Mercurial > repos > bgruening > uniprot_rest_interface

annotate uniprot.py @ 8:af5eccf83605 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit c7bbf2c24b4ec988b287a474ece740456f12d9bc
author bgruening
date Mon, 21 Nov 2022 22:02:41 +0000
parents bfdc6a7ffd3a
children 468c71dac78a
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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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11 rewitten using inspiration form: https://findwork.dev/blog/advanced-usage-python-requests-timeouts-retries-hooks/
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12 """
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13 import argparse
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14 import sys
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16 import requests
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17 from requests.adapters import HTTPAdapter
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18 from requests.packages.urllib3.util.retry import Retry
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21 DEFAULT_TIMEOUT = 5 # seconds
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22 URL = 'https://legacy.uniprot.org/'
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24 retry_strategy = Retry(
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25 total=5,
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26 backoff_factor=2,
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27 status_forcelist=[429, 500, 502, 503, 504],
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28 allowed_methods=["HEAD", "GET", "OPTIONS", "POST"]
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29 )
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32 class TimeoutHTTPAdapter(HTTPAdapter):
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33 def __init__(self, *args, **kwargs):
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34 self.timeout = DEFAULT_TIMEOUT
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35 if "timeout" in kwargs:
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36 self.timeout = kwargs["timeout"]
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37 del kwargs["timeout"]
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38 super().__init__(*args, **kwargs)
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39
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40 def send(self, request, **kwargs):
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41 timeout = kwargs.get("timeout")
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42 if timeout is None:
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43 kwargs["timeout"] = self.timeout
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44 return super().send(request, **kwargs)
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46
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47 def _map(query, f, t, format='tab', chunk_size=100):
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48 """ _map is not meant for use with the python interface, use `map` instead
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49 """
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50 tool = 'uploadlists/'
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51 data = {'format': format, 'from': f, 'to': t}
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53 req = []
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54 for i in range(0, len(query), chunk_size):
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55 q = query[i:i + chunk_size]
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56 req.append(dict([("url", URL + tool),
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57 ('data', data),
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58 ("files", {'file': ' '.join(q)})]))
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59 return req
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60 response = requests.post(URL + tool, data=data)
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61 response.raise_for_status()
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62 page = response.text
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63 if "The service is temporarily unavailable" in page:
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64 exit("The UNIPROT service is temporarily unavailable. Please try again later.")
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65 return page
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68 if __name__ == '__main__':
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69 parser = argparse.ArgumentParser(description='retrieve uniprot mapping')
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70 subparsers = parser.add_subparsers(dest='tool')
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72 mapping = subparsers.add_parser('map')
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73 mapping.add_argument('f', help='from')
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74 mapping.add_argument('t', help='to')
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75 mapping.add_argument('inp', nargs='?', type=argparse.FileType('r'),
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76 default=sys.stdin, help='input file (default: stdin)')
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77 mapping.add_argument('out', nargs='?', type=argparse.FileType('w'),
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78 default=sys.stdout, help='output file (default: stdout)')
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79 mapping.add_argument('--format', default='tab', help='output format')
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81 retrieve = subparsers.add_parser('retrieve')
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82 retrieve.add_argument('inp', metavar='in', nargs='?', type=argparse.FileType('r'),
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83 default=sys.stdin, help='input file (default: stdin)')
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84 retrieve.add_argument('out', nargs='?', type=argparse.FileType('w'),
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85 default=sys.stdout, help='output file (default: stdout)')
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86 retrieve.add_argument('-f', '--format', help='specify output format', default='txt')
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87
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88 args = parser.parse_args()
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89
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90 # get the IDs from the file as sorted list
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91 # (sorted is convenient for testing)
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92 query = set()
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93 for line in args.inp:
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94 query.add(line.strip())
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95 query = sorted(query)
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96
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97 if args.tool == 'map':
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98 pload = _map(query, args.f, args.t, chunk_size=100)
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99 elif args.tool == 'retrieve':
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100 pload = _map(query, 'ACC+ID', 'ACC', args.format, chunk_size=100)
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101
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102 adapter = TimeoutHTTPAdapter(max_retries=retry_strategy)
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103 http = requests.Session()
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104 http.mount("https://", adapter)
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105 for i, p in enumerate(pload):
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106 response = http.post(**p)
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107 args.out.write(response.text)
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108 http.close()