fixup: move gene check before trying to extract the sequence feature

scripts/newreference.py

@@ -18,17 +18,17 @@ def new_reference(referencefile, outgenbank, outfasta, gene):
                 startofgene = int(list(feature.location)[0])
                 endofgene =  int(list(feature.location)[-1])+1
 
-    record = ref[startofgene:endofgene]
-    source_feature =  SeqFeature(FeatureLocation(start=0, end=len(record)), type='source',
-                                 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"ERROR: No '{gene}' was found under 'gene' or 'CDS' features in the GenBank file.", file=sys.stderr)
         sys.exit(1)
 
+    record = ref[startofgene:endofgene]
+    source_feature =  SeqFeature(FeatureLocation(start=0, end=len(record)), type='source',
+                                 qualifiers=ref_source_feature.qualifiers)
+    record.features.append(source_feature)
+
     SeqIO.write(record, outgenbank, 'genbank')
     SeqIO.write(record, outfasta, "fasta")