Completed translation mechanism

msa_splitter.py

@@ -196,14 +196,17 @@ def trim(
             )
 
         if perform_translation:
-            aa_sequence = Seq(nt_sequence.replace("-", "n")).translate()
+            aa_sequence = (
+                s_record.seq[tru_start + start_shift - 1 : end + end_shift]
+                .replace("-", "n")
+                .translate()
+            )
+
             aa_sequence_records.append(
                 SeqRecord.SeqRecord(aa_sequence, *record_metadata)
             )
             if gen_cut_stop_codon:
-                aa_no_stop_sequence = Seq(
-                    nt_no_stop_sequence.replace("-", "n")
-                ).translate()
+                aa_no_stop_sequence = aa_sequence[:-1]
                 aa_no_stop_sequence_records.append(
                     SeqRecord.SeqRecord(aa_no_stop_sequence, *record_metadata)
                 )