Support "transcript_type" in validate_gtf.py

Made so that if ref gtf uses "transcript_type" as feature it is renamed to "transcript_biotype".
IGDRion · Nov 6, 2024 · a9352c6 · a9352c6
1 parent f83068a
commit a9352c6
Showing 1 changed file with 8 additions and 2 deletions.
diff --git a/bin/validate_gtf.py b/bin/validate_gtf.py
@@ -54,9 +54,15 @@
         record["gene_biotype"] = g_biotype
 
         #######################################################
-        if not "transcript_biotype" in record:
+        if "transcript_biotype" in record:
+            t_biotype = record["transcript_biotype"]
+        elif "transcript_type" in record:
+            record.attributes["transcript_biotype"] = record.attributes["transcript_type"]
+            del record.attributes["transcript_type"]
+            t_biotype = record["transcript_biotype"]
+        else:
             record["transcript_biotype"] = g_biotype
-        t_biotype = record["transcript_biotype"]
+            t_biotype = record["transcript_biotype"]
 
         # Check for RefSeq transcript_biotype format
         if t_biotype == "mRNA":