comparison uniprotxml_downloader.py @ 6:a371252a2cf6 draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 0c5222345ace5054df44da29cab278f4a02e2b41
author galaxyp
date Thu, 06 Jul 2023 21:15:39 +0000
parents 265c35540faa
children
comparison
equal deleted inserted replaced
5:265c35540faa 6:a371252a2cf6
45 45
46 46
47 def __main__(): 47 def __main__():
48 # Parse Command Line 48 # Parse Command Line
49 parser = optparse.OptionParser() 49 parser = optparse.OptionParser()
50 parser.add_option('-i', '--input', dest='input', default=None, help='Tabular file containing a column of NCBI Taxon IDs') 50 parser.add_option('-i', '--input', dest='input', default=None, help='Tabular file containing a column of search search_ids')
51 parser.add_option('-c', '--column', dest='column', type='int', default=0, help='The column (zero-based) in the tabular file that contains Taxon IDs') 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')
52 parser.add_option('-t', '--taxon', dest='taxon', action='append', default=[], help='NCBI taxon ID to download') 52 parser.add_option('-s', '--search-id', dest='search_id', action='append', default=[], help='ID to search in Uniprot')
53 parser.add_option('-r', '--reviewed', dest='reviewed', help='Only uniprot reviewed entries') 53 parser.add_option('-r', '--reviewed', dest='reviewed', help='Only uniprot reviewed entries')
54 parser.add_option('-f', '--format', dest='format', choices=['xml', 'fasta'], default='xml', help='output format') 54 parser.add_option('-f', '--format', dest='format', choices=['xml', 'fasta'], default='xml', help='output format')
55 parser.add_option('-k', '--field', dest='field', choices=['taxonomy_name', 'taxonomy_id'], default='taxonomy_name', help='query field') 55 parser.add_option('-k', '--field', dest='field', choices=['taxonomy_name', 'taxonomy_id', 'accession'], default='taxonomy_name', help='query field')
56 parser.add_option('-o', '--output', dest='output', help='file path for the downloaded uniprot xml') 56 parser.add_option('-o', '--output', dest='output', help='file path for the downloaded uniprot xml')
57 parser.add_option('-d', '--debug', dest='debug', action='store_true', default=False, help='Turn on wrapper debugging to stderr') 57 parser.add_option('-d', '--debug', dest='debug', action='store_true', default=False, help='Turn on wrapper debugging to stderr')
58 (options, args) = parser.parse_args() 58 (options, args) = parser.parse_args()
59 taxids = set(options.taxon) 59 search_ids = set(options.search_id)
60 if options.input: 60 if options.input:
61 with open(options.input, 'r') as inputFile: 61 with open(options.input, 'r') as inputFile:
62 for linenum, line in enumerate(inputFile): 62 for linenum, line in enumerate(inputFile):
63 if line.startswith('#'): 63 if line.startswith('#'):
64 continue 64 continue
65 fields = line.rstrip('\r\n').split('\t') 65 fields = line.rstrip('\r\n').split('\t')
66 if len(fields) > abs(options.column): 66 if len(fields) > abs(options.column):
67 taxid = fields[options.column].strip() 67 search_id = fields[options.column].strip()
68 if taxid: 68 if search_id:
69 taxids.add(taxid) 69 search_ids.add(search_id)
70 taxon_queries = [f'{options.field}:"{taxid}"' for taxid in taxids] 70 search_queries = [f'{options.field}:"{search_id}"' for search_id in search_ids]
71 taxon_query = ' OR '.join(taxon_queries) 71 search_query = ' OR '.join(search_queries)
72 if options.output: 72 if options.output:
73 dest_path = options.output 73 dest_path = options.output
74 else: 74 else:
75 dest_path = "uniprot_%s.xml" % '_'.join(taxids) 75 dest_path = "uniprot_%s.xml" % '_'.join(search_ids)
76 reviewed = " reviewed:%s" % options.reviewed if options.reviewed else '' 76 reviewed = " reviewed:%s" % options.reviewed if options.reviewed else ''
77 try: 77 try:
78 url = 'https://rest.uniprot.org/uniprotkb/stream' 78 url = 'https://rest.uniprot.org/uniprotkb/stream'
79 query = "%s%s" % (taxon_query, reviewed) 79 query = "%s%s" % (search_query, reviewed)
80 params = {'query': query, 'format': options.format} 80 params = {'query': query, 'format': options.format}
81 if options.debug: 81 if options.debug:
82 print("%s ? %s" % (url, params), file=sys.stderr) 82 print("%s ? %s" % (url, params), file=sys.stderr)
83 data = parse.urlencode(params) 83 data = parse.urlencode(params)
84 print(f"Retrieving: {url}?{data}") 84 print(f"Retrieving: {url}?{data}")
110 if re.match(pattern, line): 110 if re.match(pattern, line):
111 break 111 break
112 else: 112 else:
113 print("failed: Not a uniprot xml file", file=sys.stderr) 113 print("failed: Not a uniprot xml file", file=sys.stderr)
114 exit(1) 114 exit(1)
115 print("NCBI Taxon ID:%s" % taxids, file=sys.stdout) 115 print("Search IDs:%s" % search_ids, file=sys.stdout)
116 if 'X-UniProt-Release' in response.headers: 116 if 'X-UniProt-Release' in response.headers:
117 print("UniProt-Release:%s" % response.headers['X-UniProt-Release'], file=sys.stdout) 117 print("UniProt-Release:%s" % response.headers['X-UniProt-Release'], file=sys.stdout)
118 if 'X-Total-Results' in response.headers: 118 if 'X-Total-Results' in response.headers:
119 print("Entries:%s" % response.headers['X-Total-Results'], file=sys.stdout) 119 print("Entries:%s" % response.headers['X-Total-Results'], file=sys.stdout)
120 except Exception as e: 120 except Exception as e: