Mercurial > repos > bgruening > uniprot_rest_interface

annotate uniprot.py @ 6:f806bb47aff6 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit f7a71c09b68d85a73a7ce761b4e64d5de29daee0
author bgruening
date Sun, 16 Sep 2018 13:40:52 -0400
parents 6e9fabe16b0c
children b1cc2c5bde0e
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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 = 'uploadlists/'
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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 = {
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28 'format': format,
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29 'from': 'ACC+ID',
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30 'to': 'ACC'
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31 }
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33 responses = [requests.post(url + tool, data=data, files={'file': ' '.join(_)}) for _ in queries]
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34 page = ''.join(response.text for response in responses)
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35 return page
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38 def _map(query, f, t, format='tab'):
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39 """ _map is not meant for use with the python interface, use `map` instead
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40 """
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41 tool = 'uploadlists/'
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43 data = {
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44 'from': f,
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45 'to': t,
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46 'format': format,
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47 'query': query
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48 }
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49 response = requests.post(url + tool, data=data)
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50 page = response.text
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51 return page
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54 if __name__ == '__main__':
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55 parser = argparse.ArgumentParser(description='retrieve uniprot mapping')
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56 subparsers = parser.add_subparsers(dest='tool')
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58 mapping = subparsers.add_parser('map')
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59 mapping.add_argument('f', help='from')
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60 mapping.add_argument('t', help='to')
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61 mapping.add_argument('inp', nargs='?', type=argparse.FileType('r'),
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62 default=sys.stdin, help='input file (default: stdin)')
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63 mapping.add_argument('out', nargs='?', type=argparse.FileType('w'),
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64 default=sys.stdout, help='output file (default: stdout)')
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65 mapping.add_argument('--format', default='tab', help='output format')
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67 retrieve = subparsers.add_parser('retrieve')
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68 retrieve.add_argument('inp', metavar='in', nargs='?', type=argparse.FileType('r'),
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69 default=sys.stdin, help='input file (default: stdin)')
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70 retrieve.add_argument('out', nargs='?', type=argparse.FileType('w'),
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71 default=sys.stdout, help='output file (default: stdout)')
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72 retrieve.add_argument('-f', '--format', help='specify output format', default='txt')
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74 args = parser.parse_args()
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75 query = args.inp.read()
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77 if args.tool == 'map':
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78 args.out.write(_map(query, args.f, args.t, args.format))
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80 elif args.tool == 'retrieve':
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81 args.out.write(_retrieve(query, format=args.format))