Mercurial > repos > bgruening > uniprot_rest_interface

annotate uniprot.py @ 4:ed07130fb07c draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit 64c4336509437b9772df82a8b89046c9044b1ff5
author bgruening
date Tue, 14 Aug 2018 16:37:11 -0400
parents 357dc1f016f5
children 6e9fabe16b0c
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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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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 import argparse
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12 import sys
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14 import requests
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16 url = 'https://www.uniprot.org/'
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19 def _retrieve(query, format='txt'):
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20 """_retrieve is not meant for use with the python interface, use `retrieve`
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21 instead"""
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22 tool = 'batch/'
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24 query = list(set(query.split('\n')))
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25 queries = [query[i:i+100] for i in range(0, len(query), 100)]
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27 data = {'format': format}
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29 responses = [requests.post(url + tool, data=data, files={'file': ' '.join(_)}) for _ in queries]
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30 page = ''.join(response.text for response in responses)
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31 return page
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34 def _map(query, f, t, format='tab'):
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35 """ _map is not meant for use with the python interface, use `map` instead
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36 """
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37 tool = 'mapping/'
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39 data = {
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40 'from': f,
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41 'to': t,
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42 'format': format,
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43 'query': query
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44 }
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45 response = requests.post(url + tool, data=data)
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46 page = response.text
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47 return page
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50 if __name__ == '__main__':
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51 parser = argparse.ArgumentParser(description='retrieve uniprot mapping')
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52 subparsers = parser.add_subparsers(dest='tool')
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54 mapping = subparsers.add_parser('map')
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55 mapping.add_argument('f', help='from')
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56 mapping.add_argument('t', help='to')
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57 mapping.add_argument('inp', nargs='?', type=argparse.FileType('r'),
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58 default=sys.stdin, help='input file (default: stdin)')
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59 mapping.add_argument('out', nargs='?', type=argparse.FileType('w'),
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60 default=sys.stdout, help='output file (default: stdout)')
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61 mapping.add_argument('--format', default='tab', help='output format')
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63 retrieve = subparsers.add_parser('retrieve')
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64 retrieve.add_argument('inp', metavar='in', nargs='?', type=argparse.FileType('r'),
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65 default=sys.stdin, help='input file (default: stdin)')
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66 retrieve.add_argument('out', nargs='?', type=argparse.FileType('w'),
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67 default=sys.stdout, help='output file (default: stdout)')
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68 retrieve.add_argument('-f', '--format', help='specify output format', default='txt')
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70 args = parser.parse_args()
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71 query = args.inp.read()
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73 if args.tool == 'map':
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74 args.out.write(_map(query, args.f, args.t, args.format))
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76 elif args.tool == 'retrieve':
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77 args.out.write(_retrieve(query, format=args.format))