fix parser. Key not found when there

is no gene SYMBOL in vcf record. closes #10
icbi-lab · Aug 3, 2022 · 09d2f0c · 09d2f0c
1 parent c729c06
commit 09d2f0c
Showing 1 changed file with 3 additions and 0 deletions.
diff --git a/bin/parse_mixMHC2pred.py b/bin/parse_mixMHC2pred.py
@@ -76,6 +76,8 @@ def parse_vcf(vep_vcf, sample_name, normal_name):
         enst = CSQ[6]
         variant = CSQ[14] + CSQ[15]
 
+        gene_symbol = gene_symbol if gene_symbol else ensg
+
         vcf_record = {
             "chrom": chrom,
             "pos": pos,
@@ -94,6 +96,7 @@ def parse_vcf(vep_vcf, sample_name, normal_name):
             "variant": variant,
         }
 
+
         if "frameshift_variant" in variant_type.split("&"):
             key = gene_symbol + "_" + enst + "_" + CSQ[14] + ref + "/" + alt
         else: