commonv.py 文件源码

def main(args):
    if args.minimum_frequency is None:
        # args.table is a list of file names
        minimum_frequency = max((len(args.table) + 1) // 2, 2)
    else:
        minimum_frequency = args.minimum_frequency
    logger.info('Minimum frequency set to %s', minimum_frequency)

    # Read in tables
    tables = []
    for path in args.table:
        table = read_table(path)
        table = table.loc[:,['V_gene', 'V_SHM', 'V_nt', 'name']]
        tables.append(table)

    # Count V sequence occurrences
    counter = Counter()
    for table in tables:
        counter.update(set(table.V_nt))

    # Find most frequent occurrences and print result
    print('Frequency', 'Gene', '%SHM', 'Sequence', sep='\t')
    for sequence, frequency in counter.most_common():
        if frequency < minimum_frequency:
            break
        names = []
        gene = None
        for table in tables:
            matching_rows = table[table.V_nt == sequence]
            if matching_rows.empty:
                continue
            names.extend(matching_rows.name)
            if gene is None:
                row = matching_rows.iloc[0]
                gene = row['V_gene']
                shm = row['V_SHM']
        print(frequency, gene, shm, sequence, *names, sep='\t')