create_bigwigs.py 文件源码

def create_log2fc_bigwigs(matrix, outdir, args):
    # type: (pd.DataFrame, str, Namespace) -> None
    """Create bigwigs from matrix."""
    call("mkdir -p {}".format(outdir), shell=True)
    genome_size_dict = args.chromosome_sizes

    input_columns = matrix[args.control]
    input_rpkm_sum = (1e6 * input_columns / input_columns.sum()).sum(axis=1) / len(args.control)
    input_rpkm_sum[input_rpkm_sum == 0] = 1

    outpaths, data = [], []
    for bed_file in matrix[args.treatment]:
        outpath = join(outdir, splitext(basename(bed_file))[0] + "_log2fc.bw")
        outpaths.append(outpath)

        bed_column = matrix[bed_file]
        bed_column = 1e6 * bed_column / bed_column.sum()
        divided = bed_column / input_rpkm_sum
        divided.loc[divided == 0] = 0.01
        log2_fc_column = np.log2(divided)
        data.append(log2_fc_column)

    Parallel(n_jobs=args.number_cores)(delayed(_create_bigwig)(bed_column, outpath, genome_size_dict) for outpath, bed_column in zip(outpaths, data))