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Check for both classic and sequence_ontology name for EFF: "NON_SYNONYMOUS_CODING" or "missense_variant"
author Jim Johnson <jj@umn.edu>
date Thu, 06 Nov 2014 13:57:31 -0600
parents fcb7188fa0d2
children
files snpeff_to_peptides.py
diffstat 1 files changed, 1 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- 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]