From 6441270bd0366bc334c87d622453bd0fc322d5ba Mon Sep 17 00:00:00 2001
From: Magali Ruffier <mr6@ebi.ac.uk>
Date: Thu, 16 Oct 2014 16:35:39 +0100
Subject: [PATCH] ENSCORESW-389: when processing pairs, process dependent xrefs
as well
---
misc-scripts/xref_mapping/XrefMapper/ProcessPaired.pm | 3 +++
1 file changed, 3 insertions(+)
diff --git a/misc-scripts/xref_mapping/XrefMapper/ProcessPaired.pm b/misc-scripts/xref_mapping/XrefMapper/ProcessPaired.pm
index 583abc1834..26f06a53bc 100644
--- a/misc-scripts/xref_mapping/XrefMapper/ProcessPaired.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/ProcessPaired.pm
@@ -84,6 +84,7 @@ sub process{
my $transl_object_xrefs_sth = $self->xref->dbc->prepare("select ox.object_xref_id, ox.ensembl_id, x.accession from object_xref ox join xref x on (ox.xref_id = x.xref_id and ox.ox_status = 'DUMP_OUT' and ox.ensembl_object_type = 'Translation') join source s on (x.source_id = s.source_id and s.name like 'RefSeq\_peptide%')");
my $ox_mark_delete_sth = $self->xref->dbc->prepare("update object_xref set ox_status = 'MULTI_DELETE' where object_xref_id = ?");
+ my $ox_dx_delete_sth = $self->xref->dbc->prepare("update object_xref master_ox, object_xref dependent_ox, xref dependent, xref master, dependent_xref dx set dependent_ox.ox_status = 'MULTI_DELETE' where dependent.xref_id = dx.dependent_xref_id and master.xref_id = dx.master_xref_id and dependent.xref_id = dependent_ox.xref_id and master.xref_id = master_ox.xref_id and master_ox.object_xref_id = ? and dependent_ox.ensembl_id = ?");
$transcr_obj_xrefs_sth->execute();
@@ -168,6 +169,8 @@ sub process{
#this translations's transcript is not matched with the paired RefSeq_mRNA%,
#change the status to 'MULTI_DELETE'
$ox_mark_delete_sth->execute($translation_object_xref_id) || die("Failed to update status to 'MULTI_DELETE for object_xref_id $translation_object_xref_id");
+ $ox_dx_delete_sth->execute($translation_object_xref_id, $translation_id);
+ # Process all dependent xrefs as well
$change{'translation object xrefs removed'}++;
}
--
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