# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1415303851 21600
# Node ID 80eff5812b2af8b9299de4f096203e0df5f4e1c4
# Parent  fcb7188fa0d298c22ef7f58f5caffcebf34bc4de
Check for both classic and sequence_ontology name for EFF: "NON_SYNONYMOUS_CODING" or "missense_variant"

diff -r fcb7188fa0d2 -r 80eff5812b2a snpeff_to_peptides.py
--- a/snpeff_to_peptides.py	Fri Feb 07 15:05:20 2014 -0500
+++ b/snpeff_to_peptides.py	Thu Nov 06 13:57:31 2014 -0600
@@ -187,7 +187,7 @@
               effects = val.split(',')
               for effect in effects:
                 (eff,effs) = effect.rstrip(')').split('(')
-                if not eff == 'NON_SYNONYMOUS_CODING':
+                if not (eff == 'NON_SYNONYMOUS_CODING' or eff == 'missense_variant'):
                   continue
                 eff_fields = effs.split('|')
                 (impact,functional_class,codon_change,aa_change,aa_len,gene_name,biotype,coding,transcript,exon) = eff_fields[0:10]