Commit 522c6efb authored by Graham McVicker's avatar Graham McVicker
Browse files

moved reverse_comp method into Bio::EnsEMBL::Utils::Sequence module

parent 799274db
......@@ -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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