From 4d7119460292ed3c2a123d6a2f568611dc12beee Mon Sep 17 00:00:00 2001
From: aparton <aparton@ebi.ac.uk>
Date: Fri, 13 Sep 2019 11:49:51 +0100
Subject: [PATCH 1/4] Return subseq from correct side of seq when on reverse
 strand using a fasta file

---
 .../Bio/EnsEMBL/Variation/Utils/FastaSequence.pm    | 13 +++++++++++--
 1 file changed, 11 insertions(+), 2 deletions(-)

diff --git a/modules/Bio/EnsEMBL/Variation/Utils/FastaSequence.pm b/modules/Bio/EnsEMBL/Variation/Utils/FastaSequence.pm
index 075bf38c97..c35ae8afe9 100644
--- a/modules/Bio/EnsEMBL/Variation/Utils/FastaSequence.pm
+++ b/modules/Bio/EnsEMBL/Variation/Utils/FastaSequence.pm
@@ -361,9 +361,18 @@ sub _new_slice_seq {
     my ($self, $start, $end, $strand, $preserve_masking) = @_;
     my ($seq, $length) = ('', 0);
 
-    $start = $start ? ($self->start + $start) - 1 : $self->start;
-    $end   = $end   ? ($self->start + $end) - 1   : $self->end;
     $strand = defined($strand) ? $strand * $self->strand : $self->strand;
+    
+    if($strand == 1) {  
+      $start = $start ? ($self->start + $start) - 1 : $self->start;
+      $end   = $end   ? ($self->start + $end) - 1   : $self->end;
+    }
+    else{
+      my $old_end = $end;
+      $end = $end ? ($self->end - $start) + 1 : $self->end;
+      $start   = $start   ? ($self->end - $old_end) + 1   : $self->start;
+    }
+    
     my $sr_name = $self->seq_region_name;
 
     # indels

From 5933790bd9735016367b7ee4834614d6a4f52cc7 Mon Sep 17 00:00:00 2001
From: aparton <aparton@ebi.ac.uk>
Date: Fri, 13 Sep 2019 13:44:33 +0100
Subject: [PATCH 2/4] Call the strand in the right place

---
 modules/Bio/EnsEMBL/Variation/Utils/FastaSequence.pm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/modules/Bio/EnsEMBL/Variation/Utils/FastaSequence.pm b/modules/Bio/EnsEMBL/Variation/Utils/FastaSequence.pm
index c35ae8afe9..43e52f1e73 100644
--- a/modules/Bio/EnsEMBL/Variation/Utils/FastaSequence.pm
+++ b/modules/Bio/EnsEMBL/Variation/Utils/FastaSequence.pm
@@ -363,14 +363,14 @@ sub _new_slice_seq {
 
     $strand = defined($strand) ? $strand * $self->strand : $self->strand;
     
-    if($strand == 1) {  
+    if($self->strand == 1) {  
       $start = $start ? ($self->start + $start) - 1 : $self->start;
       $end   = $end   ? ($self->start + $end) - 1   : $self->end;
     }
     else{
-      my $old_end = $end;
+      my $input_end = $end;
       $end = $end ? ($self->end - $start) + 1 : $self->end;
-      $start   = $start   ? ($self->end - $old_end) + 1   : $self->start;
+      $start   = $start   ? ($self->end - $input_end) + 1   : $self->start;
     }
     
     my $sr_name = $self->seq_region_name;

From c7dc1eb1d40cb6c3541525d9fe6184143aea4392 Mon Sep 17 00:00:00 2001
From: aparton <aparton@ebi.ac.uk>
Date: Fri, 13 Sep 2019 14:39:01 +0100
Subject: [PATCH 3/4] Add test for slices on reverse strand

---
 modules/t/fastaSequence.t | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/modules/t/fastaSequence.t b/modules/t/fastaSequence.t
index 8a86158107..38c1cf9384 100644
--- a/modules/t/fastaSequence.t
+++ b/modules/t/fastaSequence.t
@@ -114,6 +114,14 @@ is($slice1->subseq(3, 5, -1), 'CCA', 'subseq rev');
 is($slice1->subseq(5, 4), '', 'subseq e > s');
 is($slice1->subseq(-1, 5), 'CGCATGG', "subseq overlap 5'");
 
+# test subseq on transcript feature slice on reverse strand
+my $stable_id = 'ENST00000346798';
+my $transcript_adaptor = $cdb->get_TranscriptAdaptor();
+my $transcript = $transcript_adaptor->fetch_by_stable_id($stable_id);
+my $transcript_slice = $transcript->feature_Slice;
+is($transcript_slice->subseq(1, 2), 'CA', 'subseq on slice on reverse strand');
+
+
 
 # test going off ends
 $slice1 = $sa->fetch_by_region('chromosome', 21, 1, 10);

From f68290dcf8ff20384fa409869f3ff4123ed7f763 Mon Sep 17 00:00:00 2001
From: Andrew Parton <aparton@ebi.ac.uk>
Date: Thu, 20 Feb 2020 17:02:12 +0000
Subject: [PATCH 4/4] Use correct coordinates when falling back to database for
 patch sequence

---
 modules/Bio/EnsEMBL/Variation/Utils/FastaSequence.pm | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/modules/Bio/EnsEMBL/Variation/Utils/FastaSequence.pm b/modules/Bio/EnsEMBL/Variation/Utils/FastaSequence.pm
index 43e52f1e73..55e14d685c 100644
--- a/modules/Bio/EnsEMBL/Variation/Utils/FastaSequence.pm
+++ b/modules/Bio/EnsEMBL/Variation/Utils/FastaSequence.pm
@@ -360,7 +360,10 @@ sub _new_slice_seq {
   return sub {
     my ($self, $start, $end, $strand, $preserve_masking) = @_;
     my ($seq, $length) = ('', 0);
-
+    
+    my $orig_start = $start;
+    my $orig_end = $end;
+    
     $strand = defined($strand) ? $strand * $self->strand : $self->strand;
     
     if($self->strand == 1) {  
@@ -405,7 +408,7 @@ sub _new_slice_seq {
         print STDERR "USING DATABASE\n" if $DEBUG;
         return
           scalar(@_) > 1 ?
-          $self->_fasta_old_db_subseq($start, $end, $strand) :
+          $self->_fasta_old_db_subseq($orig_start, $orig_end, $strand) :
           $self->_fasta_old_db_seq();
       }
     }