diff --git a/deeprvat/annotations/annotations.py b/deeprvat/annotations/annotations.py index 366f5dfb..e302a7e6 100644 --- a/deeprvat/annotations/annotations.py +++ b/deeprvat/annotations/annotations.py @@ -1652,7 +1652,7 @@ def merge_annotations( deepripe_hg2_file: str, deepripe_k5_file: str, variant_file: str, - vcf_file:str, + vcf_file: str, out_file: str, vepcols_to_retain: Optional[str], ): @@ -1680,7 +1680,9 @@ def merge_annotations( vep_df = pd.read_csv(vep_file, header=vep_header_line, sep="\t", na_values="-") if vepcols_to_retain is not None: vepcols_to_retain = [c for c in vepcols_to_retain.split(",")] - vep_df = process_vep(vep_file=vep_df, vcf_file = vcf_file, vepcols_to_retain=vepcols_to_retain) + vep_df = process_vep( + vep_file=vep_df, vcf_file=vcf_file, vepcols_to_retain=vepcols_to_retain + ) logger.info(f"vep_df shape is {vep_df.shape}") logger.info("load deepripe_parclip") @@ -1721,7 +1723,6 @@ def merge_annotations( ca.to_parquet(out_file, compression="zstd") - def process_deepripe(deepripe_df: pd.DataFrame, column_prefix: str) -> pd.DataFrame: """ Process the DeepRipe DataFrame, rename columns and drop duplicates.