newreference: If gene is not found, print a warning and use entire ge…

…nome

Currently, if the --gene option is used and the gene is not found, the
script will use the entire genome without printing a warning.

This commit adds a warning to notify the user of this behavior.

If the --gene option is not used, the warning is not printed.

scripts/newreference.py

@@ -22,6 +22,11 @@ def new_reference(referencefile, outgenbank, outfasta, gene):
                                  qualifiers=ref_source_feature.qualifiers)
     record.features.append(source_feature)
 
+    # 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(gene != None and startofgene==None and endofgene==None):
+        print(f"WARNING: No 'gene' or 'CDS' features found with name '{gene}', using entire genome instead.")
+
     SeqIO.write(record, outgenbank, 'genbank')
     SeqIO.write(record, outfasta, "fasta")