Bio::Tools::CodonTable::is_start_codon: check in case of ambiguous co…

…dons (#266)

In the case of ambiguous codons this method should only return true if
all possible codons are start codons (same as is_ter_codon).  This was
the behaviour in BioPerl 1.2.3 but since at least BioPerl 1.6.924 it
returns true if at least one codon is a start codon.

This change fixes that regression and makes behaviour consistent with
is_ter_codon.

Changes

@@ -13,6 +13,13 @@ Summary of important user-visible changes for BioPerl
       being used.  This update changes codon tables 3, 15, 24, 27-30,
       32, and 33 [#389, #391].
 
+    * Bio::Tools::CodonTable::is_start_codon now returns true when all
+      possible codons (in the case of ambiguous codons such as NTG)
+      are start codons.  For some recent versions it was return true
+      if any of the codons was a start codon.  This change is
+      consistent with the behaviour of is_ter_codon and returns to the
+      (very) old behaviour [#266].
+
 1.7.8     2021-02-02 23:02:18-06:00 America/Chicago
     * Bio::SeqIO::interpro has been moved to a separate repository to
       deal with issues with XML::DOM::XPath bitrot [#347]

lib/Bio/Tools/CodonTable.pm

@@ -646,7 +646,9 @@ sub reverse_translate_best {
  Title   : is_start_codon
  Usage   : $obj->is_start_codon('ATG')
  Function: returns true (1) for all codons that can be used as a
-           translation start, false (0) for others.
+           translation start, false (0) for others.  In the case of
+           ambiguous codons, e.g., 'NTG', only returns true if all
+           possible codons are true.
  Example : $myCodonTable->is_start_codon('ATG')
  Returns : boolean
  Args    : codon
@@ -662,7 +664,9 @@ sub is_start_codon{
  Title   : is_ter_codon
  Usage   : $obj->is_ter_codon('GAA')
  Function: returns true (1) for all codons that can be used as a
-           translation tarminator, false (0) for others.
+           translation terminator, false (0) for others. In the case
+           of ambiguous codons, e.g., 'TAN', only returns true if all
+           possible codons are true.
  Example : $myCodonTable->is_ter_codon('ATG')
  Returns : boolean
  Args    : codon
@@ -699,12 +703,13 @@ sub is_ter_codon{
 
 # desc: compares the passed value with a single entry in the given
 #       codon table
-# args: a value (typically a three-char string like 'atg'),
-#       a reference to the appropriate set of codon tables,
-#       a single-character value to check for at the position in the
-#       given codon table
+# args: a value (typically a three-char string like 'atg'), a
+#       reference to the appropriate set of codon tables, a
+#       single-character value to check for at the position in the
+#       given codon table.
 # ret:  boolean, true if the given codon table contains the $key at the
-#       position corresponding to $value
+#       position corresponding to $value.  In the case of ambiguous
+#       codons, only returns true if all possibilities match $key.
 sub _codon_is {
    my ($self, $value, $table, $key ) = @_;
 
@@ -714,11 +719,16 @@ sub _codon_is {
    $value  =~ tr/u/t/;
 
    my $id = $self->{'id'};
+   my $result = 0;
    for my $c ( $self->unambiguous_codons($value) ) {
        my $m = substr( $table->[$id], $CODONS->{$c}, 1 );
-       if ($m eq $key) { return 1; }
+       if ($m eq $key) {
+           $result = 1;
+       } else {
+           return 0;
+       }
    }
-   return 0;
+   return $result;
 }
 
 =head2 is_unknown_codon

t/SeqTools/CodonTable.t

@@ -6,7 +6,7 @@ use strict;
 BEGIN {
     use Bio::Root::Test;
 
-    test_begin(-tests => 91);
+    test_begin(-tests => 94);
 
     use_ok('Bio::Tools::CodonTable');
     use_ok('Bio::CodonUsage::IO');
@@ -185,6 +185,10 @@ is $myCodonTable->is_ter_codon('NNN'), 0, 'is_ter_codon, ambiguous codons should
 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';
 
+is $myCodonTable->is_start_codon('NNN'), 0, 'is_start_codon, ambiguous codons should fail, NNN';
+is $myCodonTable->is_start_codon('NTG'), 0, 'is_start_codon, ambiguous codons should fail, NTG';
+is $myCodonTable->is_start_codon('N'), 0, 'is_start_codon, incomplete codons should fail, NN';
+
 ok $myCodonTable->is_unknown_codon('jAG');
 ok $myCodonTable->is_unknown_codon('jg');
 is $myCodonTable->is_unknown_codon('UAG'), 0;