skip sequence too short <100 bp

NBISweden · Apr 17, 2019 · 6f326e9 · 6f326e9
1 parent 76916c5
commit 6f326e9
Showing 1 changed file with 3 additions and 1 deletion.
diff --git a/EMBLmyGFF3/EMBLmyGFF3.py b/EMBLmyGFF3/EMBLmyGFF3.py
@@ -1340,7 +1340,9 @@ def main():
         infile.seek(0, 0)
 
     for record in GFF.parse(infile, base_dict=seq_dict):
-
+        if len(record.seq)<100:
+            logging.warning("Sequence %s too short (%s bp)! Minimum accpeted by ENA is 100, we skip it !" % (record.name, len(record.seq) ) )
+            continue
         writer = EMBL( record, True )
 
         #To set up first