Mercurial > repos > tduigou > get_sbml_model

comparison 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
comparison
equal deleted inserted replaced
7:33be348bf9d6 8:06366f104f78
3 readSBMLFromFile 3 readSBMLFromFile
4 ) 4 )
5 from requests import get as r_get 5 from requests import get as r_get
6 6
7 7
8 def entry_point(): 8 def get_biomass_rxn(sbml_doc):
9 '''
10 Returns the biomass reaction of the model
11
12 Parameters
13 ----------
14 sbml_doc: libsbml.SBMLDocument
15 SBML model
16
17 Returns
18 -------
19 biomass_rxn: libsbml.Reaction
20 Biomass reaction
21 '''
22 reactions = sbml_doc.getModel().getListOfReactions()
23 # Search for 'biomass' keyword in reaction name
24 for rxn in reactions:
25 if 'biomass' in rxn.getName().lower():
26 return rxn
27 # Search for 'biomass' keyword in products
28 # AND not in reactants
29 for rxn in reactions:
30 in_reactants = False
31 for reac in rxn.getListOfReactants():
32 if 'biomass' in reac.getSpecies().lower():
33 in_reactants = True
34 break
35 if not in_reactants:
36 for prod in rxn.getListOfProducts():
37 if 'biomass' in prod.getSpecies().lower():
38 return rxn
39 return None
40
41
42 def get_taxon_id(hostid):
43 '''
44 Returns the taxonomy ID of the host organism
45
46 Parameters
47 ----------
48 hostid: str
49 Extended name of the host organism
50
51 Returns
52 -------
53 taxid: str
54 Taxonomy ID of the host organism
55 '''
56 taxid = get_taxon_id(hostid)
57 hostname = ''
58 # Extended Name
59 server = 'http://bigg.ucsd.edu/api/v2/models/'
60 ext = hostid
61 r = r_get(server+ext, headers={ "Content-Type" : "application/json"})
62 if not r.ok:
63 print(f"Warning: unable to retrieve host name for id {hostid}")
64 else:
65 try:
66 hostname = r.json()["organism"]
67 except KeyError:
68 print(f"Warning: unable to retrieve host name for id {hostid}")
69 if not hostname:
70 taxid = ''
71 else:
72 # TAXON ID
73 server = 'https://rest.ensembl.org'
74 ext = f'/taxonomy/id/{hostname}?'
75 r = r_get(server+ext, headers={ "Content-Type" : "application/json"})
76 if not r.ok:
77 print(f"Warning: unable to retrieve taxonomy ID for host organism {hostname}")
78 else:
79 try:
80 taxid = r.json()["id"]
81 except KeyError:
82 print(f"Warning: unable to retrieve taxonomy ID for host organism {hostname}")
83 taxid = ''
84 return taxid
85
86
87 def args():
9 parser = ArgumentParser('Returns cell informations') 88 parser = ArgumentParser('Returns cell informations')
10 parser.add_argument( 89 parser.add_argument(
11 'infile', 90 'infile',
12 type=str, 91 type=str,
13 help='SBML input file (xml)' 92 help='SBML input file (xml)'
27 '--biomass', 106 '--biomass',
28 type=str, 107 type=str,
29 help='Path to store biomass reaction ID' 108 help='Path to store biomass reaction ID'
30 ) 109 )
31 parser.add_argument( 110 parser.add_argument(
111 '--biomass-id',
112 type=str,
113 help='ID of biomass reaction'
114 )
115 parser.add_argument(
32 '--hostid', 116 '--hostid',
33 type=str, 117 type=str,
34 help='Extended name of the host organism' 118 help='Extended name of the host organism'
35 ) 119 )
36 parser.add_argument( 120 parser.add_argument(
37 '--taxid', 121 '--taxid',
38 type=str, 122 type=str,
39 help='Path to store host taxonomy ID' 123 help='Path to store host taxonomy ID'
40 ) 124 )
41 params = parser.parse_args() 125 params = parser.parse_args()
126 return params
127
128
129 def entry_point():
130
131 params = args()
42 132
43 sbml_doc = readSBMLFromFile(params.infile) 133 sbml_doc = readSBMLFromFile(params.infile)
44 134
135 compartments = sbml_doc.getModel().getListOfCompartments()
136 comp_str = ''
137 for comp in compartments:
138 comp_str += f'{comp.getId()}\t{comp.getName()}\n'
45 if params.comp: 139 if params.comp:
46 compartments = sbml_doc.getModel().getListOfCompartments()
47 with open(params.comp, 'w') as f: 140 with open(params.comp, 'w') as f:
48 f.write('#ID\tNAME\n') 141 f.write('#ID\tNAME\n')
49 for comp in compartments: 142 f.write(comp_str)
50 f.write(f'{comp.getId()}\t{comp.getName()}\n') 143 else:
144 print('Compartments:')
145 for comp in compartments:
146 print(f'{comp.getId()}\t{comp.getName()}'.replace('\n', ' | '))
51 147
148 if params.biomass_id:
149 biomass_rxn = sbml_doc.getModel().getReaction(params.biomass_id)
150 else:
151 biomass_rxn = get_biomass_rxn(sbml_doc)
152 if not biomass_rxn:
153 print('Warning: unable to retrieve biomass reaction')
154 biomass_id = ''
155 else:
156 biomass_id = biomass_rxn.getId()
52 if params.biomass: 157 if params.biomass:
53 reactions = sbml_doc.getModel().getListOfReactions()
54 with open(params.biomass, 'w') as f: 158 with open(params.biomass, 'w') as f:
55 f.write('#ID\n') 159 f.write('#ID\n')
56 for rxn in reactions: 160 f.write(f'{biomass_id}\n')
57 if 'biomass' in rxn.getId().lower(): 161 else:
58 f.write(f'{rxn.getId()}\n') 162 print(f'Biomass reaction ID: {biomass_id}')
163
164 # Model from BiGG
165 if params.bigg:
166 taxid = get_taxon_id(params.hostid)
167 # Model from user
168 else:
169 taxid = params.hostid
59 170
60 if params.taxid: 171 if params.taxid:
61 hostname = ''
62
63 # Model from BiGG
64 if params.bigg:
65 # Extended Name
66 server = 'http://bigg.ucsd.edu/api/v2/models/'
67 ext = params.hostid
68 r = r_get(server+ext, headers={ "Content-Type" : "application/json"})
69 if not r.ok:
70 print(f"Warning: unable to retrieve host name for id {params.hostid}")
71 else:
72 try:
73 hostname = r.json()["organism"]
74 except KeyError:
75 print(f"Warning: unable to retrieve host name for id {params.hostid}")
76 if not hostname:
77 taxid = ''
78 else:
79 # TAXON ID
80 server = 'https://rest.ensembl.org'
81 ext = f'/taxonomy/id/{hostname}?'
82 r = r_get(server+ext, headers={ "Content-Type" : "application/json"})
83 if not r.ok:
84 print(f"Warning: unable to retrieve taxonomy ID for host organism {hostname}")
85 else:
86 try:
87 taxid = r.json()["id"]
88 except KeyError:
89 print(f"Warning: unable to retrieve taxonomy ID for host organism {hostname}")
90 taxid = ''
91
92 # Model from user
93 else:
94 taxid = params.hostid
95
96 with open(params.taxid, 'w') as f: 172 with open(params.taxid, 'w') as f:
97 f.write('#ID\n') 173 f.write('#ID\n')
98 f.write(f'{taxid}\n') 174 f.write(f'{taxid}\n')
175 else:
176 print(f'Taxonomy ID: {taxid}')
99 177
100 178
101 if __name__ == "__main__": 179 if __name__ == "__main__":
102 entry_point() 180 entry_point()