Allows for CDS (as well as gene) features to generate a new gene refe…

…rence

The newreference.py script processes a GenBank file, producing new gene
reference files (GenBank and FASTA) which are required for creating the
Nextstrain gene tree views.

As we intend to use this script as a template for other viruses (e.g. dengue, measles),
it was necessary to allow the use of CDS features in the GenBank file, not just the gene.

scripts/newreference.py

@@ -6,10 +6,12 @@
 
 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])