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