view @ 0:0bd2688166a5 draft

planemo upload for repository commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty
author galaxyp
date Tue, 08 Mar 2016 12:03:49 -0500
children e1abc9a35c64
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#!/usr/bin/env python
#                         University of Minnesota
#         Copyright 2016, Regents of the University of Minnesota
# Author:
#  James E Johnson
import sys
import re
import optparse
import urllib

def __main__():
    # Parse Command Line
    parser = optparse.OptionParser()
    parser.add_option('-t', '--taxon', dest='taxon', action='append', default=[], help='NCBI taxon ID to download')
    parser.add_option('-r', '--reviewed', dest='reviewed', help='file path for th downloaed uniprot xml')
    parser.add_option('-o', '--output', dest='output', help='file path for th downloaed uniprot xml')
    parser.add_option('-v', '--verbose', dest='verbose', action='store_true', default=False, help='Print UniProt Info')
    parser.add_option('-d', '--debug', dest='debug', action='store_true', default=False, help='Turn on wrapper debugging to stderr')
    (options, args) = parser.parse_args()

    taxids = options.taxon if options.taxon else ['9606']
    taxon_queries = ['taxonomy:"%s"' % taxid for taxid in taxids]
    taxon_query = ' OR '.join(taxon_queries)
    if options.output:
        dest_path = options.output
        dest_path = "uniprot_%s.xml" % '_'.join(taxids)
    reviewed = " reviewed:%s" % options.reviewed if options.reviewed else ''
    url = '' % (taxon_query, reviewed)
    if options.debug:
        print >> sys.stderr, url
        (fname, msg) = urllib.urlretrieve(url, dest_path)
        headers = {j[0]: j[1].strip() for j in [i.split(':', 1) for i in str(msg).strip().splitlines()]}
        if 'Content-Length' in headers and headers['Content-Length'] == 0:
            print >> sys.stderr, url
            print >> sys.stderr, msg
        elif True:
            with open(dest_path, 'r') as contents:
                while True:
                    line = contents.readline()
                    if options.debug:
                        print >> sys.stderr, line
                    if line is None or not line.startswith('<?'):
                    # pattern match <root or <ns:root for any ns string
                    pattern = '^<(\w*:)?uniprot'
                    if re.match(pattern, line):
                        print >> sys.stderr, "failed: Not a uniprot xml file"

        if options.verbose:
            print >> sys.stdout, "NCBI Taxon ID:%s" % taxids
            if 'X-UniProt-Release' in headers:
                print >> sys.stdout, "UniProt-Release:%s" % headers['X-UniProt-Release']
            if 'X-Total-Results' in headers:
                print >> sys.stdout, "Entries:%s" % headers['X-Total-Results']
            print >> sys.stdout, "%s" % url
    except Exception, e:
        print >> sys.stderr, "failed: %s" % e

if __name__ == "__main__":