annotate uniprotxml_downloader.py @ 0:0bd2688166a5 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit fa07533e9216dc40133a98e3129be9b87a963e80-dirty

#!/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
    else:
        dest_path = "uniprot_%s.xml" % '_'.join(taxids)
    reviewed = " reviewed:%s" % options.reviewed if options.reviewed else ''
    url = 'http://www.uniprot.org/uniprot/?query=%s%s&force=yes&format=xml' % (taxon_query, reviewed)
    if options.debug:
        print >> sys.stderr, url
    try:
        (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
            exit(1)
        elif True:
            pass
        else:
            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('<?'):
                        break
                    # pattern match <root or <ns:root for any ns string
                    pattern = '^<(\w*:)?uniprot'
                    if re.match(pattern, line):
                        break
                    else:
                        print >> sys.stderr, "failed: Not a uniprot xml file"
                        exit(1)

        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__":
    __main__()