From 2331a63c39aa77483638acc30164cb2c29b6943f Mon Sep 17 00:00:00 2001
From: Magali Ruffier <mr6@ebi.ac.uk>
Date: Mon, 22 Feb 2016 11:49:47 +0000
Subject: [PATCH] clean up transcripts without translations
---
.../xref_mapping/XrefMapper/BasicMapper.pm | 16 ++++++++++++++++
1 file changed, 16 insertions(+)
diff --git a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
index 4f7295ed75..711469bcab 100644
--- a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
@@ -720,6 +720,22 @@ EOF
EOF2
$result = $xref_dbc->do($sql);
+
+# Special tidying up for transcripts without translation
+# The resulting object_xref does not have an ensembl_id to map to
+
+ $sql=(<<"EOF4");
+ DELETE object_xref, identity_xref, go_xref
+ FROM object_xref, xref, source, identity_xref, go_xref
+ WHERE object_xref.ensembl_object_type = "$to" AND
+ identity_xref.object_xref_id = object_xref.object_xref_id AND
+ xref.xref_id = object_xref.xref_id AND
+ go_xref.object_xref_id = object_xref.object_xref_id AND
+ xref.source_id = source.source_id AND
+ object_xref.ensembl_id = 0 AND
+ object_xref.ox_status = "DUMP_OUT" AND
+ source.name = "$db_name";
+EOF4
}
else{
$sql =(<<"EOF3");
--
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