Interpret : or = for gene token in fasta files

davidemms · Jan 6, 2021 · 425347e · 425347e
1 parent cab6c69
commit 425347e
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/tools/primary_transcript.py b/tools/primary_transcript.py
@@ -43,7 +43,7 @@ def ScanTags_with_fn(fn, gene_name_fn):
     # print(sorted(genes)[:10])
 
 def GetGeneName(acc_line):
-    tokens = [t.split(":")[1] for t in acc_line.rstrip().split() if "gene:" in t]
+    tokens = [(t.split("=") if "=" in t else t.split(":"))[1] for t in acc_line.rstrip().split() if ("gene:" in t or "gene=" in t)]
     if len(tokens) != 1: return None
     return tokens[0]