- is_ter_codon was incorrectly returning ambiguous codons as stop cod…

…ons (ie. NNN was being returned true), any failure in the list of unambiguous codons should return false, the opposite was occuring

- U was not being remapped to T, it's needed for UAG and such
- Added tests for better coverage of corner cases

Bio/Tools/CodonTable.pm

@@ -726,7 +726,31 @@ sub is_start_codon{
 =cut
 
 sub is_ter_codon{
-    shift->_codon_is( shift, \@TABLES, $TERMINATOR );
+   my ($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;
+   }
 }
 
 # desc: compares the passed value with a single entry in the given

t/SeqTools/CodonTable.t

@@ -160,16 +160,21 @@ ok $test;
 # boolean tests
 $myCodonTable->id(1); # Standard table
 
-ok $myCodonTable->is_start_codon('ATG');
-is $myCodonTable->is_start_codon('GGH'), 0;
-ok $myCodonTable->is_start_codon('HTG');
-is $myCodonTable->is_start_codon('CCC'), 0;
-
-ok $myCodonTable->is_ter_codon('UAG');
-ok $myCodonTable->is_ter_codon('TaG');
-ok $myCodonTable->is_ter_codon('TaR');
-ok $myCodonTable->is_ter_codon('tRa');
-is $myCodonTable->is_ter_codon('ttA'), 0;
+ok $myCodonTable->is_start_codon('ATG'), 'is_start_codon, ATG';
+is $myCodonTable->is_start_codon('GGH'), 0, 'is_start_codon, GGH';
+ok $myCodonTable->is_start_codon('HTG'), 'is_start_codon, HTG';
+is $myCodonTable->is_start_codon('CCC'), 0, 'is_start_codon, CCC';
+
+ok $myCodonTable->is_ter_codon('UAG'), 'is_ter_codon, U should map to T, UAG';
+ok $myCodonTable->is_ter_codon('TaG'), 'is_ter_codon,TaG';
+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';
+is $myCodonTable->is_ter_codon('CC'), 0, 'is_ter_codon, incomplete codons should fail, CC';
 
 ok $myCodonTable->is_unknown_codon('jAG');
 ok $myCodonTable->is_unknown_codon('jg');