comparison data_manager/twobit_builder.py @ 6:62359a151521 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_twobit_builder commit 18d696a933873372ae5c77257fd31eaf2cd4ed13

5:625fd9476402

        if not sequence_name:
            sequence_name = dbkey
    return sequence_id, sequence_name


def build_twobit(data_manager_dict, fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name):
    twobit_base_name = "%s.2bit" % (sequence_id)
    twobit_filename = os.path.join(target_directory, twobit_base_name)

    args = ['faToTwoBit', fasta_filename, twobit_filename]
    tmp_stderr = tempfile.NamedTemporaryFile(prefix="tmp-data-manager-twobit-builder-stderr")
    proc = subprocess.Popen(args=args, shell=False, cwd=target_directory, stderr=tmp_stderr.fileno())
    return_code = proc.wait()
    if return_code:
        tmp_stderr.flush()

        print("Error building index:", file=sys.stderr)
        while True:
            chunk = tmp_stderr.read(CHUNK_SIZE)
            if not chunk:
                break
            sys.stderr.write(chunk)
        sys.exit(return_code)
    tmp_stderr.close()
    # lastz_seqs
    data_table_entry = dict(value=sequence_id, name=sequence_name, path=twobit_base_name)

def main():
    parser = optparse.OptionParser()
    parser.add_option('-f', '--fasta_filename', dest='fasta_filename', action='store', type="string", default=None, help='fasta_filename')
    parser.add_option('-d', '--fasta_dbkey', dest='fasta_dbkey', action='store', type="string", default=None, help='fasta_dbkey')
    parser.add_option('-t', '--fasta_description', dest='fasta_description', action='store', type="string", default=None, help='fasta_description')
    (options, args) = parser.parse_args()

    filename = args[0]

    with open(filename) as fh:

        raise Exception('"%s" is not a valid dbkey. You must specify a valid dbkey.' % (dbkey))

    sequence_id, sequence_name = get_id_name(params, dbkey=dbkey, fasta_description=options.fasta_description)

    # build the index
    build_twobit(data_manager_dict, options.fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name)

    # save info to json file
    with open(filename, 'w') as fh:
        json.dump(data_manager_dict, fh, sort_keys=True)

6:62359a151521

        if not sequence_name:
            sequence_name = dbkey
    return sequence_id, sequence_name


def build_twobit(data_manager_dict, fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, long):
    twobit_base_name = "%s.2bit" % (sequence_id)
    twobit_filename = os.path.join(target_directory, twobit_base_name)

    args = ['faToTwoBit']
    if long:
        args.append('-long')
    args.extend([fasta_filename, twobit_filename])
    tmp_stderr = tempfile.NamedTemporaryFile(prefix="tmp-data-manager-twobit-builder-stderr")
    proc = subprocess.Popen(args=args, shell=False, cwd=target_directory, stderr=tmp_stderr.fileno())
    return_code = proc.wait()
    if return_code:
        tmp_stderr.flush()

        print("Error building index:", file=sys.stderr)
        while True:
            chunk = tmp_stderr.read(CHUNK_SIZE)
            if not chunk:
                break
            sys.stderr.write(chunk.decode('utf-8'))
        sys.exit(return_code)
    tmp_stderr.close()
    # lastz_seqs
    data_table_entry = dict(value=sequence_id, name=sequence_name, path=twobit_base_name)

def main():
    parser = optparse.OptionParser()
    parser.add_option('-f', '--fasta_filename', dest='fasta_filename', action='store', type="string", default=None, help='fasta_filename')
    parser.add_option('-d', '--fasta_dbkey', dest='fasta_dbkey', action='store', type="string", default=None, help='fasta_dbkey')
    parser.add_option('-t', '--fasta_description', dest='fasta_description', action='store', type="string", default=None, help='fasta_description')
    parser.add_option('-l', '--long', dest='long', action="store_true", default=False, help='For big genomes you need to pass the -long option.')

    (options, args) = parser.parse_args()

    filename = args[0]

    with open(filename) as fh:

        raise Exception('"%s" is not a valid dbkey. You must specify a valid dbkey.' % (dbkey))

    sequence_id, sequence_name = get_id_name(params, dbkey=dbkey, fasta_description=options.fasta_description)

    # build the index
    build_twobit(data_manager_dict, options.fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, options.long)

    # save info to json file
    with open(filename, 'w') as fh:
        json.dump(data_manager_dict, fh, sort_keys=True)