From ce90f95874ac2e0eb2d032b5639ad26d2a0bbb72 Mon Sep 17 00:00:00 2001
From: Eugene Kulesha <ek@ebi.ac.uk>
Date: Fri, 1 Oct 2010 16:27:27 +0000
Subject: [PATCH] exons of the genes overlapping chromosome origin are attached
to the normal slice, but with negative coordinates
---
modules/Bio/EnsEMBL/Exon.pm | 41 +++++++++++++++++++------------------
1 file changed, 21 insertions(+), 20 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Exon.pm b/modules/Bio/EnsEMBL/Exon.pm
index 2181223b15..df5494ac0d 100755
--- a/modules/Bio/EnsEMBL/Exon.pm
+++ b/modules/Bio/EnsEMBL/Exon.pm
@@ -1441,27 +1441,28 @@ sub seq {
return undef;
}
- if ( $self->slice->start() > $self->slice->end()
- && $self->slice->is_circular() )
- {
- my $mid_point =
- $self->slice()->seq_region_length() -
- $self->slice()->start() + 1;
-
- my $seq1 =
- $self->slice()
- ->subseq( $self->start(), $mid_point, $self->strand() );
-
- my $seq2 =
- $self->slice()
- ->subseq( $mid_point + 1, $self->end(), $self->strand() );
-
- $seq = $self->strand() > 0 ? "$seq1$seq2" : "$seq2$seq1";
-
+ if ($self->slice->is_circular() ) {
+ if ( $self->slice->start > $self->slice->end) {
+# Normally exons overlapping chromosome origin will have negative feature start, but slice will be from 1 .. length
+# But in case you got an exon attached to a sub slice try this
+ my $mid_point = $self->slice()->seq_region_length() - $self->slice()->start() + 1;
+ my $seq1 = $self->slice()->subseq( $self->start(), $mid_point, $self->strand() );
+
+ my $seq2 = $self->slice()->subseq( $mid_point + 1, $self->end(), $self->strand() );
+
+ $seq = $self->strand() > 0 ? "$seq1$seq2" : "$seq2$seq1";
+ } elsif ( $self->start < 0) {
+# Normally exons overlapping chromosome origin will have negative start
+ my $start_point = $self->slice->seq_region_length + $self->slice->start;
+ my $mid_point = $self->slice->seq_region_length;
+ my $seq1 = $self->slice->subseq( $self->start, $mid_point, $self->strand);
+ my $seq2 = $self->slice->subseq(1, $self->end, $self->strand );
+ $seq = $self->strand > 0 ? "$seq1$seq2" : "$seq2$seq1";
+ } else {
+ $seq = $self->slice()->subseq( $self->start(), $self->end(), $self->strand() );
+ }
} else {
- $seq =
- $self->slice()
- ->subseq( $self->start(), $self->end(), $self->strand() );
+ $seq = $self->slice()->subseq( $self->start(), $self->end(), $self->strand() );
}
$self->{'_seq_cache'} = $seq;
--
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