From 2d207ed0eb8b9087f4089ea8a5b53ee79e75e684 Mon Sep 17 00:00:00 2001
From: Ian Longden <ianl@sanger.ac.uk>
Date: Fri, 15 Jun 2007 15:02:53 +0000
Subject: [PATCH] new code to work out the cmp seq regions that have multuple
assemblys. This is now stored in the seq_region_attrib table
---
.../Bio/EnsEMBL/DBSQL/AssemblyMapperAdaptor.pm | 17 +++++++----------
1 file changed, 7 insertions(+), 10 deletions(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/AssemblyMapperAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/AssemblyMapperAdaptor.pm
index e99d420399..dd8039ed98 100644
--- a/modules/Bio/EnsEMBL/DBSQL/AssemblyMapperAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/AssemblyMapperAdaptor.pm
@@ -126,28 +126,25 @@ sub cache_seq_ids_with_mult_assemblys{
my %multis;
return if (defined($self->{'multi_seq_ids'}));
+
$self->{'multi_seq_ids'} = {};
my $sql=(<<SQL);
- SELECT a.cmp_seq_region_id, count(*) as count
- FROM assembly a, seq_region s, coord_system c
- WHERE a.asm_seq_region_id=s.seq_region_id and
- c.coord_system_id = s.coord_system_id
- GROUP BY a.cmp_seq_region_id, s.coord_system_id HAVING count >= 2
+ SELECT seq_region_id
+ FROM seq_region_attrib sra, attrib_type at
+ WHERE sra.attrib_type_id = at.attrib_type_id and code = "MultAssem"
SQL
my $sth = $self->prepare($sql);
$sth->execute();
- my ($seq_region_id, $count);
-
- $sth->bind_columns(\$seq_region_id, \$count);
+ my ($seq_region_id);
- my %asm_registered;
+ $sth->bind_columns(\$seq_region_id);
while($sth->fetch()) {
- $self->{'multi_seq_ids'}->{$seq_region_id} = $count;
+ $self->{'multi_seq_ids'}->{$seq_region_id} = 1;
}
$sth->finish;
}
--
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