main

Call peaks for the given Calling Cards data.

:param args: the command line arguments. :type args: Namespace

Source code in callingcardstools/PeakCalling/yeast/call_peaks.py

def main(args: argparse.Namespace) -> None:
    """
    Call peaks for the given Calling Cards data.

    :param args: the command line arguments.
    :type args: Namespace
    """
    check_files = [
        args.experiment_data_path,
        args.promoter_data_path,
        args.background_data_path,
        args.chrmap_data_path,
    ]
    for file in check_files:
        if not os.path.isfile(file):
            raise FileNotFoundError("The following path " f"does not exist: {file}")

    result_df = call_peaks(
        args.experiment_data_path,
        args.experiment_orig_chr_convention,
        args.promoter_data_path,
        args.promoter_orig_chr_convention,
        args.background_data_path,
        args.background_orig_chr_convention,
        args.chrmap_data_path,
        args.unified_chr_convention,
        args.deduplicate_experiment,
    )

    result_df.to_csv(
        args.output_path,
        compression="gzip" if args.compress_output else None,
        index=False,
    )