Mercurial > repos > bgruening > uniprot_rest_interface

comparison uniprot.py @ 0:ddcc8591ddfb draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit 2b8ad1bbfe098129ae32cd8311a755dff58ae97b-dirty
author bgruening
date Fri, 09 Oct 2015 16:39:30 -0400
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children 357dc1f016f5
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-1:000000000000 0:ddcc8591ddfb
1 #!/usr/bin/env python
2 """
3 uniprot python interface
4 to access the uniprot database
5
6 Based on work from Jan Rudolph: https://github.com/jdrudolph/uniprot
7 available services:
8 map
9 retrieve
10 """
11
12 import requests
13 import sys, argparse
14
15 url = 'http://www.uniprot.org/'
16
17 def _retrieve(query, format='txt'):
18 """_retrieve is not meant for use with the python interface, use `retrieve`
19 instead"""
20 tool = 'batch/'
21
22 query = list(set(query.split('\n')))
23 queries = [query[i:i+100] for i in range(0, len(query), 100)]
24
25 data = {'format':format}
26
27 responses = [requests.post(url + tool, data=data, files={'file':' '.join(query)}) for query in queries]
28 page = ''.join([response.text for response in responses])
29 return page
30
31 def retrieve(ids, format='txt'):
32 """ request entries by uniprot acc using batch retrieval
33
34 Args:
35 query: list of ids to retrieve
36 format: txt by default
37
38 Help:
39 possible formats:
40 txt, xml, rdf, fasta, gff"""
41 if type(ids) is not list:
42 ids = [ids]
43 return _retrieve(' '.join(ids), format)
44
45 def _map(query, f, t, format='tab'):
46 """ _map is not meant for use with the python interface, use `map` instead
47 """
48 tool = 'mapping/'
49
50 data = {
51 'from':f,
52 'to':t,
53 'format':format,
54 'query': query
55 }
56 response = requests.post(url + tool, data=data)
57 page = response.text
58 return page
59
60 def map(ids, f, t, format='tab'):
61 """ map a list of ids from one format onto another using uniprots mapping api
62
63 Args:
64 query: id or list of ids to be mapped
65 f: from ACC | P_ENTREZGENEID | ...
66 t: to ...
67 format: tab by default
68
69 Help:
70 for a list of all possible mappings visit
71 'http://www.uniprot.org/faq/28'
72 """
73 if type(ids) is not list:
74 ids = [ids]
75 page = _map(' '.join(ids), f, t, format)
76 result = dict()
77 for row in page.splitlines()[1:]:
78 key, value = row.split('\t')
79 if key in result:
80 result[key].add(value)
81 else:
82 result[key] = set([value])
83 return result
84
85 if __name__ == '__main__':
86 import argparse
87 import sys
88
89 parser = argparse.ArgumentParser(description='retrieve uniprot mapping')
90 subparsers = parser.add_subparsers(dest='tool')
91
92 mapping = subparsers.add_parser('map')
93 mapping.add_argument('f', help='from')
94 mapping.add_argument('t', help='to')
95 mapping.add_argument('inp', nargs='?', type=argparse.FileType('r'),
96 default=sys.stdin, help='input file (default: stdin)')
97 mapping.add_argument('out', nargs='?', type=argparse.FileType('w'),
98 default=sys.stdout, help='output file (default: stdout)')
99 mapping.add_argument('--format', default='tab', help='output format')
100
101 retrieve = subparsers.add_parser('retrieve')
102 retrieve.add_argument('inp', metavar = 'in', nargs='?', type=argparse.FileType('r'),
103 default=sys.stdin, help='input file (default: stdin)')
104 retrieve.add_argument('out', nargs='?', type=argparse.FileType('w'),
105 default=sys.stdout, help='output file (default: stdout)')
106 retrieve.add_argument('-f', '--format', help='specify output format', default='txt')
107
108 args = parser.parse_args()
109 query = args.inp.read()
110
111 if args.tool == 'map':
112 args.out.write(_map(query, args.f, args.t, args.format))
113
114 elif args.tool == 'retrieve':
115 args.out.write(_retrieve(query, format=args.format))
116
117