From 522c6efb8f092ac2dcaec6fbca93977e0cf8f900 Mon Sep 17 00:00:00 2001
From: Graham McVicker <mcvicker@sanger.ac.uk>
Date: Mon, 23 Feb 2004 15:29:32 +0000
Subject: [PATCH] moved reverse_comp method into Bio::EnsEMBL::Utils::Sequence
module
---
modules/Bio/EnsEMBL/DBSQL/SequenceAdaptor.pm | 30 +++-----------------
1 file changed, 4 insertions(+), 26 deletions(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/SequenceAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/SequenceAdaptor.pm
index 94fd5ef64b..1ebe0694b8 100644
--- a/modules/Bio/EnsEMBL/DBSQL/SequenceAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/SequenceAdaptor.pm
@@ -36,6 +36,7 @@ use strict;
use Bio::EnsEMBL::DBSQL::BaseAdaptor;
use Bio::EnsEMBL::Utils::Exception qw(throw deprecate);
+use Bio::EnsEMBL::Utils::Sequence qw(reverse_comp);
@ISA = qw(Bio::EnsEMBL::DBSQL::BaseAdaptor);
@@ -110,7 +111,7 @@ sub fetch_by_Slice_start_end_strand {
1,undef,1)};
}
if($strand == -1) {
- _reverse_comp(\$seq);
+ reverse_comp(\$seq);
}
return \$seq;
}
@@ -144,7 +145,7 @@ sub fetch_by_Slice_start_end_strand {
#reverse compliment on negatively oriented slices
if($seq_slice->strand == -1) {
- _reverse_comp(\$tmp_seq);
+ reverse_comp(\$tmp_seq);
}
$seq .= $tmp_seq;
@@ -166,7 +167,7 @@ sub fetch_by_Slice_start_end_strand {
}
#if they asked for the negative slice strand revcomp the whole thing
- _reverse_comp(\$seq) if($strand == -1);
+ reverse_comp(\$seq) if($strand == -1);
return \$seq;
}
@@ -230,29 +231,6 @@ sub store {
}
-=head2 _reverse_comp
-
- Arg [1] : reference to a string $seqref
- Example : $self->_reverse_comp(\$seqref);
- Description: Does an in place reverse compliment of a passed in string
- reference. The string is passed by reference
- rather than by value for memory efficiency.
- Returntype : none
- Exceptions : none
- Caller : internal
-
-=cut
-
-sub _reverse_comp {
- my $seqref = shift;
-
- $$seqref = reverse( $$seqref );
- $$seqref =~
- tr/acgtrymkswhbvdnxACGTRYMKSWHBVDNX/tgcayrkmswdvbhnxTGCAYRKMSWDVBHNX/;
-
- return undef;
-}
-
=head2 fetch_by_assembly_location
--
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