From d7ceb81493491d445311a69a421114b405ad441a Mon Sep 17 00:00:00 2001
From: Glenn Proctor <gp1@sanger.ac.uk>
Date: Tue, 8 Feb 2005 08:46:40 +0000
Subject: [PATCH] Improved DB handling in CCDS dumping. Seems to work now.
---
.../xref_mapping/XrefMapper/BasicMapper.pm | 59 +++++++++++++++++--
1 file changed, 53 insertions(+), 6 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
index 45a1c5090f..b46d5b1e9d 100644
--- a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
@@ -905,6 +905,21 @@ sub dump_direct_xrefs {
open (XREF, ">>" . $self->dir() . "/xref.txt");
open (OBJECT_XREF, ">>" . $self->dir() . "/object_xref.txt");
+ # Will need to look up translation stable ID from transcript stable ID, build hash table
+ print "Building transcript stable ID -> translation stable ID lookup table\n";
+ my %transcript_stable_id_to_translation_stable_id;
+ my $trans_sth = $self->dbi()->prepare("SELECT tss.stable_id as transcript, tls.stable_id AS translation FROM translation tl, translation_stable_id tls, transcript_stable_id tss WHERE tss.transcript_id=tl.transcript_id AND tl.translation_id=tls.translation_id");
+ $trans_sth->execute();
+ my ($transcript_stable_id, $translation_stable_id);
+ $trans_sth->bind_columns(\$transcript_stable_id, \$translation_stable_id);
+ while ($trans_sth->fetch()) {
+ $transcript_stable_id_to_translation_stable_id{$transcript_stable_id} = $translation_stable_id;
+ }
+ $trans_sth->finish();
+
+ # Will need lookup tables for gene/transcript/translation stable ID to internal ID
+ my $stable_id_to_internal_id = $self->build_stable_id_to_internal_id_hash();
+
# SQL / statement handle for getting all direct xrefs
my $xref_sql = "SELECT dx.general_xref_id, dx.ensembl_stable_id, dx.type, dx.linkage_xref, x.accession, x.version, x.label, x.description, x.source_id, x.species_id FROM direct_xref dx, xref x WHERE dx.general_xref_id=x.xref_id";
my $xref_sth = $self->xref()->dbi()->prepare($xref_sql);
@@ -919,12 +934,17 @@ sub dump_direct_xrefs {
my $external_db_id = $source_to_external_db{$source_id};
if ($external_db_id) {
- # Look up Ensembl internal ID from stable ID. No joins, so quick.
- my $core_sql = "SELECT ${type}_id FROM ${type}_stable_id WHERE stable_id=\'$ensembl_stable_id\'" ;
- my $core_sth = $self->dbi()->prepare($core_sql);
- $core_sth->execute();
- my @row = $core_sth->fetchrow_array();
- my $ensembl_internal_id = $row[0];
+ # In the case of CCDS xrefs, direct_xref is to transcript but we want
+ # the mapping in the core db to be to the *translation*
+ if ($source_id == get_source_id_from_source_name($self->xref(), "CCDS")) {
+ $type = 'translation';
+ my $tmp_esid = $ensembl_stable_id;
+ $ensembl_stable_id = $transcript_stable_id_to_translation_stable_id{$tmp_esid};
+ warn "Can't find translation for transcript $tmp_esid" if (!$ensembl_stable_id);
+ #print "CCDS: transcript $tmp_esid -> translation $ensembl_stable_id\n";
+ }
+
+ my $ensembl_internal_id = $stable_id_to_internal_id->{$type}->{$ensembl_stable_id};
if ($ensembl_internal_id) {
if (!$xrefs_written{$xref_id}) {
@@ -976,6 +996,33 @@ sub dump_interpro {
}
+sub build_stable_id_to_internal_id_hash {
+
+ my $self = shift;
+
+ my %stable_id_to_internal_id;
+
+ foreach my $type ('gene', 'transcript', 'translation') { # Add exon here if required
+
+ print "Caching stable ID -> internal ID links for ${type}s\n";
+
+ my $core_sql = "SELECT ${type}_id, stable_id FROM ${type}_stable_id" ;
+ my $sth = $self->dbi()->prepare($core_sql);
+ $sth->execute();
+ my ($internal_id, $stable_id);
+ $sth->bind_columns(\$internal_id, \$stable_id);
+
+ while ($sth->fetch) {
+
+ $stable_id_to_internal_id{$type}{$stable_id} = $internal_id;
+
+ }
+
+ }
+
+ return \%stable_id_to_internal_id;
+
+}
sub get_ensembl_object_type {
--
GitLab