Mercurial > repos > tduigou > get_sbml_model

comparison 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
comparison
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6:9b5947d48192 7:8dc4d3964ab5
9 parser = ArgumentParser('Returns cell informations') 9 parser = ArgumentParser('Returns cell informations')
10 parser.add_argument( 10 parser.add_argument(
11 'infile', 11 'infile',
12 type=str, 12 type=str,
13 help='SBML input file (xml)' 13 help='SBML input file (xml)'
14 )
15 # argument to tag file from BiGG
16 parser.add_argument(
17 '--bigg',
18 action='store_true',
19 help='Tag file from BiGG'
14 ) 20 )
15 parser.add_argument( 21 parser.add_argument(
16 '--comp', 22 '--comp',
17 type=str, 23 type=str,
18 help='Path to store cell compartments' 24 help='Path to store cell compartments'
50 for rxn in reactions: 56 for rxn in reactions:
51 if 'biomass' in rxn.getId().lower(): 57 if 'biomass' in rxn.getId().lower():
52 f.write(f'{rxn.getId()}\n') 58 f.write(f'{rxn.getId()}\n')
53 59
54 if params.taxid: 60 if params.taxid:
55 # Extended Name 61 hostname = ''
56 server = 'http://bigg.ucsd.edu/api/v2/models/' 62
57 ext = params.hostid 63 # Model from BiGG
58 r = r_get(server+ext, headers={ "Content-Type" : "application/json"}) 64 if params.bigg:
59 if not r.ok: 65 # Extended Name
60 print(f"Warning: unable to retrieve host name for id {params.hostid}") 66 server = 'http://bigg.ucsd.edu/api/v2/models/'
61 else: 67 ext = params.hostid
62 try:
63 hostname = r.json()["organism"]
64 except KeyError:
65 print(f"Warning: unable to retrieve host name for id {params.hostid}")
66 hostname = ''
67 if not hostname:
68 taxid = ''
69 else:
70 # TAXON ID
71 server = 'https://rest.ensembl.org'
72 ext = f'/taxonomy/id/{hostname}?'
73 r = r_get(server+ext, headers={ "Content-Type" : "application/json"}) 68 r = r_get(server+ext, headers={ "Content-Type" : "application/json"})
74 if not r.ok: 69 if not r.ok:
75 print(f"Warning: unable to retrieve taxonomy ID for host organism {hostname}") 70 print(f"Warning: unable to retrieve host name for id {params.hostid}")
76 else: 71 else:
77 try: 72 try:
78 taxid = r.json()["id"] 73 hostname = r.json()["organism"]
79 except KeyError: 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:
80 print(f"Warning: unable to retrieve taxonomy ID for host organism {hostname}") 84 print(f"Warning: unable to retrieve taxonomy ID for host organism {hostname}")
81 taxid = '' 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
82 with open(params.taxid, 'w') as f: 96 with open(params.taxid, 'w') as f:
83 f.write('#ID\n') 97 f.write('#ID\n')
84 f.write(f'{taxid}\n') 98 f.write(f'{taxid}\n')
85 99
86 100