From e9bd0fad035f0976772600c1061454e1b421e926 Mon Sep 17 00:00:00 2001
From: Florent Angly <florent.angly@gmail.com>
Date: Wed, 31 Oct 2012 12:20:55 +1000
Subject: [PATCH] Avoid new() just to revcom() a sequence

... use Bio::PrimarySeqI::_revcom_from_string instead
---
 Bio/PrimarySeq.pm  | 14 +++++++-------
 t/Seq/PrimarySeq.t |  2 +-
 2 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/Bio/PrimarySeq.pm b/Bio/PrimarySeq.pm
index 3cf012583..a53169126 100644
--- a/Bio/PrimarySeq.pm
+++ b/Bio/PrimarySeq.pm
@@ -378,15 +378,15 @@ sub subseq {
 
     if( ref($start) && $start->isa('Bio::LocationI') ) {
         my $loc = $start;
-        my $seq = "";
+        my $seq = '';
         foreach my $subloc ($loc->each_Location()) {
-            my $piece = $self->subseq(-START        => $subloc->start(),
-                                      -END          => $subloc->end(),
-                                      -REPLACE_WITH => $replace,
-                                      -NOGAP        => $nogap);
+            my $piece = $self->subseq(-start        => $subloc->start(),
+                                      -end          => $subloc->end(),
+                                      -replace_with => $replace,
+                                      -nogap        => $nogap);
             $piece =~ s/[$GAP_SYMBOLS]//g if $nogap;
-            if($subloc->strand() < 0) {
-                $piece = Bio::PrimarySeq->new( -seq => $piece)->revcom()->seq();
+            if ($subloc->strand() < 0) {
+                $piece = $self->_revcom_from_string($piece, $self->alphabet);
             }
             $seq .= $piece;
         }
diff --git a/t/Seq/PrimarySeq.t b/t/Seq/PrimarySeq.t
index aa93875b5..549a125fe 100644
--- a/t/Seq/PrimarySeq.t
+++ b/t/Seq/PrimarySeq.t
@@ -8,7 +8,7 @@ BEGIN {
     use lib '.';
     use Bio::Root::Test;
 
-    test_begin( -tests => 163 );
+    test_begin( -tests => 164 );
 
     use_ok('Bio::PrimarySeq');
     use_ok('Bio::Location::Simple');
-- 
2.11.4.GIT