.write('#ID\n')
4c773948a490 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 4a0b08beb8cdf51ab295a1f5f8c586d6bbaf5586
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98 f.write(f'{taxid}\n')
2
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99
52649039cf3f planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit d1f5bac36c249e0767ed0bb968a1f4b5843256e3
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100
1
e276119e73c8 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
tduigou
parents:
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101 if __name__ == "__main__":
e276119e73c8 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
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102 entry_point()