Mercurial > repos > galaxyp > uniprotxml_downloader

annotate uniprotxml_downloader.py @ 5:7be8e30d536f draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 0c5222345ace5054df44da29cab278f4a02e2b41
author galaxyp
date Thu, 06 Jul 2023 21:15:29 +0000
parents e1ffb00a0436
children c4a0f3badafe
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1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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1 #!/usr/bin/env python
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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2 """
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3 #
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4 #------------------------------------------------------------------------------
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5 # University of Minnesota
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6 # Copyright 2016, Regents of the University of Minnesota
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7 #------------------------------------------------------------------------------
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8 # Author:
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9 #
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10 # James E Johnson
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11 #
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12 #------------------------------------------------------------------------------
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13 """
3
b0abab8e78eb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 62afd9de6db50f4314e49d9f24881b6d3778a0a5"
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14 import optparse
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15 import re
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16 import sys
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17 from urllib import parse
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19 import requests
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20 from requests.adapters import HTTPAdapter
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21 from requests.packages.urllib3.util.retry import Retry
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23 DEFAULT_TIMEOUT = 5 # seconds
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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 __main__():
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48 # Parse Command Line
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49 parser = optparse.OptionParser()
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50 parser.add_option('-i', '--input', dest='input', default=None, help='Tabular file containing a column of search search_ids')
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51 parser.add_option('-c', '--column', dest='column', type='int', default=0, help='The column (zero-based) in the tabular file that contains search search_ids')
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52 parser.add_option('-s', '--search-id', dest='search_id', action='append', default=[], help='ID to search in Uniprot')
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53 parser.add_option('-r', '--reviewed', dest='reviewed', help='Only uniprot reviewed entries')
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54 parser.add_option('-f', '--format', dest='format', choices=['xml', 'fasta'], default='xml', help='output format')
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55 parser.add_option('-k', '--field', dest='field', choices=['taxonomy_name', 'taxonomy_id', 'accession'], default='taxonomy_name', help='query field')
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56 parser.add_option('-o', '--output', dest='output', help='file path for the downloaded uniprot xml')
0
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57 parser.add_option('-d', '--debug', dest='debug', action='store_true', default=False, help='Turn on wrapper debugging to stderr')
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58 (options, args) = parser.parse_args()
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59 search_ids = set(options.search_id)
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60 if options.input:
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61 with open(options.input, 'r') as inputFile:
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62 for linenum, line in enumerate(inputFile):
1
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63 if line.startswith('#'):
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64 continue
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65 fields = line.rstrip('\r\n').split('\t')
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66 if len(fields) > abs(options.column):
5
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67 search_id = fields[options.column].strip()
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68 if search_id:
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69 search_ids.add(search_id)
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70 search_queries = [f'{options.field}:"{search_id}"' for search_id in search_ids]
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71 search_query = ' OR '.join(search_queries)
0
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72 if options.output:
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73 dest_path = options.output
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74 else:
5
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75 dest_path = "uniprot_%s.xml" % '_'.join(search_ids)
0
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76 reviewed = " reviewed:%s" % options.reviewed if options.reviewed else ''
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77 try:
4
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78 url = 'https://rest.uniprot.org/uniprotkb/stream'
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79 query = "%s%s" % (search_query, reviewed)
4
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80 params = {'query': query, 'format': options.format}
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81 if options.debug:
3
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82 print("%s ? %s" % (url, params), file=sys.stderr)
b0abab8e78eb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 62afd9de6db50f4314e49d9f24881b6d3778a0a5"
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83 data = parse.urlencode(params)
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84 print(f"Retrieving: {url}?{data}")
3
b0abab8e78eb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 62afd9de6db50f4314e49d9f24881b6d3778a0a5"
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85 adapter = TimeoutHTTPAdapter(max_retries=retry_strategy)
4
e1ffb00a0436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit ba0d41c2dc0dbc0a0d3d200f51e67c6598c7e4e9
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86
3
b0abab8e78eb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 62afd9de6db50f4314e49d9f24881b6d3778a0a5"
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87 http = requests.Session()
b0abab8e78eb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 62afd9de6db50f4314e49d9f24881b6d3778a0a5"
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88 http.mount("https://", adapter)
4
e1ffb00a0436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit ba0d41c2dc0dbc0a0d3d200f51e67c6598c7e4e9
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89 response = http.get(url, params=params)
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b0abab8e78eb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 62afd9de6db50f4314e49d9f24881b6d3778a0a5"
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90 http.close()
4
e1ffb00a0436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit ba0d41c2dc0dbc0a0d3d200f51e67c6598c7e4e9
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91
e1ffb00a0436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit ba0d41c2dc0dbc0a0d3d200f51e67c6598c7e4e9
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92 if response.status_code != 200:
e1ffb00a0436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit ba0d41c2dc0dbc0a0d3d200f51e67c6598c7e4e9
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93 exit(f"Request failed with status code {response.status_code}:\n{response.text}")
e1ffb00a0436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit ba0d41c2dc0dbc0a0d3d200f51e67c6598c7e4e9
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94
3
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95 with open(dest_path, 'w') as fh:
b0abab8e78eb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 62afd9de6db50f4314e49d9f24881b6d3778a0a5"
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96 fh.write(response.text)
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97
1
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98 if options.format == 'xml':
0
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99 with open(dest_path, 'r') as contents:
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100 while True:
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101 line = contents.readline()
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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102 if options.debug:
3
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103 print(line, file=sys.stderr)
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104 if line is None:
0
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105 break
1
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106 if line.startswith('<?'):
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107 continue
0
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108 # pattern match <root or <ns:root for any ns string
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109 pattern = r'^<(\w*:)?uniprot'
0
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110 if re.match(pattern, line):
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111 break
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112 else:
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113 print("failed: Not a uniprot xml file", file=sys.stderr)
0
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114 exit(1)
5
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115 print("Search IDs:%s" % search_ids, file=sys.stdout)
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116 if 'X-UniProt-Release' in response.headers:
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117 print("UniProt-Release:%s" % response.headers['X-UniProt-Release'], file=sys.stdout)
b0abab8e78eb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 62afd9de6db50f4314e49d9f24881b6d3778a0a5"
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118 if 'X-Total-Results' in response.headers:
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119 print("Entries:%s" % response.headers['X-Total-Results'], file=sys.stdout)
b0abab8e78eb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 62afd9de6db50f4314e49d9f24881b6d3778a0a5"
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120 except Exception as e:
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121 exit("%s" % e)
0
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122
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123
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124 if __name__ == "__main__":
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125 __main__()