From c8c6133b9d5fb45e31a7d6e89e13777df0ce4b24 Mon Sep 17 00:00:00 2001
From: Ian Longden <ianl@sanger.ac.uk>
Date: Mon, 1 Jun 2009 12:17:56 +0000
Subject: [PATCH] rememebr to remove old synonyms and identity xrefs

---
 misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
index ac4cde7699..91fe98b92c 100644
--- a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
@@ -608,7 +608,19 @@ FSQL
   # Delete the old ones.
   ###########################
 
+  # delete the synonyms first
 
+  my $del_synonym_sql = "delete s from synonym s, xref x where s.xref_id = x.xref_id and x.source_id in ( $odn_curated_gene_id, $odn_automatic_gene_id, $clone_based_vega_gene_id, $clone_based_ensembl_gene_id,$odn_automatic_tran_id, $clone_based_ensembl_tran_id)";
+
+  $sth = $self->xref->dbc->prepare($del_synonym_sql);
+  $sth->execute();
+
+ 
+  my $del_identity_sql = "delete i from object_xref o, xref x, identity_xref i where i.object_xref_id = o.object_xref_id and x.xref_id = o.xref_id and x.source_id in ( $odn_curated_gene_id, $odn_automatic_gene_id, $clone_based_vega_gene_id, $clone_based_ensembl_gene_id,$odn_automatic_tran_id, $clone_based_ensembl_tran_id)";
+
+  $sth = $self->xref->dbc->prepare($del_identity_sql);
+  $sth->execute();
+ 
   my $del_vega_sql = "delete o from object_xref o, xref x where x.xref_id = o.xref_id and x.source_id in ( $odn_curated_gene_id, $odn_automatic_gene_id, $clone_based_vega_gene_id, $clone_based_ensembl_gene_id,$odn_automatic_tran_id, $clone_based_ensembl_tran_id)";
 
   $sth = $self->xref->dbc->prepare($del_vega_sql);
-- 
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