Mercurial > repos > galaxyp > uniprotxml_downloader

annotate uniprotxml_downloader.py @ 6:c4a0f3badafe draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
author galaxyp
date Wed, 11 Dec 2024 13:34:46 +0000
parents 7be8e30d536f
children
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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
0
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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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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b0abab8e78eb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 62afd9de6db50f4314e49d9f24881b6d3778a0a5"
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19 import requests
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c4a0f3badafe planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
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20 from requests.adapters import HTTPAdapter, Retry
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23 def __main__():
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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24 # Parse Command Line
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25 parser = optparse.OptionParser()
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26 parser.add_option('-i', '--input', dest='input', default=None, help='Tabular file containing a column of search search_ids')
7be8e30d536f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 0c5222345ace5054df44da29cab278f4a02e2b41
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27 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')
7be8e30d536f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 0c5222345ace5054df44da29cab278f4a02e2b41
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28 parser.add_option('-s', '--search-id', dest='search_id', action='append', default=[], help='ID to search in Uniprot')
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29 parser.add_option('-r', '--reviewed', dest='reviewed', help='Only uniprot reviewed entries')
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30 parser.add_option('-f', '--format', dest='format', choices=['xml', 'fasta', 'tsv'], default='xml', help='output format')
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31 parser.add_option('-k', '--field', dest='field', choices=['taxonomy_name', 'taxonomy_id', 'accession'], default='taxonomy_name', help='query field')
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32 parser.add_option('-o', '--output', dest='output', help='file path for the downloaded uniprot xml')
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33 parser.add_option('--output_columns', dest='output_columns', help='Columns to include in output (tsv)')
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34 parser.add_option('-d', '--debug', dest='debug', action='store_true', default=False, help='Turn on wrapper debugging to stderr')
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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35 (options, args) = parser.parse_args()
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7be8e30d536f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 0c5222345ace5054df44da29cab278f4a02e2b41
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36 search_ids = set(options.search_id)
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37 if options.input:
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38 with open(options.input, 'r') as inputFile:
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39 for linenum, line in enumerate(inputFile):
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40 if line.startswith('#'):
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41 continue
7fd760c99ec5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
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42 fields = line.rstrip('\r\n').split('\t')
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43 if len(fields) > abs(options.column):
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44 search_id = fields[options.column].strip()
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45 if search_id:
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46 search_ids.add(search_id)
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47 search_queries = [f'{options.field}:"{search_id}"' for search_id in search_ids]
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48 search_query = ' OR '.join(search_queries)
0
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49 if options.output:
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50 dest_path = options.output
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51 else:
5
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52 dest_path = "uniprot_%s.xml" % '_'.join(search_ids)
0
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53 reviewed = " reviewed:%s" % options.reviewed if options.reviewed else ''
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54 try:
6
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55 re_next_link = re.compile(r'<(.+)>; rel="next"')
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56 retries = Retry(total=5, backoff_factor=0.25, status_forcelist=[500, 502, 503, 504])
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57 session = requests.Session()
c4a0f3badafe planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
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58 session.mount("https://", HTTPAdapter(max_retries=retries))
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59
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60 def get_next_link(headers):
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61 if "Link" in headers:
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62 match = re_next_link.match(headers["Link"])
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63 if match:
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64 return match.group(1)
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65
6
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66 def get_batch(batch_url):
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67 while batch_url:
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68 response = session.get(batch_url)
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69 response.raise_for_status()
c4a0f3badafe planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
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70 total = response.headers["x-total-results"]
c4a0f3badafe planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
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71 release = response.headers["x-uniprot-release"]
c4a0f3badafe planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
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72 yield response, total, release
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73 batch_url = get_next_link(response.headers)
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74
6
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75 params = {'size': 500, 'format': options.format, 'query': search_query + reviewed}
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76 if options.output_columns:
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77 params['fields'] = options.output_columns
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78 url = f'https://rest.uniprot.org/uniprotkb/search?{parse.urlencode(params)}'
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79 print(f"Downloading from:{url}")
4
e1ffb00a0436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit ba0d41c2dc0dbc0a0d3d200f51e67c6598c7e4e9
galaxyp
parents: 3
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80
3
b0abab8e78eb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 62afd9de6db50f4314e49d9f24881b6d3778a0a5"
galaxyp
parents: 2
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81 with open(dest_path, 'w') as fh:
6
c4a0f3badafe planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 5
diff changeset
82 for batch, total, release in get_batch(url):
c4a0f3badafe planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
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83 fh.write(batch.text)
4
e1ffb00a0436 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit ba0d41c2dc0dbc0a0d3d200f51e67c6598c7e4e9
galaxyp
parents: 3
diff changeset
84
1
7fd760c99ec5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
parents: 0
diff changeset
85 if options.format == 'xml':
0
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
86 with open(dest_path, 'r') as contents:
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
87 while True:
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
88 line = contents.readline()
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
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diff changeset
89 if options.debug:
3
b0abab8e78eb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 62afd9de6db50f4314e49d9f24881b6d3778a0a5"
galaxyp
parents: 2
diff changeset
90 print(line, file=sys.stderr)
1
7fd760c99ec5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
parents: 0
diff changeset
91 if line is None:
0
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
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92 break
1
7fd760c99ec5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
parents: 0
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93 if line.startswith('<?'):
7fd760c99ec5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
parents: 0
diff changeset
94 continue
0
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
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diff changeset
95 # pattern match <root or <ns:root for any ns string
3
b0abab8e78eb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 62afd9de6db50f4314e49d9f24881b6d3778a0a5"
galaxyp
parents: 2
diff changeset
96 pattern = r'^<(\w*:)?uniprot'
0
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
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diff changeset
97 if re.match(pattern, line):
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
98 break
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
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diff changeset
99 else:
3
b0abab8e78eb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 62afd9de6db50f4314e49d9f24881b6d3778a0a5"
galaxyp
parents: 2
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100 print("failed: Not a uniprot xml file", file=sys.stderr)
0
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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parents:
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101 exit(1)
6
c4a0f3badafe planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 5
diff changeset
102 print(f"Search IDs:{search_ids}")
c4a0f3badafe planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 5
diff changeset
103 print(f"UniProt-Release:{release}")
c4a0f3badafe planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 91705a9789b30878a55d1044c654e39a7726cf60
galaxyp
parents: 5
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104 print(f"Entries:{total}")
3
b0abab8e78eb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 62afd9de6db50f4314e49d9f24881b6d3778a0a5"
galaxyp
parents: 2
diff changeset
105 except Exception as e:
b0abab8e78eb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 62afd9de6db50f4314e49d9f24881b6d3778a0a5"
galaxyp
parents: 2
diff changeset
106 exit("%s" % e)
0
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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107
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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108
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
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109 if __name__ == "__main__":
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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110 __main__()