From 824f954474a33f58c74eab4d1a0affbd6c4f4325 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20Kusalananda=20K=C3=A4h=C3=A4ri?=
<ak4@sanger.ac.uk>
Date: Fri, 13 Aug 2010 16:20:51 +0000
Subject: [PATCH] Make _objs_from_sth() aware of circular chromosomes. Patch
from EG.
---
.../Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm | 80 +++++++++++++++----
1 file changed, 66 insertions(+), 14 deletions(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm
index 4cbba25717..18ede60db1 100644
--- a/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm
@@ -312,8 +312,12 @@ sub fetch_all_by_Gene {
throw("Gene must have attached slice to retrieve transcripts.");
}
- if ($gene->start() < 1 || $gene->end() > $gslice->length()) {
- $slice = $self->db->get_SliceAdaptor->fetch_by_Feature($gene);
+ if ( $gene->start() < 1 || $gene->end() > $gslice->length() ) {
+ if ( $gslice->is_circular() ) {
+ $slice = $gslice;
+ } else {
+ $slice = $self->db->get_SliceAdaptor->fetch_by_Feature($gene);
+ }
} else {
$slice = $gslice;
}
@@ -1486,31 +1490,79 @@ sub _objs_from_sth {
}
#
- # If a destination slice was provided convert the coords
- # If the dest_slice starts at 1 and is foward strand, nothing needs doing
+ # If a destination slice was provided convert the coords.
#
- if ($dest_slice) {
- if ( $dest_slice_start != 1 || $dest_slice_strand != 1 ) {
- if ( $dest_slice_strand == 1 ) {
- $seq_region_start = $seq_region_start - $dest_slice_start + 1;
- $seq_region_end = $seq_region_end - $dest_slice_start + 1;
+ if (defined($dest_slice)) {
+ if ( $dest_slice_strand == 1 ) {
+ $seq_region_start = $seq_region_start - $dest_slice_start + 1;
+ $seq_region_end = $seq_region_end - $dest_slice_start + 1;
+
+ if ( $dest_slice->is_circular ) {
+ if ( $seq_region_start > $seq_region_end ) {
+ # Looking at a feature overlapping the chromsome origin.
+ if ( $seq_region_end > $dest_slice_start ) {
+ # Looking at the region in the beginning of the chromosome
+ $seq_region_start -= $dest_slice->seq_region_length();
+ }
+ if ( $seq_region_end < 0 ) {
+ $seq_region_end += $dest_slice->seq_region_length();
+ }
+ } else {
+ if ( $dest_slice_start > $dest_slice_end
+ && $seq_region_end < 0 )
+ {
+ # Looking at the region overlapping the chromosome
+ # origin and a feature which is at the beginning of the
+ # chromosome.
+ $seq_region_start += $dest_slice->seq_region_length();
+ $seq_region_end += $dest_slice->seq_region_length();
+ }
+ }
+ }
+ } else {
+ if ( $dest_slice->is_circular()
+ && $seq_region_start > $seq_region_end )
+ {
+ if ( $seq_region_end > $dest_slice_start ) {
+ # Looking at the region in the beginning of the chromosome.
+ $seq_region_start = $dest_slice_end - $seq_region_end + 1;
+ $seq_region_end =
+ $seq_region_end -
+ $dest_slice->seq_region_length() -
+ $dest_slice_start + 1;
+ } else {
+ my $tmp_seq_region_start = $seq_region_start;
+ $seq_region_start =
+ $dest_slice_end -
+ $seq_region_end -
+ $dest_slice->seq_region_length() + 1;
+ $seq_region_end =
+ $dest_slice_end - $tmp_seq_region_start + 1;
+ }
+
} else {
my $tmp_seq_region_start = $seq_region_start;
$seq_region_start = $dest_slice_end - $seq_region_end + 1;
$seq_region_end = $dest_slice_end - $tmp_seq_region_start + 1;
- $seq_region_strand *= -1;
}
- }
+
+ $seq_region_strand = -$seq_region_strand;
+ } ## end else [ if ( $dest_slice_strand...)]
# Throw away features off the end of the requested slice
- if ( $seq_region_end < 1
- || $seq_region_start > $dest_slice_length
- || ( $dest_slice_sr_id ne $seq_region_id ) )
+ if ( $seq_region_end < 1
+ || $seq_region_start > $dest_slice_length
+ || ( $dest_slice_sr_id ne $seq_region_id ) )
{
next FEATURE;
}
$slice = $dest_slice;
+ } else {
+ $slice =
+ $sa->fetch_by_seq_region_id( $seq_region_id, $seq_region_start,
+ $seq_region_end, $seq_region_strand
+ );
}
my $display_xref;
--
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