From c4088d2ea1e28db9da1931cf624d14da1f56b23c Mon Sep 17 00:00:00 2001
From: Ian Longden <ianl@sanger.ac.uk>
Date: Thu, 28 Jan 2010 10:06:15 +0000
Subject: [PATCH] a) added unused_priority to the order list as this now
contains the number of times that trancript name was used and is need to make
sure that the gene name is the same as the transcripts. b) make sure there is
a description else we get a ton of warning regarding undefined vars
---
misc-scripts/xref_mapping/XrefMapper/DisplayXrefs.pm | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefMapper/DisplayXrefs.pm b/misc-scripts/xref_mapping/XrefMapper/DisplayXrefs.pm
index 3f00f79a71..1983a140e3 100644
--- a/misc-scripts/xref_mapping/XrefMapper/DisplayXrefs.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/DisplayXrefs.pm
@@ -1158,7 +1158,7 @@ from ( display_xref_prioritys p
left join gene_transcript_translation gtt_translation
on (gtt_translation.translation_id = ox.ensembl_id)
where ox.ox_status = 'DUMP_OUT'
-order by gene_id DESC, p.priority DESC, (ix.target_identity+ix.query_identity) DESC
+order by gene_id DESC, p.priority DESC, (ix.target_identity+ix.query_identity) DESC, ox.unused_priority DESC
DXS
# SELECT gtt.gene_id, gtt.transcript_id, p.priority, x.xref_id, ox.ensembl_object_type, x.label
@@ -1212,7 +1212,7 @@ DXS
$update_tran_sth->finish;
#
- # reset the staus to DUMP_OUT fro thise that where ignored for the display_xref;
+ # reset the status to DUMP_OUT fro thise that where ignored for the display_xref;
#
my $reset_status_sth = $self->xref->dbc->prepare('UPDATE object_xref SET ox_status = "DUMP_OUT" where ox_status = "NO_DISPLAY"');
@@ -1416,7 +1416,7 @@ DXS
while($gene_desc_sth->fetch()){
# print "$gene_id, $transcript_id, $p, $xref_id, $type, $label\n";
- if($gene_id != $last_gene){
+ if($gene_id != $last_gene and defined($desc) ){
my $filtered_description = $self->filter_by_regexp($desc, \@regexps);
if ($filtered_description ne "") {
$desc .= " [Source:".$source_id_to_external_name{$source_id}.";Acc:".$label."]";
--
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