comparison iedb_api.py @ 3:e95d3221b7f0 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 863578373c7dadc5880633115b0c348f73dac782"

2:a09849898387

                      'processing': range(8, 15),
                      'mhcnp': range(8, 12),
                      'bcell': range(8, 16)}


def parse_alleles(allelefile, lengths):
    alleles = []
    lengths = []
    with open(allelefile, 'r') as fh:
        for i, line in enumerate(fh):
            fields = line.strip().split(',')

            if allele:
                if len(fields) > 1:
                    for alen in fields[1:]:
                        alleles.append(allele)
                        lengths.append(alen)
                elif lengths:
                    for alen in str(lengths).split(','):
                        alleles.append(allele)
                        lengths.append(alen)
                else:
                    alleles.append(allele)
    return (alleles, lengths)

                        default=None,
                        help='File of HLA alleles')
    parser.add_argument('-l', '--length',
                        action="append",
                        default=[],
                        help='lengths for which to make predictions, '
                             '1 per allele')
    parser.add_argument('-w', '--window_size',
                        type=int,
                        default=None,
                        help='window_size for bcell prediction')
    parser.add_argument('-i', '--input',
                        default=None,
                        help='Input file for peptide sequences '
                             '(fasta or tabular)')
    parser.add_argument('-c', '--column',
                        default=None,
                        help='Peptide Column in a tabular input file')
    parser.add_argument('-C', '--id_column',
                        default=None,

        if not args.allele and not args.allelefile:
            warn_err('-a allele or -A allelefile required\n', exit_code=1)

    if not (args.sequence or args.input):
        warn_err('NO Sequences given: '
                 'either -s sequence or -i input_file is required\n',
                 exit_code=1)

    if args.output is not None:
        try:
            outputPath = os.path.abspath(args.output)

        if args.allelefile:
            (alleles, lengths) = parse_alleles(args.allelefile, args.length)
        if args.allele:
            for i, allele in enumerate(args.allele):
                alleles.append(allele)
                alen = args.length[i] if i < len(args.length) else args.length[-1]
                lengths.append(alen)
    allele = ','.join(alleles) if alleles else None
    length = ','.join(lengths) if lengths else None
    method = args.method
    proteasome = args.proteasome if args.prediction == 'processcing' else None
    url = 'http://tools-cluster-interface.iedb.org/tools_api/%s/' %\
        args.prediction

    # results
    results = {'prediction': {'header': None, 'entries': []}, 'detail': {'header': None, 'entries': []}}

    if args.sequence:
        for i, seq in enumerate(args.sequence):
            seqid = 'pep_%d' % i
            query(url, args.prediction, seq, allele, length, results,

3:e95d3221b7f0

                      'processing': range(8, 15),
                      'mhcnp': range(8, 12),
                      'bcell': range(8, 16)}


def parse_alleles(allelefile, query_lengths):
    alleles = []
    lengths = []
    with open(allelefile, 'r') as fh:
        for i, line in enumerate(fh):
            fields = line.strip().split(',')

            if allele:
                if len(fields) > 1:
                    for alen in fields[1:]:
                        alleles.append(allele)
                        lengths.append(alen)
                elif query_lengths:
                    lens = []
                    for ql in query_lengths:
                        lens.extend(str(ql).split(','))
                    for alen in lens:
                        alleles.append(allele)
                        lengths.append(alen)
                else:
                    alleles.append(allele)
    return (alleles, lengths)

                        default=None,
                        help='File of HLA alleles')
    parser.add_argument('-l', '--length',
                        action="append",
                        default=[],
                        help='lengths for which to make predictions for alleles')
    parser.add_argument('-w', '--window_size',
                        type=int,
                        default=None,
                        help='window_size for bcell prediction')
    parser.add_argument('-i', '--input',
                        default=None,
                        help='Input file for peptide sequences '
                             + '(fasta or tabular)')
    parser.add_argument('-c', '--column',
                        default=None,
                        help='Peptide Column in a tabular input file')
    parser.add_argument('-C', '--id_column',
                        default=None,

        if not args.allele and not args.allelefile:
            warn_err('-a allele or -A allelefile required\n', exit_code=1)

    if not (args.sequence or args.input):
        warn_err('NO Sequences given: '
                 + 'either -s sequence or -i input_file is required\n',
                 exit_code=1)

    if args.output is not None:
        try:
            outputPath = os.path.abspath(args.output)

        if args.allelefile:
            (alleles, lengths) = parse_alleles(args.allelefile, args.length)
        if args.allele:
            for i, allele in enumerate(args.allele):
                alleles.append(allele)
                alen = args.length[i] if i < len(args.length)\
                    else args.length[-1]
                lengths.append(alen)
    allele = ','.join(alleles) if alleles else None
    length = ','.join(lengths) if lengths else None
    method = args.method
    proteasome = args.proteasome if args.prediction == 'processcing' else None
    url = 'http://tools-cluster-interface.iedb.org/tools_api/%s/' %\
        args.prediction

    # results
    results = {'prediction': {'header': None, 'entries': []},
               'detail': {'header': None, 'entries': []}}

    if args.sequence:
        for i, seq in enumerate(args.sequence):
            seqid = 'pep_%d' % i
            query(url, args.prediction, seq, allele, length, results,