diff --git a/scripts/iso_name_tagging.py b/scripts/iso_name_tagging.py index 035cb1b..caa5f55 100755 --- a/scripts/iso_name_tagging.py +++ b/scripts/iso_name_tagging.py @@ -157,7 +157,7 @@ def attributes_dictionary(attr: str) -> Dict[str, str]: def parse_intersect_output( - intersect_file: Path, id: str = "name", extension: int = 0 + intersect_file: Path, ID: str = "name", extension: int = 0 ) -> Optional[Dict[Optional[str], list]]: """Parse intersect BED file. @@ -205,7 +205,7 @@ def parse_intersect_output( for line in bedfile: fields = Fields(*line.strip().split("\t")) - miRNA_name = attributes_dictionary(fields.feat_attributes)[id] + miRNA_name = attributes_dictionary(fields.feat_attributes)[ID] miRNA_start = int(fields.feat_start) + extension miRNA_end = int(fields.feat_end) - extension @@ -268,7 +268,7 @@ def main(args) -> None: """Add intersecting feature(s) into a SAM file as a tag.""" intersect_data = parse_intersect_output( intersect_file=args.bed, - id=args.id, + ID=args.id, extension=args.extension, )