diff --git a/update_sc_name/update_scientific_name.py b/update_sc_name/update_scientific_name.py index dcccd703..849d95ce 100644 --- a/update_sc_name/update_scientific_name.py +++ b/update_sc_name/update_scientific_name.py @@ -80,8 +80,6 @@ def main(): argparser.add_argument("--profile", help="ex: development, production_processing", default="production_processing", required=False) argparser.add_argument("--taxonomy", type=int, help="taxonomy id e.g. 9606", required=True) - argparser.add_argument("--scientific-name", help=f"""new scientific name for taxonomy - (put in "" for names having space in between)""", required=False) argparser.add_argument("--ref-seq-dir", help="path to reference seq directory", required=True) argparser.add_argument("--ref-seq-dir-name", help="name of the reference directory if it could not be " "derived by normalizing scientific name in table", required=False) @@ -91,7 +89,7 @@ def main(): # update directory name in reference sequence directory old_sc_name = get_scientific_name_from_eva(args.taxonomy, args.private_config_xml_file, args.profile) - new_sc_name = args.scientific_name or get_scientific_name_from_ensembl(args.taxonomy) + new_sc_name = get_scientific_name_from_ensembl(args.taxonomy) logger.info(f"old scientific name: {old_sc_name}, new scientific name: {new_sc_name}") update_path_reference_sequence(args.taxonomy, old_sc_name, new_sc_name, args.ref_seq_dir, args.ref_seq_dir_name,