From 11b639c618b6b5a65283f5102eb464689416ed75 Mon Sep 17 00:00:00 2001
From: Glenn Proctor <gp1@sanger.ac.uk>
Date: Mon, 20 Dec 2004 10:11:55 +0000
Subject: [PATCH] Fix for species that have all xrefs mapped directly to
translations.
Make all external_synonym entries unique.
Corrected location from which display_xref .sql files are uploaded.
---
misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm | 8 +++++---
1 file changed, 5 insertions(+), 3 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
index a06460b20c..3dac1c5d26 100644
--- a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
@@ -1021,7 +1021,7 @@ sub dump_core_xrefs {
}
# Now get the synonyms for each of these xrefs and write them to the external_synonym table
- $sql = "SELECT xref_id, synonym FROM synonym WHERE xref_id $id_str";
+ $sql = "SELECT DISTINCT xref_id, synonym FROM synonym WHERE xref_id $id_str";
my $syn_sth = $xref_dbi->prepare($sql);
$syn_sth->execute();
@@ -1182,12 +1182,14 @@ sub build_transcript_display_xrefs {
foreach my $key (keys %obj_to_best_xref) {
my ($type, $object_id) = split /\|/, $key;
- my ($best_xref, $best_xref_priority_idx) = split /\|/, $obj_to_best_xref{$object_id};
+
+ my ($best_xref, $best_xref_priority_idx) = split /\|/, $obj_to_best_xref{$key};
# If transcript has a translation, use the best xref out of the transcript & translation
if ($type =~ /Transcript/i) {
my $transcript_id = $object_id;
my $translation_id = $transcript_to_translation{$transcript_id};
+
if ($translation_id) {
my ($translation_xref, $translation_priority) = split /\|/, $obj_to_best_xref{"Translation|$translation_id"};
my ($transcript_xref, $transcript_priority) = split /\|/, $obj_to_best_xref{"Transcript|$transcript_id"};
@@ -1436,7 +1438,7 @@ sub do_upload {
# gene_display_xref.sql etc
foreach my $table ("gene", "transcript") {
- my $file = getcwd() . "/" . $table . "_display_xref.txt";
+ my $file = $self->dir() . "/" . $table . "_display_xref.txt";
my $sth;
if ($deleteexisting) {
--
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