run_repeat_expansion_variants.py

#!/usr/bin/env python3
"""A wrapper script for running the repeat expansion pipeline."""

import argparse
import repeat_expansion_variants.pipeline

parser = argparse.ArgumentParser(description=__doc__)
parser.add_argument(
    '--clinvar-summary-tsv', required=True,
    help='ClinVar summary TSV dump file (variant_summary.txt.gz)'
)
parser.add_argument(
    '--output-consequences', required=True,
    help='File to output functional consequences to. Format is compatible with the main VEP mapping pipeline.'
)
parser.add_argument(
    '--output-dataframe', required=True,
    help='File to output full dataframe for subsequent analysis and debugging.'
)
args = parser.parse_args()
repeat_expansion_variants.pipeline.main(args.clinvar_summary_tsv, args.output_consequences, args.output_dataframe)