# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1410779627 18000
# Node ID fbb6510186dfee585825d7c1f7a8c3eb0406ea57
# Parent  a64ef06111176118a4684d0698469b61c0dae273
when codon has ambiguous nucleotide translate to X

diff -r a64ef0611117 -r fbb6510186df snpEff_cds_report.py
--- a/snpEff_cds_report.py	Thu Jun 13 11:37:34 2013 -0500
+++ b/snpEff_cds_report.py	Mon Sep 15 06:13:47 2014 -0500
@@ -37,7 +37,8 @@
   rna = seq.upper().replace('T','U')
   aa = []
   for i in range(0,len(rna) - 2, 3):
-    aa.append(codon_map[rna[i:i+3]])
+    codon = rna[i:i+3]
+    aa.append(codon_map[codon] if codon in codon_map else 'X')
   return ''.join(aa)
 
 """