Allows CDS (as well as gene) features to create new gene references f…

…iles #55

scripts/newreference.py

@@ -3,18 +3,27 @@
 from Bio.SeqFeature import SeqFeature, FeatureLocation, Seq
 import shutil
 import argparse
+import sys
 
 def new_reference(referencefile, outgenbank, outfasta, gene):
  ref = SeqIO.read(referencefile, "genbank")
+ startofgene = None
+ endofgene = None
  for feature in ref.features:
  if feature.type == 'source':
  ref_source_feature = feature
- if feature.type =='gene':
+ if feature.type =='gene' or feature.type == 'CDS':
  a = list(feature.qualifiers.items())[0][-1][0]
  if a == 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(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)
+
  record = ref[startofgene:endofgene]
  source_feature = SeqFeature(FeatureLocation(start=0, end=len(record)), type='source',
  qualifiers=ref_source_feature.qualifiers)