updated make_ref to set gene symbol instead of ensg in sym2ref when using ensembl

SCRIPTS/make_ref.py

@@ -278,12 +278,21 @@ def processEnsembl(fastaString, fastaOut, annotOut):
             # Split track name by ' '. Transcript ID is on 1st field, gene symbol is on 7th field.
             ls = line.decode("utf-8").split(" ")
             fastaMod += ls[0]+"\n"
-            geneField = 1
+            geneSymbol = 1
+            enst = 1
+            found = False
             for i in range(1,len(ls)):
                 if(ls[i].startswith("gene:")):
-                    geneField = i
+                    enst = i
+                    continue
+                if(ls[i].startswith("gene_symbol:")):
+                    geneSymbol = i
+                    found = True
                     break
-            geneName = ls[geneField].split(":")[1].rstrip('\n')
+            if(not found):
+                geneName = ls[enst].split(":")[1].rstrip('\n')
+            else:
+                geneName = ls[geneSymbol].split(":")[1].rstrip('\n')
             if(not geneName in gene2transcripts):
                 gene2transcripts[geneName] = set()
             gene2transcripts[geneName].add(ls[0][1:])