comparison galaxy-tools/biobank/utils/check_tsv_header.py @ 3:43be74e62bfe draft

Uploaded

3:43be74e62bfe

"""
"""
import csv, sys, argparse, logging


LOG_FORMAT = '%(asctime)s|%(levelname)-8s|%(message)s'
LOG_DATEFMT = '%Y-%m-%d %H:%M:%S'
LOG_LEVELS = ['DEBUG', 'INFO', 'WARNING', 'ERROR', 'CRITICAL']

def make_parser():
    parser = argparse.ArgumentParser(description='prepare inputs for VLUTIL.prepare_seq_dsample_inputs')
    parser.add_argument('--logfile', type=str, help='log file (default=stderr)')
    parser.add_argument('--loglevel', type=str, choices=LOG_LEVELS,
                        help='logging level', default='INFO')
    parser.add_argument('--in-file', '-i', type=str, required=True,
                        help='input file')
    return parser

def read_samplesheet(in_file):
    with open(in_file, 'rU') as f:
        reader = csv.DictReader(f, delimiter='\t')
        recs = [r for r in reader]
        fieldnames = reader.fieldnames
    return recs, fieldnames

def is_header_different(titer_plate_header, header_to_be_checked):
    result = set(header_to_be_checked).difference(frozenset(titer_plate_header))
    if len(result) > 0:
        return True
    else:
        return False

def main(argv):
    parser = make_parser()
    args = parser.parse_args(argv)

    log_level = getattr(logging, args.loglevel)
    kwargs = {'format': LOG_FORMAT,
              'datefmt': LOG_DATEFMT,
              'level': log_level}
    if args.logfile:
        kwargs['filename'] = args.logfile
    logging.basicConfig(**kwargs)
    logger = logging.getLogger('check tsv header')

    logger.info('Loading data from file %s' % args.in_file)
    recs, file_header = read_samplesheet(args.in_file)
    logger.debug('Retrieved %d records', len(recs))

    titer_plate_header = ['study', 'label', 'barcode', 'rows', 'columns']

    if is_header_different(titer_plate_header, file_header):
        logger.info("Tsv file header has to have this elements: {}".format(titer_plate_header))
        # hack to support old galaxy
        sys.stderr.write("Headers not compliant to: {}".format(titer_plate_header))
        sys.exit(2)     
    else:
        logger.info("Header check passed")

if __name__ == '__main__':
    main(sys.argv[1:])