diff --git a/scripts/newreference.py b/scripts/newreference.py index 063dafb..a89c819 100644 --- a/scripts/newreference.py +++ b/scripts/newreference.py @@ -18,8 +18,8 @@ def new_reference(referencefile, outgenbank, outfasta, gene): startofgene = int(list(feature.location)[0]) endofgene = int(list(feature.location)[-1])+1 - # If user provides a --gene 'some name' is not found, print a warning and use the entire genome. - # Otherwise do not print a warning. + # If user provides a --gene 'some name' that is not found, error out as this may indicate that + # the gene name is misspelled or the user may be using the wrong GenBank file. if(gene is not None and startofgene is None and endofgene is None): print(f"ERROR: No '{gene}' was found under 'gene' or 'CDS' features in the GenBank file.", file=sys.stderr) sys.exit(1)