Mercurial > repos > tduigou > get_sbml_model

annotate get_infos.py @ 8:06366f104f78 draft default tip

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planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit aa5a9ac47997d9c1718b9c7eaff1b83c63ac1d58
author tduigou
date Fri, 29 Sep 2023 09:05:17 +0000
parents 33be348bf9d6
children
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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
tduigou
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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
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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
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6
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7
8
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8 def get_biomass_rxn(sbml_doc):
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tduigou
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9 '''
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tduigou
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10 Returns the biomass reaction of the model
06366f104f78 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit aa5a9ac47997d9c1718b9c7eaff1b83c63ac1d58
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11
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12 Parameters
06366f104f78 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit aa5a9ac47997d9c1718b9c7eaff1b83c63ac1d58
tduigou
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13 ----------
06366f104f78 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit aa5a9ac47997d9c1718b9c7eaff1b83c63ac1d58
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14 sbml_doc: libsbml.SBMLDocument
06366f104f78 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit aa5a9ac47997d9c1718b9c7eaff1b83c63ac1d58
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15 SBML model
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16
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17 Returns
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18 -------
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19 biomass_rxn: libsbml.Reaction
06366f104f78 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit aa5a9ac47997d9c1718b9c7eaff1b83c63ac1d58
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20 Biomass reaction
06366f104f78 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit aa5a9ac47997d9c1718b9c7eaff1b83c63ac1d58
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21 '''
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22 reactions = sbml_doc.getModel().getListOfReactions()
06366f104f78 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit aa5a9ac47997d9c1718b9c7eaff1b83c63ac1d58
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23 # Search for 'biomass' keyword in reaction name
06366f104f78 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit aa5a9ac47997d9c1718b9c7eaff1b83c63ac1d58
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24 for rxn in reactions:
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25 if 'biomass' in rxn.getName().lower():
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26 return rxn
06366f104f78 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit aa5a9ac47997d9c1718b9c7eaff1b83c63ac1d58
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27 # Search for 'biomass' keyword in products
06366f104f78 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit aa5a9ac47997d9c1718b9c7eaff1b83c63ac1d58
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28 # AND not in reactants
06366f104f78 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit aa5a9ac47997d9c1718b9c7eaff1b83c63ac1d58
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29 for rxn in reactions:
06366f104f78 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit aa5a9ac47997d9c1718b9c7eaff1b83c63ac1d58
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30 in_reactants = False
06366f104f78 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit aa5a9ac47997d9c1718b9c7eaff1b83c63ac1d58
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31 for reac in rxn.getListOfReactants():
06366f104f78 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit aa5a9ac47997d9c1718b9c7eaff1b83c63ac1d58
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32 if 'biomass' in reac.getSpecies().lower():
06366f104f78 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit aa5a9ac47997d9c1718b9c7eaff1b83c63ac1d58
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33 in_reactants = True
06366f104f78 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit aa5a9ac47997d9c1718b9c7eaff1b83c63ac1d58
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34 break
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35 if not in_reactants:
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36 for prod in rxn.getListOfProducts():
06366f104f78 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit aa5a9ac47997d9c1718b9c7eaff1b83c63ac1d58
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37 if 'biomass' in prod.getSpecies().lower():
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38 return rxn
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39 return None
06366f104f78 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit aa5a9ac47997d9c1718b9c7eaff1b83c63ac1d58
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40
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41
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42 def get_taxon_id(hostid):
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43 '''
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44 Returns the taxonomy ID of the host organism
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45
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46 Parameters
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47 ----------
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48 hostid: str
06366f104f78 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit aa5a9ac47997d9c1718b9c7eaff1b83c63ac1d58
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49 Extended name of the host organism
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50
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51 Returns
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52 -------
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53 taxid: str
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54 Taxonomy ID of the host organism
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55 '''
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56 taxid = get_taxon_id(hostid)
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57 hostname = ''
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58 # Extended Name
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59 server = 'http://bigg.ucsd.edu/api/v2/models/'
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60 ext = hostid
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61 r = r_get(server+ext, headers={ "Content-Type" : "application/json"})
06366f104f78 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit aa5a9ac47997d9c1718b9c7eaff1b83c63ac1d58
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62 if not r.ok:
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63 print(f"Warning: unable to retrieve host name for id {hostid}")
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64 else:
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65 try:
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66 hostname = r.json()["organism"]
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67 except KeyError:
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68 print(f"Warning: unable to retrieve host name for id {hostid}")
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69 if not hostname:
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70 taxid = ''
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71 else:
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72 # TAXON ID
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73 server = 'https://rest.ensembl.org'
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74 ext = f'/taxonomy/id/{hostname}?'
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75 r = r_get(server+ext, headers={ "Content-Type" : "application/json"})
06366f104f78 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit aa5a9ac47997d9c1718b9c7eaff1b83c63ac1d58
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76 if not r.ok:
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77 print(f"Warning: unable to retrieve taxonomy ID for host organism {hostname}")
06366f104f78 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit aa5a9ac47997d9c1718b9c7eaff1b83c63ac1d58
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78 else:
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79 try:
06366f104f78 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit aa5a9ac47997d9c1718b9c7eaff1b83c63ac1d58
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80 taxid = r.json()["id"]
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81 except KeyError:
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82 print(f"Warning: unable to retrieve taxonomy ID for host organism {hostname}")
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83 taxid = ''
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84 return taxid
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85
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86
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87 def args():
1
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88 parser = ArgumentParser('Returns cell informations')
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89 parser.add_argument(
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90 'infile',
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91 type=str,
e276119e73c8 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
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92 help='SBML input file (xml)'
e276119e73c8 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
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93 )
7
33be348bf9d6 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 1a86e55d9e8c539de5fe8110ba85a2489473bde4
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94 # argument to tag file from BiGG
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95 parser.add_argument(
33be348bf9d6 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 1a86e55d9e8c539de5fe8110ba85a2489473bde4
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96 '--bigg',
33be348bf9d6 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 1a86e55d9e8c539de5fe8110ba85a2489473bde4
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97 action='store_true',
33be348bf9d6 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 1a86e55d9e8c539de5fe8110ba85a2489473bde4
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98 help='Tag file from BiGG'
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99 )
1
e276119e73c8 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
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100 parser.add_argument(
e276119e73c8 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
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101 '--comp',
e276119e73c8 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
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102 type=str,
e276119e73c8 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
tduigou
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103 help='Path to store cell compartments'
e276119e73c8 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
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104 )
e276119e73c8 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
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105 parser.add_argument(
e276119e73c8 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
tduigou
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106 '--biomass',
e276119e73c8 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
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107 type=str,
e276119e73c8 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
tduigou
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108 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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109 )
2
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110 parser.add_argument(
8
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111 '--biomass-id',
06366f104f78 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit aa5a9ac47997d9c1718b9c7eaff1b83c63ac1d58
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112 type=str,
06366f104f78 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit aa5a9ac47997d9c1718b9c7eaff1b83c63ac1d58
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113 help='ID of biomass reaction'
06366f104f78 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit aa5a9ac47997d9c1718b9c7eaff1b83c63ac1d58
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114 )
06366f104f78 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit aa5a9ac47997d9c1718b9c7eaff1b83c63ac1d58
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115 parser.add_argument(
2
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116 '--hostid',
52649039cf3f planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit d1f5bac36c249e0767ed0bb968a1f4b5843256e3
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117 type=str,
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118 help='Extended name of the host organism'
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119 )
52649039cf3f planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit d1f5bac36c249e0767ed0bb968a1f4b5843256e3
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120 parser.add_argument(
52649039cf3f planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit d1f5bac36c249e0767ed0bb968a1f4b5843256e3
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121 '--taxid',
52649039cf3f planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit d1f5bac36c249e0767ed0bb968a1f4b5843256e3
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122 type=str,
52649039cf3f planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit d1f5bac36c249e0767ed0bb968a1f4b5843256e3
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123 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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124 )
1
e276119e73c8 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
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125 params = parser.parse_args()
8
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126 return params
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127
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128
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129 def entry_point():
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130
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131 params = args()
1
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132
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133 sbml_doc = readSBMLFromFile(params.infile)
e276119e73c8 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
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134
8
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135 compartments = sbml_doc.getModel().getListOfCompartments()
06366f104f78 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit aa5a9ac47997d9c1718b9c7eaff1b83c63ac1d58
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136 comp_str = ''
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137 for comp in compartments:
06366f104f78 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit aa5a9ac47997d9c1718b9c7eaff1b83c63ac1d58
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138 comp_str += f'{comp.getId()}\t{comp.getName()}\n'
1
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139 if params.comp:
e276119e73c8 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3
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140 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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141 f.write('#ID\tNAME\n')
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142 f.write(comp_str)
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143 else:
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144 print('Compartments:')
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145 for comp in compartments:
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146 print(f'{comp.getId()}\t{comp.getName()}'.replace('\n', ' | '))
1
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147
8
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148 if params.biomass_id:
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149 biomass_rxn = sbml_doc.getModel().getReaction(params.biomass_id)
06366f104f78 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit aa5a9ac47997d9c1718b9c7eaff1b83c63ac1d58
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150 else:
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151 biomass_rxn = get_biomass_rxn(sbml_doc)
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152 if not biomass_rxn:
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153 print('Warning: unable to retrieve biomass reaction')
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154 biomass_id = ''
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155 else:
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156 biomass_id = biomass_rxn.getId()
1
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157 if params.biomass:
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158 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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159 f.write('#ID\n')
8
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160 f.write(f'{biomass_id}\n')
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161 else:
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162 print(f'Biomass reaction ID: {biomass_id}')
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163
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164 # Model from BiGG
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165 if params.bigg:
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166 taxid = get_taxon_id(params.hostid)
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167 # Model from user
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168 else:
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169 taxid = params.hostid
1
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170
2
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171 if params.taxid:
4
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172 with open(params.taxid, 'w') as f:
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173 f.write('#ID\n')
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174 f.write(f'{taxid}\n')
8
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175 else:
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176 print(f'Taxonomy ID: {taxid}')
2
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177
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178
1
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179 if __name__ == "__main__":
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180 entry_point()