From 3c2b7d36ae1c88ddf6fff491c663a5431f998952 Mon Sep 17 00:00:00 2001
From: Graham McVicker <mcvicker@sanger.ac.uk>
Date: Mon, 23 Feb 2004 15:27:50 +0000
Subject: [PATCH] corrected bug in Slice::subseq which did not correctly obtain
sequence when slice sequence was manually loaded
---
modules/Bio/EnsEMBL/Slice.pm | 6 ++++--
1 file changed, 4 insertions(+), 2 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Slice.pm b/modules/Bio/EnsEMBL/Slice.pm
index f18186787c..b1115e00e1 100644
--- a/modules/Bio/EnsEMBL/Slice.pm
+++ b/modules/Bio/EnsEMBL/Slice.pm
@@ -70,6 +70,7 @@ use Bio::EnsEMBL::Utils::Argument qw(rearrange);
use Bio::EnsEMBL::Utils::Exception qw(throw deprecate warning);
use Bio::EnsEMBL::RepeatMaskedSlice;
+use Bio::EnsEMBL::Utils::Sequence qw(reverse_comp);
#inheritance to Bio::EnsEMBL::Root will eventually be removed
@ISA = qw(Bio::EnsEMBL::Root Bio::PrimarySeqI);
@@ -474,8 +475,9 @@ sub subseq {
$subseq = ${$seqAdaptor->fetch_by_Slice_start_end_strand
( $self, $start,
$end, $strand )};
- }else{
- $subseq = substr ($self->seq(), ($start-1), $end);
+ } else {
+ $subseq = substr ($self->seq(), $start-1, $end - $start + 1);
+ reverse_comp(\$subseq) if($strand == -1);
}
return $subseq;
}
--
GitLab