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Commit 71a2ee81 authored by Graham McVicker's avatar Graham McVicker
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use arg strand in Slice::subseq so that SequenceAdaptor does reverse...

use arg strand in Slice::subseq so that SequenceAdaptor does reverse complimenting (it has more complete transliteration) rather than exon code
parent ace95e66
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......@@ -791,22 +791,14 @@ sub seq {
if ( ! defined $self->slice ) {
warning(" this exon doesn't have a slice you won't get a seq \n");
return undef;
} else {
$seq = $self->slice()->subseq($self->start, $self->end, $self->strand);
}
else {
$seq = $self->slice()->subseq($self->start, $self->end);
if($self->strand == -1){
$seq =~ tr/ATGCatgc/TACGtacg/;
$seq = reverse($seq);
}
}
$self->{'_seq_cache'} = $seq;
return Bio::Seq->new(-seq => $self->{'_seq_cache'},
-id => $self->stable_id,
-moltype => 'dna');
-id => $self->stable_id,
-moltype => 'dna');
}
......
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