INNER CODE UNIT · Python

run_summary_to_file

MariaNattestad/assemblytics · assemblytics/cli.py:43

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(
        file=bed_path,
        minimum_variant_size=minimum_size,
        maximum_variant_size=maximum_size,
    )
    buffer = io.StringIO()
    stdout = sys.stdout
    sys.stdout = buffer
    try:
        run_summary(summary_args)
    finally:
        sys.stdout = stdout
    with open(summary_path, "w") as summary:
        summary.write(buffer.getvalue())

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