get last tests passing

cjfields · Sep 2, 2014 · efe000a · efe000a
1 parent 837b7ba
commit efe000a
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Showing 2 changed files with 14 additions and 16 deletions.
diff --git a/lib/Bio/Tools/CodonTable.pm6 b/lib/Bio/Tools/CodonTable.pm6
@@ -117,15 +117,14 @@ method name() {
 }
 
 method tables() {
-  my %tables;
-  for  1 .. @!NAMES ->  $id {
-    my $name = @!NAMES[$id-1];
-    %tables{$id} = $name if $name;
-  }
-  return %tables;
+    my %tables;
+    for  1 .. @!NAMES ->  $id {
+      my $name = @!NAMES[$id-1];
+      %tables{$id} = $name if $name;
+    }
+    return %tables;
 }
 
-
 method translate($seq is copy,
                 :$terminator? is copy,
                 :$unknown is copy) {
@@ -151,10 +150,9 @@ method translate($seq is copy,
     }
 
     # any leftover?  TODO: this doesn't account for possible gaps
-    my $partial = $seq.chars % CODONSIZE;
-
-    if $partial == 2 {
-        $protein ~= self!translate_ambiguous_codon( $seq.substr(*-2, 2).lc ~ 'n' );
+    if $seq.chars % CODONSIZE == 2 {
+        my $aa = self!translate_ambiguous_codon( $seq.substr(*-2, 2).lc ~ 'n' );
+        $protein ~= $aa if $aa ne 'X';
     }
 
     return $protein;

diff --git a/t/Tools/CodonTable.t b/t/Tools/CodonTable.t
@@ -47,11 +47,11 @@ for @ii Z @res -> $dna,$aa {
     is($myCodonTable.translate($dna), $aa, "$dna: $aa");
 }
 ok ($test);
-is $myCodonTable.translate('ag'), '';
-is $myCodonTable.translate('jj'), '';
-is $myCodonTable.translate('jjg'), 'X';
-is $myCodonTable.translate('gt'), 'V';
-is $myCodonTable.translate('g'), '';
+is $myCodonTable.translate('ag'), '', 'ag:';
+is $myCodonTable.translate('jj'), '', 'jj:';
+is $myCodonTable.translate('jjg'), 'X', 'jjg:Z';
+is $myCodonTable.translate('gt'), 'V', 'gt:V';
+is $myCodonTable.translate('g'), '', 'gt:V';
 
 # a more comprehensive test on ambiguous codes
 my $seq = "