From 120a20ad837458e825e150e6a52d1431b7726e9d Mon Sep 17 00:00:00 2001
From: Jacques Dainat <jacques.dainat@ird.fr>
Date: Fri, 16 Feb 2024 18:13:09 +0100
Subject: [PATCH 1/2] is_ter_codon and is_start_codon do not behaves thesame.
 Now it does. is_ter_codon was not verifying all unambiguous_codons, but only
 the first.

---
 lib/Bio/Tools/CodonTable.pm | 29 +++--------------------------
 1 file changed, 3 insertions(+), 26 deletions(-)

diff --git a/lib/Bio/Tools/CodonTable.pm b/lib/Bio/Tools/CodonTable.pm
index 315c541d48..0cfdfbf845 100644
--- a/lib/Bio/Tools/CodonTable.pm
+++ b/lib/Bio/Tools/CodonTable.pm
@@ -735,10 +735,10 @@ sub is_start_codon{
 =head2 is_ter_codon
 
  Title   : is_ter_codon
- Usage   : $obj->is_ter_codon('GAA')
+ Usage   : $obj->is_ter_codon('TGA')
  Function: returns true (1) for all codons that can be used as a
            translation tarminator, false (0) for others.
- Example : $myCodonTable->is_ter_codon('ATG')
+ Example : $myCodonTable->is_ter_codon('TGA')
  Returns : boolean
  Args    : codon
 
@@ -746,30 +746,7 @@ sub is_start_codon{
 
 sub is_ter_codon{
    my ($self, $value) = @_;
-   my $id = $self->{'id'};
-
-   # We need to ensure U is mapped to T (ie. UAG)
-   $value = uc $value;
-   $value =~ tr/U/T/;
-
-   if (length $value != 3  )  {
-       # Incomplete codons are not stop codons
-       return 0;
-   } else {
-       my $result = 0;
-
-       # For all the possible codons, if any are not a stop
-       # codon, fail immediately
-       for my $c ( $self->unambiguous_codons($value) ) {
-	   my $m = substr( $TABLES[$id], $CODONS->{$c}, 1 );
-	   if($m eq $TERMINATOR) {
-	       $result = 1;
-	   } else {
-	       return 0;
-	   }
-       }
-       return $result;
-   }
+   shift->_codon_is( shift, \@STARTS, '*' );
 }
 
 # desc: compares the passed value with a single entry in the given

From d3ae01edbcbf175f60af714dc0cdba363bc845b4 Mon Sep 17 00:00:00 2001
From: Jacques Dainat <jacques.dainat@ird.fr>
Date: Wed, 21 Feb 2024 11:44:13 +0100
Subject: [PATCH 2/2] add ambiguous codons tests for is_start_codon and modify
 ambiguous codons tests for is_ter_codon

---
 t/SeqTools/CodonTable.t | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

diff --git a/t/SeqTools/CodonTable.t b/t/SeqTools/CodonTable.t
index f8cba9c4e6..6fd5edbb1a 100644
--- a/t/SeqTools/CodonTable.t
+++ b/t/SeqTools/CodonTable.t
@@ -6,7 +6,7 @@ use strict;
 BEGIN {
     use Bio::Root::Test;
 
-    test_begin(-tests => 84);
+    test_begin(-tests => 87);
 
     use_ok('Bio::Tools::CodonTable');
     use_ok('Bio::CodonUsage::IO');
@@ -170,9 +170,13 @@ ok $myCodonTable->is_ter_codon('TaR'), 'is_ter_codon,TaR';
 ok $myCodonTable->is_ter_codon('tRa'), 'is_ter_codon,tRa';
 is $myCodonTable->is_ter_codon('ttA'), 0, 'is_ter_codon,ttA';
 
-# Ambiguous codons should fail
-is $myCodonTable->is_ter_codon('NNN'), 0, 'is_ter_codon, ambiguous codons should fail, NNN';
-is $myCodonTable->is_ter_codon('TAN'), 0, 'is_ter_codon, ambiguous codons should fail, TAN';
+# Ambiguous codons
+is $myCodonTable->is_start_codon('NNN'), 1, 'is_start_codon, ambiguous codons should succeed, NNN';
+is $myCodonTable->is_start_codon('ATN'), 1, 'is_start_codon, ambiguous codons should succeed, ATN';
+is $myCodonTable->is_start_codon('CC'), 0, 'is_ter_codon, incomplete codons should fail, CC';
+
+is $myCodonTable->is_ter_codon('NNN'), 1, 'is_ter_codon, ambiguous codons should succeed, NNN';
+is $myCodonTable->is_ter_codon('TAN'), 1, 'is_ter_codon, ambiguous codons should succeed, TAN';
 is $myCodonTable->is_ter_codon('CC'), 0, 'is_ter_codon, incomplete codons should fail, CC';
 
 ok $myCodonTable->is_unknown_codon('jAG');