comparison data_manager/shapeit_ref.py @ 4:094bd0114876 draft

planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit 06f9376308b504cd2ab7a4ff0126ae70d73faacc

3:203133a92000

assert_prefix_exists.__annotations__ = {'prefix': str, 'path': str, 'prefix_type': str, 'return': None}

if __name__ == '__main__':
    parser = argparse.ArgumentParser(description='Generate a data manager output for SHAPEIT reference data')
    parser.add_argument('key', help='Short key to identify this reference set (no spaces)')
    parser.add_argument('description', help='Description of reference set')
    parser.add_argument('path', help='Filesystem path to directory containing this reference set')
    parser.add_argument('reference_prefix', help='Filename prefix for the reference (.hap / .legend / .sample) files')
    parser.add_argument('map_prefix', help='Filename prefix for map files in this reference set')
    parser.add_argument('output_file', type=argparse.FileType('w'), help='JSON file used to write data manager values to')
    args = parser.parse_args()

        exit("Unable to find specified path {}".format(args.path))

    assert_prefix_exists(args.reference_prefix, args.path, 'reference')
    assert_prefix_exists(args.map_prefix, args.path, 'map')

    for column in ('key', 'description', 'path', 'reference_prefix', 'map_prefix'):
        value = getattr(args, column)
        if '\t' in value:
            exit("TAB character found in {} argument".format(column))

    data_manager_dict = {}
    data_table_entry = dict(value=args.key, description=args.description, path=args.path,
                            reference_prefix=args.reference_prefix, map_prefix=args.map_prefix)
    _add_data_table_entry(data_manager_dict, 'shapeit_ref', data_table_entry)

    args.output_file.write(json.dumps(data_manager_dict, sort_keys=True) + '\n')

4:094bd0114876

assert_prefix_exists.__annotations__ = {'prefix': str, 'path': str, 'prefix_type': str, 'return': None}

if __name__ == '__main__':
    parser = argparse.ArgumentParser(description='Generate a data manager output for SHAPEIT reference data')
    parser.add_argument('key', help='Short key to identify this reference set (no spaces)')
    parser.add_argument('name', help='Description of reference set')
    parser.add_argument('path', help='Filesystem path to directory containing this reference set')
    parser.add_argument('reference_prefix', help='Filename prefix for the reference (.hap / .legend / .sample) files')
    parser.add_argument('map_prefix', help='Filename prefix for map files in this reference set')
    parser.add_argument('output_file', type=argparse.FileType('w'), help='JSON file used to write data manager values to')
    args = parser.parse_args()

        exit("Unable to find specified path {}".format(args.path))

    assert_prefix_exists(args.reference_prefix, args.path, 'reference')
    assert_prefix_exists(args.map_prefix, args.path, 'map')

    for column in ('key', 'name', 'path', 'reference_prefix', 'map_prefix'):
        value = getattr(args, column)
        if '\t' in value:
            exit("TAB character found in {} argument".format(column))

    data_manager_dict = {}
    data_table_entry = dict(value=args.key, name=args.name, path=args.path,
                            reference_prefix=args.reference_prefix, map_prefix=args.map_prefix)
    _add_data_table_entry(data_manager_dict, 'shapeit_ref', data_table_entry)

    args.output_file.write(json.dumps(data_manager_dict, sort_keys=True) + '\n')