diff --git a/src/pyrodigal/cli.py b/src/pyrodigal/cli.py index efe293b..0334dd4 100644 --- a/src/pyrodigal/cli.py +++ b/src/pyrodigal/cli.py @@ -192,9 +192,9 @@ def argument_parser( parser.add_argument( "--no-stop-codon", required=False, - action="store_false", + action="store_true", help="Disables translation of stop codons into star characters (*) for complete genes.", - default=True, + default=False, ) parser.add_argument( "--pool", @@ -310,7 +310,7 @@ def main( preds.write_genes(nuc_file, seq_id) # if asked, write amino acid sequences of proteins if prot_file is not None: - preds.write_translations(prot_file, seq_id, include_stop=args.no_stop_codon) + preds.write_translations(prot_file, seq_id, include_stop=not args.no_stop_codon) # if asked, write scores if scores_file is not None: preds.write_scores(scores_file, seq_id)