From 799133f94523f962135e0d6a3dcc295f09d1b143 Mon Sep 17 00:00:00 2001
From: Andrew Yates <ayates@ebi.ac.uk>
Date: Tue, 12 Mar 2013 06:43:45 +0000
Subject: [PATCH] [ENSCORESW-377]. Fixing the seq region synonym as mentioned
by Steve S. Also added a test case which looks for synonyms with a coordinate
system not as before which only worked when we had no coordinate system)
---
modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm | 4 ++--
modules/t/sliceAdaptor.t | 2 ++
2 files changed, 4 insertions(+), 2 deletions(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
index 85d4072175..28d29f286f 100644
--- a/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
@@ -301,9 +301,9 @@ sub fetch_by_region {
if($syn_sql_sth->fetch){
$syn_sql_sth->finish;
- if (not defined($cs)) {
+ if ((not defined($cs)) || ($cs->name eq $new_coord_system)) {
return $self->fetch_by_region($new_coord_system, $new_name, $start, $end, $strand, $new_version, $no_fuzz);
- } elsif ($cs->dbID != $new_coord_system) {
+ } elsif ($cs->name ne $new_coord_system) {
warning("Searched for a known feature on coordinate system: ".$cs->dbID." but found it on: ".$new_coord_system.
"\n No result returned, consider searching without coordinate system or use toplevel.");
return;
diff --git a/modules/t/sliceAdaptor.t b/modules/t/sliceAdaptor.t
index 726f6f7518..9efad50ab8 100644
--- a/modules/t/sliceAdaptor.t
+++ b/modules/t/sliceAdaptor.t
@@ -426,6 +426,8 @@ ok($slice->seq_region_name =~ /$clone_name\.\d+/);
{
my $syn_slice = $slice_adaptor->fetch_by_region(undef, 'anoth_20');
is($syn_slice->seq_region_name(), '20', 'Ensuring slice is Chr20 as expected');
+ my $chr_syn_slice = $slice_adaptor->fetch_by_region('chromosome', 'anoth_20');
+ is($chr_syn_slice->seq_region_name(), '20', 'Ensuring slice is Chr20 as expected');
}
#{
--
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