run_IGV_snapshot_automator.py 文件源码

def summary_table_to_bed_long(sample_summary_table, output_file, filename_suffix = 'long', min_frequency = 1):
    '''
    Write out the low frequency variants

    NOTE: See 'check_for_IGV_long_regions_snapshot' function in run_parser.py
    UPDATE: Naima wants long snapshots for ALL variants from now on.
    '''
    import csv
    print('Find low frequency variants...')
    print('input file: {0}'.format(sample_summary_table))
    print('output file: {0}'.format(output_file))
    with open(sample_summary_table, 'r') as tsvin, open(output_file, 'w') as bedout:
        reader = csv.DictReader(tsvin, delimiter='\t')
        writer = csv.writer(bedout, delimiter='\t')
        for row in reader:
            if float(row['Frequency']) < min_frequency:
                print(row['Frequency'])
                filename = make_snapshot_filename(summary_dict = row, filename_suffix = filename_suffix)
                entry = [row['Chrom'], row['Position'], row['Position'], filename]
                print(entry)
                writer.writerow(entry)