Updated trunk to 0.5.5

git-svn-id: https://jcvi-tools.svn.sourceforge.net/svnroot/jcvi-tools/JCVI-Translator/trunk@24 a16988d2-67c9-4db9-a897-0603be59747b
kgalinsky · Oct 28, 2009 · b70f30e · b70f30e
1 parent 3e7a1bf
commit b70f30e
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Showing 4 changed files with 13 additions and 10 deletions.
diff --git a/Changes b/Changes
@@ -1,5 +1,8 @@
 Revision history for JCVI-Translator
 
+0.5.5   Apr 23 2009
+  - Fixed bug in Base where Xs weren't being put in when base isn't found
+
 0.5.4   Apr 15 2009
   - Put use version on same line as $VERSION declared
   - Added META.yml so make dist would work

diff --git a/lib/JCVI/Translator.pm b/lib/JCVI/Translator.pm
@@ -66,7 +66,7 @@ package JCVI::Translator;
 use strict;
 use warnings;
 
-use version; our $VERSION = qv('0.5.4');
+use version; our $VERSION = qv('0.5.5');
 
 use base qw(Class::Accessor::Fast);
 __PACKAGE__->mk_accessors(qw(table base));

diff --git a/lib/JCVI/Translator/Base.pm b/lib/JCVI/Translator/Base.pm
@@ -193,7 +193,7 @@ sub translate {
 
         # Grab the codon, and look it up in the translation table
         my $codon = substr( $$seq_ref, $index, 3 );
-        push @residues, $self->{table}->{$codon};
+        push @residues, $self->{table}->{$codon} || 'X';
 
         # Increment the index
         $index += $self->{increment};
@@ -212,7 +212,7 @@ sub start {
     my ($self) = @_;
 
     # If start == stop, don't do anything
-    return '' if ( $self->{start} == $self->{stop} );
+    return () if ( $self->{start} == $self->{stop} );
 
     my $seq_ref = $self->{seq_ref};
 
@@ -221,7 +221,7 @@ sub start {
     my $start   = $self->{starts}->{$codon};
 
     # Return the empty string if start isn't found in the translation table
-    return '' unless ($start);
+    return () unless ($start);
 
     # Increment the start location and return the start codon
     $self->{start} += $self->{increment};

diff --git a/t/01-translate.t b/t/01-translate.t
@@ -26,11 +26,8 @@ is( ${ $translator->translate( \$seq, { strand => -1, upper => 59 } ) },
 is( ${ $translator->translate( \$seq, { strand => -1, upper => 58 } ) },
     'MGPRGTGGA*RSRMACMIS', 'Translate frame -3' );
 
-is(
-    ${ $translator->translate( \$seq, { partial => 1 } ) },
-    'LISCMPFSTAMRLLFLVGPK',
-    q{Translate 5' partial frame 1}
-);
+is( ${ $translator->translate( \$seq, { partial => 1 } ) },
+    'LISCMPFSTAMRLLFLVGPK', q{Translate 5' partial frame 1} );
 
 is(
     ${
@@ -39,4 +36,7 @@ is(
       },
     'LGPRGTGGA*RSRMACMIS',
     q{Translate 5' partial frame -3}
-);
+);
+
+is( ${ $translator->translate( \'NNN' ) }, 'X',
+    q{Translate not found as 'X'} )