Mercurial > repos > galaxyp > uniprotxml_downloader

annotate uniprotxml_downloader.py @ 1:7fd760c99ec5 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
author galaxyp
date Fri, 16 Dec 2016 17:32:53 -0500
parents 1af0f7987741
children 366bf2635603
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
1 #!/usr/bin/env python
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
2 """
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
3 #
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
4 #------------------------------------------------------------------------------
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
5 # University of Minnesota
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
6 # Copyright 2016, Regents of the University of Minnesota
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
7 #------------------------------------------------------------------------------
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
8 # Author:
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
9 #
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
10 # James E Johnson
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
11 #
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
12 #------------------------------------------------------------------------------
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
13 """
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
14 import sys
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
15 import re
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
16 import optparse
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
17 import urllib
1
7fd760c99ec5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
parents: 0
diff changeset
18 import urllib2
0
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
19
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
20
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
21 def __main__():
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
22 # Parse Command Line
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
23 parser = optparse.OptionParser()
1
7fd760c99ec5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
parents: 0
diff changeset
24 parser.add_option('-i', '--input', dest='input', default=None, help='Tabular file containing a column of NCBI Taxon IDs')
7fd760c99ec5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
parents: 0
diff changeset
25 parser.add_option('-c', '--column', dest='column', type='int', default=0, help='The column (zero-based) in the tabular file that contains Taxon IDs' )
0
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
26 parser.add_option('-t', '--taxon', dest='taxon', action='append', default=[], help='NCBI taxon ID to download')
1
7fd760c99ec5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
parents: 0
diff changeset
27 parser.add_option('-r', '--reviewed', dest='reviewed', help='Only uniprot reviewed entries')
7fd760c99ec5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
parents: 0
diff changeset
28 parser.add_option('-f', '--format', dest='format', choices=['xml', 'fasta'], default='xml',help='output format')
0
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
29 parser.add_option('-o', '--output', dest='output', help='file path for th downloaed uniprot xml')
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
30 parser.add_option('-v', '--verbose', dest='verbose', action='store_true', default=False, help='Print UniProt Info')
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
31 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
galaxyp
parents:
diff changeset
32 (options, args) = parser.parse_args()
1
7fd760c99ec5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
parents: 0
diff changeset
33 taxids = set(options.taxon)
7fd760c99ec5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
parents: 0
diff changeset
34 if options.input:
7fd760c99ec5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
parents: 0
diff changeset
35 with open(options.input,'r') as inputFile:
7fd760c99ec5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
parents: 0
diff changeset
36 for linenum,line in enumerate(inputFile):
7fd760c99ec5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
parents: 0
diff changeset
37 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
38 continue
7fd760c99ec5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
parents: 0
diff changeset
39 fields = line.rstrip('\r\n').split('\t')
7fd760c99ec5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
parents: 0
diff changeset
40 if len(fields) > abs(options.column):
7fd760c99ec5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
parents: 0
diff changeset
41 taxid = fields[options.column].strip()
7fd760c99ec5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
parents: 0
diff changeset
42 if taxid:
7fd760c99ec5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
parents: 0
diff changeset
43 taxids.add(taxid)
0
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
44 taxon_queries = ['taxonomy:"%s"' % taxid for taxid in taxids]
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
45 taxon_query = ' OR '.join(taxon_queries)
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
46 if options.output:
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
47 dest_path = options.output
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
48 else:
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
49 dest_path = "uniprot_%s.xml" % '_'.join(taxids)
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
50 reviewed = " reviewed:%s" % options.reviewed if options.reviewed else ''
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
51 try:
1
7fd760c99ec5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
parents: 0
diff changeset
52 def reporthook(n1,n2,n3):
7fd760c99ec5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
parents: 0
diff changeset
53 pass
7fd760c99ec5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
parents: 0
diff changeset
54 url = 'http://www.uniprot.org/uniprot/'
7fd760c99ec5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
parents: 0
diff changeset
55 query = "%s%s" % (taxon_query, reviewed)
7fd760c99ec5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
parents: 0
diff changeset
56 params = {'query' : query, 'force' : 'yes' , 'format' : options.format}
7fd760c99ec5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
parents: 0
diff changeset
57 if options.debug:
7fd760c99ec5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
parents: 0
diff changeset
58 print >> sys.stderr, "%s ? %s" % (url,params)
7fd760c99ec5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
parents: 0
diff changeset
59 data = urllib.urlencode(params)
7fd760c99ec5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
parents: 0
diff changeset
60 (fname, msg) = urllib.urlretrieve(url, dest_path,reporthook,data)
0
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
61 headers = {j[0]: j[1].strip() for j in [i.split(':', 1) for i in str(msg).strip().splitlines()]}
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
62 if 'Content-Length' in headers and headers['Content-Length'] == 0:
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
63 print >> sys.stderr, url
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
64 print >> sys.stderr, msg
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
65 exit(1)
1
7fd760c99ec5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
parents: 0
diff changeset
66 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
67 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
68 while True:
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
69 line = contents.readline()
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
70 if options.debug:
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
71 print >> sys.stderr, line
1
7fd760c99ec5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
parents: 0
diff changeset
72 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:
diff changeset
73 break
1
7fd760c99ec5 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 15c2d28359584bcee25cdb456cff50892fff7347
galaxyp
parents: 0
diff changeset
74 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
75 continue
0
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
76 # pattern match <root or <ns:root for any ns string
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
77 pattern = '^<(\w*:)?uniprot'
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
78 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
79 break
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
80 else:
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
81 print >> sys.stderr, "failed: Not a uniprot xml file"
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
82 exit(1)
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
83 if options.verbose:
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
84 print >> sys.stdout, "NCBI Taxon ID:%s" % taxids
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
85 if 'X-UniProt-Release' in headers:
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
86 print >> sys.stdout, "UniProt-Release:%s" % headers['X-UniProt-Release']
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
87 if 'X-Total-Results' in headers:
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
88 print >> sys.stdout, "Entries:%s" % headers['X-Total-Results']
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
89 print >> sys.stdout, "%s" % url
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
90 except Exception, e:
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
91 print >> sys.stderr, "failed: %s" % e
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
92
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
93
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
94 if __name__ == "__main__":
1af0f7987741 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
parents:
diff changeset
95 __main__()