Mercurial > repos > tduigou > get_sbml_model

comparison get_infos.py @ 9:6a2871e89352 draft default tip

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planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 537d7fefe58984b8f7ca66010153a2fdc35ddf4b
author tduigou
date Wed, 14 Feb 2024 15:25:38 +0000
parents 768ed7cc0978
children
comparison
equal deleted inserted replaced
8:768ed7cc0978 9:6a2871e89352
1 from argparse import ArgumentParser 1 from argparse import ArgumentParser
2 from libsbml import ( 2 from libsbml import (
3 readSBMLFromFile 3 readSBMLFromFile
4 ) 4 )
5 from requests import get as r_get 5 from taxonid import get_taxonid
6 6
7 7
8 def get_biomass_rxn(sbml_doc): 8 def get_biomass_rxn(sbml_doc):
9 ''' 9 '''
10 Returns the biomass reaction of the model 10 Returns the biomass reaction of the model
37 if 'biomass' in prod.getSpecies().lower(): 37 if 'biomass' in prod.getSpecies().lower():
38 return rxn 38 return rxn
39 return None 39 return None
40 40
41 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(): 42 def args():
88 parser = ArgumentParser('Returns cell informations') 43 parser = ArgumentParser('Returns cell informations')
89 parser.add_argument( 44 parser.add_argument(
90 'infile', 45 'infile',
91 type=str, 46 type=str,
111 '--biomass-id', 66 '--biomass-id',
112 type=str, 67 type=str,
113 help='ID of biomass reaction' 68 help='ID of biomass reaction'
114 ) 69 )
115 parser.add_argument( 70 parser.add_argument(
116 '--hostid', 71 '--hostname',
117 type=str, 72 type=str,
118 help='Extended name of the host organism' 73 help='Name of the host organism'
119 ) 74 )
120 parser.add_argument( 75 parser.add_argument(
121 '--taxid', 76 '--taxid',
122 type=str, 77 type=str,
123 help='Path to store host taxonomy ID' 78 help='Path to store host taxonomy ID'
124 ) 79 )
125 params = parser.parse_args() 80 params = parser.parse_args()
126 return params 81 return params
82
83
84 def get_taxon_id(hostid: str, bigg: bool):
85 '''
86 Returns the taxonomy ID of the host organism
87
88 Parameters
89 ----------
90 hostid: str
91 Extended name of the host organism or host ID if from BiGG
92 bigg: bool
93 True if the model is from BiGG
94
95 Returns
96 -------
97 taxid: str
98 Taxonomy ID of the host organism
99 '''
100 if not bigg:
101 return get_taxonid(hostid)
102
103 hostname = ''
104 # Extended Name
105 server = 'http://bigg.ucsd.edu/api/v2/models/'
106 ext = hostid
107 r = r_get(server+ext, headers={ "Content-Type" : "application/json"})
108 if not r.ok:
109 print(f"Warning: unable to retrieve host name for id {hostid}")
110 else:
111 try:
112 hostname = r.json()["organism"]
113 except KeyError:
114 print(f"Warning: unable to retrieve host name for id {hostid}")
115 if not hostname:
116 taxid = ''
117 else:
118 # TAXON ID
119 server = 'https://rest.ensembl.org'
120 ext = f'/taxonomy/id/{hostname}?'
121 r = r_get(server+ext, headers={ "Content-Type" : "application/json"})
122 if not r.ok:
123 print(f"Warning: unable to retrieve taxonomy ID for host organism {hostname}")
124 else:
125 try:
126 taxid = r.json()["id"]
127 except KeyError:
128 print(f"Warning: unable to retrieve taxonomy ID for host organism {hostname}")
129 taxid = ''
130 return taxid
127 131
128 132
129 def entry_point(): 133 def entry_point():
130 134
131 params = args() 135 params = args()
159 f.write('#ID\n') 163 f.write('#ID\n')
160 f.write(f'{biomass_id}\n') 164 f.write(f'{biomass_id}\n')
161 else: 165 else:
162 print(f'Biomass reaction ID: {biomass_id}') 166 print(f'Biomass reaction ID: {biomass_id}')
163 167
164 # Model from BiGG 168 taxid = get_taxon_id(params.hostname, params.bigg)
165 if params.bigg:
166 taxid = get_taxon_id(params.hostid)
167 # Model from user
168 else:
169 taxid = params.hostid
170 169
171 if params.taxid: 170 if params.taxid:
172 with open(params.taxid, 'w') as f: 171 with open(params.taxid, 'w') as f:
173 f.write('#ID\n') 172 f.write('#ID\n')
174 f.write(f'{taxid}\n') 173 f.write(f'{taxid}\n')