From 36705e45ed6ef10b80f599b5c81eff0666e463a5 Mon Sep 17 00:00:00 2001
From: Steve Trevanion <st3@sanger.ac.uk>
Date: Wed, 6 Oct 2004 17:12:21 +0000
Subject: [PATCH] removes all traces of supercontigs
---
.../SeqStoreConverter/vega/HomoSapiens.pm | 23 +++++++++++++++++++
.../SeqStoreConverter/vega/MusMusculus.pm | 21 +++++++++++++++++
2 files changed, 44 insertions(+)
diff --git a/misc-scripts/surgery/SeqStoreConverter/vega/HomoSapiens.pm b/misc-scripts/surgery/SeqStoreConverter/vega/HomoSapiens.pm
index 4b907f96eb..379ec13a40 100644
--- a/misc-scripts/surgery/SeqStoreConverter/vega/HomoSapiens.pm
+++ b/misc-scripts/surgery/SeqStoreConverter/vega/HomoSapiens.pm
@@ -61,4 +61,27 @@ sub update_clone_info {
return;
}
+sub remove_supercontigs {
+ my $self = shift;
+
+ my $target = $self->target();
+ my $dbh = $self->dbh();
+ $self->debug("Vega mouse specific - removing supercontigs from $target");
+
+ $dbh->do("DELETE FROM $target.meta ".
+ "WHERE meta_value like '%supercontig%'");
+
+ $dbh->do("DELETE FROM $target.coord_system ".
+ "WHERE name like 'supercontig'");
+
+ $dbh->do("DELETE $target.assembly ".
+ "FROM $target.assembly a, $target.seq_region sr ".
+ "WHERE sr.coord_system_id = 2 ".
+ "and a.asm_seq_region_id = sr.seq_region_id");
+
+ $dbh->do("DELETE FROM $target.seq_region ".
+ "WHERE coord_system_id = 2");
+}
+
+
1;
diff --git a/misc-scripts/surgery/SeqStoreConverter/vega/MusMusculus.pm b/misc-scripts/surgery/SeqStoreConverter/vega/MusMusculus.pm
index 7f30fea1ae..8a77eb679d 100644
--- a/misc-scripts/surgery/SeqStoreConverter/vega/MusMusculus.pm
+++ b/misc-scripts/surgery/SeqStoreConverter/vega/MusMusculus.pm
@@ -60,5 +60,26 @@ sub update_clone_info {
return;
}
+sub remove_supercontigs {
+ my $self = shift;
+
+ my $target = $self->target();
+ my $dbh = $self->dbh();
+ $self->debug("Vega mouse specific - removing supercontigs from $target");
+
+ $dbh->do("DELETE FROM $target.meta ".
+ "WHERE meta_value like '%supercontig%'");
+
+ $dbh->do("DELETE FROM $target.coord_system ".
+ "WHERE name like 'supercontig'");
+
+ $dbh->do("DELETE $target.assembly ".
+ "FROM $target.assembly a, $target.seq_region sr ".
+ "WHERE sr.coord_system_id = 2 ".
+ "and a.asm_seq_region_id = sr.seq_region_id");
+
+ $dbh->do("DELETE FROM $target.seq_region ".
+ "WHERE coord_system_id = 2");
+}
1;
--
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