INNER CODE UNIT · Python

fail

MariaNattestad/assemblytics · assemblytics/cli.py:29

def fail(log_file, step, message, exit_code=1):
    log_progress(log_file, step)
    sys.exit(exit_code)


def zip_results(output_dir):
    zip_path = os.path.join(output_dir, "assemblytics_results.zip")
    zip_filename = os.path.basename(zip_path)
    with zipfile.ZipFile(zip_path, "w", zipfile.ZIP_DEFLATED) as archive:
        for filename in os.listdir(output_dir):
            if filename.startswith("assemblytics_") and filename != zip_filename:
                archive.write(os.path.join(output_dir, filename), filename)


def run_summary_to_file(output_dir, minimum_size, maximum_size):
    summary_path = os.path.join(output_dir, "assemblytics_structural_variants_summary.txt")
    bed_path = os.path.join(output_dir, "assemblytics_structural_variants.bed")
    summary_args = argparse.Namespace(

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