Merge pull request #222 from udp3f/master

add VEP format for version 73
arq5x · Oct 7, 2013 · b252630 · b252630
2 parents 0ba53e7 + 7bebc6a
commit b252630
Showing 1 changed file with 5 additions and 1 deletion.
diff --git a/gemini/gemini_load_chunk.py b/gemini/gemini_load_chunk.py
@@ -171,10 +171,14 @@ def _is_proper_vep_input(self):
         Test whether the VCF header meets expectations for
         proper execution of VEP for use with Gemini.
         """
+        #support versions >2.4<73
         format = "Consequence|Codons|Amino_acids|Gene|HGNC|Feature|EXON|PolyPhen|SIFT".upper()
+        #support version 73
+        format73 = "Consequence|Codons|Amino_acids|Gene|SYMBOL|Feature|EXON|PolyPhen|SIFT".upper()
 
         if 'CSQ' in self.vcf_reader.infos and \
-                format in str(self.vcf_reader.infos['CSQ']).upper():
+                (format in str(self.vcf_reader.infos['CSQ']).upper() or \
+                format73 in str(self.vcf_reader.infos['CSQ']).upper()):
             return True
         return False