main

Call peaks for the given Calling Cards data.

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

def main(args: argparse.Namespace) -> None:
    """
    Call peaks for the given Calling Cards data.
    """
    # note the * -- unpack the list of paths
    check_files = [
        *args.experiment_data_paths,
        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(f"The following path does not exist: {file}")

    try:
        result_df = call_peaks(
            args.experiment_data_paths,
            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,
            genomic_only=args.genomic_only,
            pseudocount=args.pseudocount,
        )

        result_df.to_csv(
            args.output_path,
            compression="gzip" if args.compress_output else None,
            index=False,
        )
    except Exception as e:
        logger.error(
            "Error processing experiment files: %s. Error: %s",
            args.experiment_data_paths,
            e,
        )
        raise