Completed translation mechanism

2023-03-28 15:56:50 -05:00 · 2023-03-28 15:56:50 -05:00 · 0c5f188b80
commit 0c5f188b80
parent 03d87a670f
2 changed files with 34641 additions and 4 deletions
--- a/msa_splitter.py
+++ b/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)
                )
--- a/tests/resources/test_msa_transl.aln
+++ b/tests/resources/test_msa_transl.aln