From 3930d05adb2498ff5d05a2a07cd4949b5c90c528 Mon Sep 17 00:00:00 2001
From: Monika Komorowska <mk8@sanger.ac.uk>
Date: Wed, 12 Oct 2011 11:18:25 +0000
Subject: [PATCH] stable_id merge changes
---
misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm | 6 +++---
misc-scripts/xref_mapping/XrefMapper/CoreInfo.pm | 2 +-
misc-scripts/xref_mapping/XrefMapper/DisplayXrefs.pm | 4 ++--
.../XrefMapper/caenorhabditis_elegans.pm | 2 +-
.../XrefMapper/saccharomyces_cerevisiae.pm | 2 +-
.../XrefMapper/schizosaccharomyces_pombe.pm | 2 +-
misc-scripts/xref_mapping/XrefParser/CCDSParser.pm | 6 +++---
misc-scripts/xref_mapping/XrefParser/OTTTParser.pm | 6 +++---
.../XrefParser/VegaOfficialNameParser.pm | 12 +++++-------
.../XrefParser/WormbaseDatabaseStableIDParser.pm | 2 +-
.../XrefParser/curated_transcriptParser.pm | 8 ++++----
misc-scripts/xref_mapping/compare_xrefs_by_source.pl | 2 +-
misc-scripts/xref_mapping/core_vega_link_check.pl | 2 +-
13 files changed, 27 insertions(+), 29 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
index 30e6ebd6fe..69bc80a771 100644
--- a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
@@ -613,13 +613,13 @@ SEQ
#
my $sql =(<<'LRG');
-SELECT ox.ensembl_id, gsi.gene_id
- FROM xref x, object_xref ox, external_db e, gene_stable_id gsi
+SELECT ox.ensembl_id, g.gene_id
+ FROM xref x, object_xref ox, external_db e, gene g
WHERE x.xref_id = ox.xref_id AND
e.external_db_id = x.external_db_id AND
e.db_name like "Ens_Hs_gene" AND
ox.ensembl_object_type = "Gene" AND
- x.display_label = gsi.stable_id
+ x.display_label = g.stable_id
LRG
$sth = $self->core->dbc->prepare($sql);
diff --git a/misc-scripts/xref_mapping/XrefMapper/CoreInfo.pm b/misc-scripts/xref_mapping/XrefMapper/CoreInfo.pm
index 171bf6860e..fbcde51443 100644
--- a/misc-scripts/xref_mapping/XrefMapper/CoreInfo.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/CoreInfo.pm
@@ -123,7 +123,7 @@ sub load_stable_ids{
my ($id, $stable_id);
foreach my $table (qw(gene transcript translation)){
- my $sth = $self->core->dbc->prepare("select ".$table."_id, stable_id from ".$table."_stable_id");
+ my $sth = $self->core->dbc->prepare("select ".$table."_id, stable_id from ".$table);
my $ins_sth = $self->xref->dbc->prepare("insert into ".$table."_stable_id (internal_id, stable_id) values(?, ?)");
$sth->execute();
$sth->bind_columns(\$id, \$stable_id);
diff --git a/misc-scripts/xref_mapping/XrefMapper/DisplayXrefs.pm b/misc-scripts/xref_mapping/XrefMapper/DisplayXrefs.pm
index 7b67eedfc7..37f9a38922 100644
--- a/misc-scripts/xref_mapping/XrefMapper/DisplayXrefs.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/DisplayXrefs.pm
@@ -186,10 +186,10 @@ sub genes_and_transcripts_attributes_set{
# Special removal of LRG transcript display xref, xref and object_xrefs;
- my $sth_lrg = $self->core->dbc->prepare('DELETE ox, x FROM object_xref ox, xref x, transcript t, transcript_stable_id tsi WHERE ox.xref_id = x.xref_id and tsi.transcript_id = t.transcript_id and t.display_xref_id = x.xref_id and tsi.stable_id like "LRG%"');
+ my $sth_lrg = $self->core->dbc->prepare('DELETE ox, x FROM object_xref ox, xref x, transcript t WHERE ox.xref_id = x.xref_id and t.display_xref_id = x.xref_id and t.stable_id like "LRG%"');
$sth_lrg->execute;
- $sth_lrg = $self->core->dbc->prepare('UPDATE transcript t, transcript_stable_id tsi SET t.display_xref_id = null WHERE tsi.stable_id like "LRG%" and tsi.transcript_id = t.transcript_id');
+ $sth_lrg = $self->core->dbc->prepare('UPDATE transcript SET display_xref_id = null WHERE stable_id like "LRG%" ');
$sth_lrg->execute;
#End of Special
diff --git a/misc-scripts/xref_mapping/XrefMapper/caenorhabditis_elegans.pm b/misc-scripts/xref_mapping/XrefMapper/caenorhabditis_elegans.pm
index cd39c05b5e..d7cdb15402 100644
--- a/misc-scripts/xref_mapping/XrefMapper/caenorhabditis_elegans.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/caenorhabditis_elegans.pm
@@ -27,7 +27,7 @@ sub build_display_xrefs {
print "Setting $type display_xrefs from $type stable IDs\n";
my $dir = $self->core()->dir();
- my $sql = "UPDATE $type t, ${type}_stable_id s, xref x, external_db e SET t.display_xref_id=x.xref_id WHERE t.${type}_id=s.${type}_id AND s.stable_id=x.dbprimary_acc AND e.external_db_id=x.external_db_id AND e.db_name=\'${external_db}\'\n";
+ my $sql = "UPDATE $type t, xref x, external_db e SET t.display_xref_id=x.xref_id WHERE t.stable_id=x.dbprimary_acc AND e.external_db_id=x.external_db_id AND e.db_name=\'${external_db}\'\n";
open (SQL, ">$dir/${type}_display_xref.sql");
diff --git a/misc-scripts/xref_mapping/XrefMapper/saccharomyces_cerevisiae.pm b/misc-scripts/xref_mapping/XrefMapper/saccharomyces_cerevisiae.pm
index eda28d7427..deb9a063b9 100644
--- a/misc-scripts/xref_mapping/XrefMapper/saccharomyces_cerevisiae.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/saccharomyces_cerevisiae.pm
@@ -27,7 +27,7 @@ sub build_display_xrefs {
print "Setting $type display_xrefs from $type stable IDs\n";
my $dir = $self->core()->dir();
- my $sql = "UPDATE $type t, ${type}_stable_id s, xref x, external_db e SET t.display_xref_id=x.xref_id WHERE t.${type}_id=s.${type}_id AND s.stable_id=x.dbprimary_acc AND e.external_db_id=x.external_db_id AND e.db_name=\'${external_db}\'\n";
+ my $sql = "UPDATE $type t, xref x, external_db e SET t.display_xref_id=x.xref_id WHERE t.stable_id=x.dbprimary_acc AND e.external_db_id=x.external_db_id AND e.db_name=\'${external_db}\'\n";
open (SQL, ">$dir/${type}_display_xref.sql");
diff --git a/misc-scripts/xref_mapping/XrefMapper/schizosaccharomyces_pombe.pm b/misc-scripts/xref_mapping/XrefMapper/schizosaccharomyces_pombe.pm
index 7d81e95001..971f14ab46 100644
--- a/misc-scripts/xref_mapping/XrefMapper/schizosaccharomyces_pombe.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/schizosaccharomyces_pombe.pm
@@ -26,7 +26,7 @@ sub build_display_xrefs {
print "Setting $type display_xrefs from $type stable IDs\n";
my $dir = $self->core()->dir();
- my $sql = "UPDATE $type t, ${type}_stable_id s, xref x, external_db e SET t.display_xref_id=x.xref_id WHERE t.${type}_id=s.${type}_id AND s.stable_id=x.dbprimary_acc AND e.external_db_id=x.external_db_id AND e.db_name=\'${external_db}\'\n";
+ my $sql = "UPDATE $type t, xref x, external_db e SET t.display_xref_id=x.xref_id WHERE t.stable_id=x.dbprimary_acc AND e.external_db_id=x.external_db_id AND e.db_name=\'${external_db}\'\n";
open (SQL, ">$dir/${type}_display_xref.sql");
diff --git a/misc-scripts/xref_mapping/XrefParser/CCDSParser.pm b/misc-scripts/xref_mapping/XrefParser/CCDSParser.pm
index fef1ae2979..3d2075e3b2 100644
--- a/misc-scripts/xref_mapping/XrefParser/CCDSParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/CCDSParser.pm
@@ -60,11 +60,11 @@ sub run_script {
my $xref_count = 0;
my $sql =(<<'SCD');
-SELECT tsi.stable_id, x.dbprimary_acc
- FROM xref x, object_xref ox, transcript_stable_id tsi, external_db e
+SELECT t.stable_id, x.dbprimary_acc
+ FROM xref x, object_xref ox, transcript t, external_db e
WHERE x.xref_id=ox.xref_id AND
ox.ensembl_object_type = "Transcript" AND
- ox.ensembl_id = tsi.transcript_id AND
+ ox.ensembl_id = t.transcript_id AND
e.external_db_id = x.external_db_id AND
e.db_name like "Ens_%_transcript"
SCD
diff --git a/misc-scripts/xref_mapping/XrefParser/OTTTParser.pm b/misc-scripts/xref_mapping/XrefParser/OTTTParser.pm
index 923f22e8ff..46654cb75c 100644
--- a/misc-scripts/xref_mapping/XrefParser/OTTTParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/OTTTParser.pm
@@ -44,11 +44,11 @@ sub run_script {
my $sql =(<<'SQL');
-SELECT tsi.stable_id, x.display_label
- FROM xref x, object_xref ox , transcript_stable_id tsi, external_db e
+SELECT t.stable_id, x.display_label
+ FROM xref x, object_xref ox , transcript t, external_db e
WHERE e.external_db_id = x.external_db_id AND
x.xref_id = ox.xref_id AND
- tsi.transcript_id = ox.ensembl_id AND
+ t.transcript_id = ox.ensembl_id AND
e.db_name like ?
SQL
diff --git a/misc-scripts/xref_mapping/XrefParser/VegaOfficialNameParser.pm b/misc-scripts/xref_mapping/XrefParser/VegaOfficialNameParser.pm
index 00d771f1d7..a94bb18ccf 100644
--- a/misc-scripts/xref_mapping/XrefParser/VegaOfficialNameParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/VegaOfficialNameParser.pm
@@ -162,23 +162,21 @@ sub run_script {
my $sql =(<<SQL);
-SELECT tsi.stable_id, x.display_label
- FROM analysis a, xref x, object_xref ox , transcript_stable_id tsi, external_db e , transcript t
+SELECT t.stable_id, x.display_label
+ FROM analysis a, xref x, object_xref ox , transcript t, external_db e
WHERE a.analysis_id = t.analysis_id and
- t.transcript_id = tsi.transcript_id and
e.external_db_id = x.external_db_id and
x.xref_id = ox.xref_id and
- tsi.transcript_id = ox.ensembl_id and
+ t.transcript_id = ox.ensembl_id and
a.logic_name like "%havana%" and
e.db_name like ?
SQL
my $ext_sql =(<<EXT);
-SELECT tsi.stable_id, x.dbprimary_acc
- FROM xref x, object_xref ox , transcript_stable_id tsi, gene g, external_db e, transcript t
+SELECT t.stable_id, x.dbprimary_acc
+ FROM xref x, object_xref ox , transcript t, gene g, external_db e
WHERE t.gene_id = g.gene_id and
g.gene_id = ox.ensembl_id and
- tsi.transcript_id = t.transcript_id and
e.external_db_id = x.external_db_id and
x.xref_id = ox.xref_id and
ox.ensembl_object_type = "Gene" and
diff --git a/misc-scripts/xref_mapping/XrefParser/WormbaseDatabaseStableIDParser.pm b/misc-scripts/xref_mapping/XrefParser/WormbaseDatabaseStableIDParser.pm
index 125cec3fe3..c38fd700e8 100644
--- a/misc-scripts/xref_mapping/XrefParser/WormbaseDatabaseStableIDParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/WormbaseDatabaseStableIDParser.pm
@@ -39,7 +39,7 @@ sub run {
my $wb_source_id = $self->get_source_id_for_source_name("wormbase_$type");
- my $sth = $db->prepare( "SELECT stable_id FROM ${type}_stable_id" );
+ my $sth = $db->prepare( "SELECT stable_id FROM ${type}" );
$sth->execute();
while(my @row = $sth->fetchrow_array()) {
diff --git a/misc-scripts/xref_mapping/XrefParser/curated_transcriptParser.pm b/misc-scripts/xref_mapping/XrefParser/curated_transcriptParser.pm
index 68dd9ad2ae..c3600ca957 100644
--- a/misc-scripts/xref_mapping/XrefParser/curated_transcriptParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/curated_transcriptParser.pm
@@ -156,9 +156,9 @@ sub run_script {
print "source id is $source_id, curated_source_id is $curated_source_id\n";
- my $sql = 'select tsi.stable_id, x.display_label, t.status from analysis a, xref x, object_xref ox , transcript_stable_id tsi, external_db e, transcript t where t.analysis_id = a.analysis_id and a.logic_name like "%havana%" and e.external_db_id = x.external_db_id and x.xref_id = ox.xref_id and tsi.transcript_id = ox.ensembl_id and t.transcript_id = tsi.transcript_id and e.db_name like ?';
+ my $sql = 'select t.stable_id, x.display_label, t.status from analysis a, xref x, object_xref ox , external_db e, transcript t where t.analysis_id = a.analysis_id and a.logic_name like "%havana%" and e.external_db_id = x.external_db_id and x.xref_id = ox.xref_id and t.transcript_id = ox.ensembl_id and e.db_name like ?';
- my $sql_vega = 'select tsi.stable_id, x.display_label, t.status from xref x, object_xref ox , transcript_stable_id tsi, external_db e, transcript t where e.external_db_id = x.external_db_id and x.xref_id = ox.xref_id and tsi.transcript_id = ox.ensembl_id and t.transcript_id = tsi.transcript_id and tsi.stable_id <> x.display_label and e.db_name like ?';
+ my $sql_vega = 'select t.stable_id, x.display_label, t.status from xref x, object_xref ox , external_db e, transcript t where e.external_db_id = x.external_db_id and x.xref_id = ox.xref_id and t.transcript_id = ox.ensembl_id and t.stable_id <> x.display_label and e.db_name like ?';
my %ott_to_vega_name;
@@ -220,7 +220,7 @@ sub run_script {
# need to add gene info to havana_status table
- $sql = 'select gsi.stable_id, x.display_label from xref x, object_xref ox , gene_stable_id gsi, external_db e, gene g where e.external_db_id = x.external_db_id and x.xref_id = ox.xref_id and gsi.gene_id = ox.ensembl_id and g.gene_id = gsi.gene_id and e.db_name like "OTTG"';
+ $sql = 'select g.stable_id, x.display_label from xref x, object_xref ox , external_db e, gene g where e.external_db_id = x.external_db_id and x.xref_id = ox.xref_id and g.gene_id = ox.ensembl_id and e.db_name like "OTTG"';
$sth = $core_dbc->prepare($sql) || die "Could not prepare for core $sql\n";
$sth->execute() or croak( $core_dbc->errstr());
@@ -229,7 +229,7 @@ sub run_script {
$ottg_to_ensg{$row[1]} = $row[0];
}
- $sth = $vega_dbc->prepare("select gsi.stable_id, g.status from gene g, gene_stable_id gsi where g.gene_id = gsi.gene_id");
+ $sth = $vega_dbc->prepare("select stable_id, status from gene");
$sth->execute() or croak( $core_dbc->errstr());
while ( my @row = $sth->fetchrow_array() ) {
if(defined($ottg_to_ensg{$row[0]}) and defined($row[1])){
diff --git a/misc-scripts/xref_mapping/compare_xrefs_by_source.pl b/misc-scripts/xref_mapping/compare_xrefs_by_source.pl
index 83e87ea72d..41ead1f851 100644
--- a/misc-scripts/xref_mapping/compare_xrefs_by_source.pl
+++ b/misc-scripts/xref_mapping/compare_xrefs_by_source.pl
@@ -64,7 +64,7 @@ sub compare {
#print "Caching old gene stable ID - $source display_xref mappings from $old_dbname\n";
- my $sql = "SELECT gsi.stable_id, x.dbprimary_acc FROM xref x, gene_stable_id gsi, gene g, external_db e WHERE gsi.gene_id=g.gene_id AND g.display_xref_id=x.xref_id AND e.external_db_id=x.external_db_id AND e.db_name='" . $source . "'";
+ my $sql = "SELECT g.stable_id, x.dbprimary_acc FROM xref x, gene g, external_db e WHERE g.display_xref_id=x.xref_id AND e.external_db_id=x.external_db_id AND e.db_name='" . $source . "'";
#print "\n\n$sql\n\n";
my $old_sth = $old_dbi->prepare($sql);
diff --git a/misc-scripts/xref_mapping/core_vega_link_check.pl b/misc-scripts/xref_mapping/core_vega_link_check.pl
index 15606ef8b6..e0ed13c69c 100644
--- a/misc-scripts/xref_mapping/core_vega_link_check.pl
+++ b/misc-scripts/xref_mapping/core_vega_link_check.pl
@@ -29,7 +29,7 @@ if(!defined($vega_sa)){
}
-my $sql = 'select tsi.stable_id, x.display_label from xref x, object_xref ox , transcript_stable_id tsi, external_db e where e.external_db_id = x.external_db_id and x.xref_id = ox.xref_id and tsi.transcript_id = ox.ensembl_id and e.db_name like ?';
+my $sql = 'select t.stable_id, x.display_label from xref x, object_xref ox , transcript t, external_db e where e.external_db_id = x.external_db_id and x.xref_id = ox.xref_id and t.transcript_id = ox.ensembl_id and e.db_name like ?';
--
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