comparison uniprotxml_downloader.py @ 3:1a5690a5eedc draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit 6aac77a68426533c8c18c9f6aabd2df56a82de24

2:e1abc9a35c64

    parser = optparse.OptionParser()
    parser.add_option('-i', '--input', dest='input', default=None, help='Tabular file containing a column of NCBI Taxon IDs')
    parser.add_option('-c', '--column', dest='column', type='int', default=0, help='The column (zero-based) in the tabular file that contains Taxon IDs' )
    parser.add_option('-t', '--taxon', dest='taxon', action='append', default=[], help='NCBI taxon ID to download')
    parser.add_option('-r', '--reviewed', dest='reviewed', help='Only uniprot reviewed entries')
    parser.add_option('-f', '--format', dest='format', choices=['xml', 'fasta'], default='xml',help='output format')
    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 = set(options.taxon)
    if options.input:

        dest_path = "uniprot_%s.xml" % '_'.join(taxids)
    reviewed = " reviewed:%s" % options.reviewed if options.reviewed else ''
    try:
        def reporthook(n1,n2,n3):
            pass   
        url = 'http://www.uniprot.org/uniprot/'
        query = "%s%s" % (taxon_query, reviewed)
        params = {'query' : query, 'force' : 'yes' , 'format' : options.format}
        if options.debug:
            print >> sys.stderr, "%s ? %s" % (url,params)
        data = urllib.urlencode(params)

3:1a5690a5eedc

    parser = optparse.OptionParser()
    parser.add_option('-i', '--input', dest='input', default=None, help='Tabular file containing a column of NCBI Taxon IDs')
    parser.add_option('-c', '--column', dest='column', type='int', default=0, help='The column (zero-based) in the tabular file that contains Taxon IDs' )
    parser.add_option('-t', '--taxon', dest='taxon', action='append', default=[], help='NCBI taxon ID to download')
    parser.add_option('-r', '--reviewed', dest='reviewed', help='Only uniprot reviewed entries')
    parser.add_option('-f', '--format', dest='format', choices=['xml', 'fasta'], default='xml', help='output format')
    parser.add_option('-o', '--output', dest='output', help='file path for the downloaded 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 = set(options.taxon)
    if options.input:

        dest_path = "uniprot_%s.xml" % '_'.join(taxids)
    reviewed = " reviewed:%s" % options.reviewed if options.reviewed else ''
    try:
        def reporthook(n1,n2,n3):
            pass   
        url = 'https://www.uniprot.org/uniprot/'
        query = "%s%s" % (taxon_query, reviewed)
        params = {'query' : query, 'force' : 'yes' , 'format' : options.format}
        if options.debug:
            print >> sys.stderr, "%s ? %s" % (url,params)
        data = urllib.urlencode(params)