fix: replace gaps in nucleotide-seq with "N" characters to ensure val…

…id translation when `--keep-gaps` flag is given. (forces ambigious AA call)

AminoExtract/args.py

@@ -153,7 +153,7 @@ def get_args(givenargs: list[str] | None = None) -> argparse.Namespace:
         "-kg",
         action="store_true",
         default=False,
-        help='If this flag is set then the amino acid translation will be done including gaps in the nucleotide sequence.\nThis results in an "X" on gap positions in the aminoacid sequence.\n [underline]By default, gaps are removed before translation.[/underline]',
+        help='If this flag is set then the amino acid translation will be done including gaps in the nucleotide sequence.\n This results in an "X" on gapped positions in the aminoacid sequence as gap characters ("-") will be replaced by "N" in the nucleotide sequence.\n  [underline]By default, gaps are removed before translation.[/underline]',
         required=False,
     )
 

AminoExtract/sequences.py

@@ -82,7 +82,7 @@ def Extract_AminoAcids(
 
         # get the sequence slice from the start to the end position
         seq_slice = (
-            NucSequence[start:end]
+            NucSequence[start:end].replace("-", "N")
             if keep_gaps
             else NucSequence[start:end].replace("-", "")
         )