fix for synonymous+inframe variant change type

jodyphelan · Sep 7, 2019 · 6586bb1 · 6586bb1
1 parent 07d5ff2
commit 6586bb1
Showing 1 changed file with 4 additions and 4 deletions.
diff --git a/pathogenprofiler/vcf.py b/pathogenprofiler/vcf.py
@@ -106,17 +106,17 @@ def load_csq(self,ann_file=None):
 					variants[sample].append({"sample":sample,"gene_id":ann_gene,"chr":chrom,"genome_pos":pos,"type":"non_coding","change":cng,"freq":adr[call2], "nucleotide_change":cng})
 				elif  "missense" in info[0] or "start_lost" in info[0] or "stop_gained" in info[0]:
 					variants[sample].append({"sample":sample,"gene_id":gene_id,"gene_name":gene_name,"chr":chrom,"genome_pos":pos,"type":info[0],"change":info[5],"freq":adr[call2], "nucleotide_change":info[6]})
-				elif "synonymous" in info[0] or info[0]=="stop_retained":
-					change_num,ref_nuc,alt_nuc =  parse_mutation(info[6])
-					change = "%s%s>%s" % (ann_pos,ref_nuc,alt_nuc) if ann_pos else "%s%s>%s" % (pos,ref_nuc,alt_nuc)
-					variants[sample].append({"sample":sample,"gene_id":gene_id,"gene_name":gene_name,"chr":chrom,"genome_pos":pos,"type":info[0],"change":change,"freq":adr[call2],"nucleotide_change":info[6]})
 				elif "frame" in info[0] or "stop_lost" in info[0]:
 					if len(info)<6:
 						if chrom in ann and pos in ann[chrom]:
 							change = "%s%s>%s" % (pos,ref,call2)
 							variants[sample].append({"sample":sample,"gene_id":gene_id,"gene_name":gene_name,"chr":chrom,"genome_pos":pos,"type":info[0],"change":change,"freq":adr[call2],"nucleotide_change":change})
 					else:
 						variants[sample].append({"sample":sample,"gene_id":gene_id,"gene_name":gene_name,"chr":chrom,"genome_pos":pos,"type":info[0],"change":info[6],"freq":adr[call2],"nucleotide_change":info[6]})
+				elif "synonymous" in info[0] or info[0]=="stop_retained":
+					change_num,ref_nuc,alt_nuc =  parse_mutation(info[6])
+					change = "%s%s>%s" % (ann_pos,ref_nuc,alt_nuc) if ann_pos else "%s%s>%s" % (pos,ref_nuc,alt_nuc)
+					variants[sample].append({"sample":sample,"gene_id":gene_id,"gene_name":gene_name,"chr":chrom,"genome_pos":pos,"type":info[0],"change":change,"freq":adr[call2],"nucleotide_change":info[6]})
 				elif info[0]=="non_coding":
 					if chrom in ann and pos in ann[chrom]:
 						gene = ann[chrom][pos][0]