Print error in append_primers if primers are contained in the original sequence

Author: Donaim

micall/utils/append_primers.py

@@ -43,6 +43,16 @@ def append_primers_to_record(record: SeqRecord,
     is the forward primer + original sequence + reverse primer.
     """
 
+    if fwd_primer in record.seq:
+        pos = record.seq.index(fwd_primer)
+        logger.error("Sequence %r contains the forward primer at position %s.",
+                     record.name, pos)
+
+    if rev_primer in record.seq:
+        pos = record.seq.index(rev_primer)
+        logger.error("Sequence %r contains the reverse primer at position %s.",
+                     record.name, pos)
+
     new_seq = Seq(fwd_primer + str(record.seq) + rev_primer)
     new_record = SeqRecord(
         new_seq,