From c6f4b5d2542452b166482042fbd33ef4531a256d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20Kusalananda=20K=C3=A4h=C3=A4ri?=
<ak4@sanger.ac.uk>
Date: Wed, 23 Apr 2008 17:52:23 +0000
Subject: [PATCH] Performance improvement by *not* splitting OR into multiple
queries (MySQL v5 knows how to do index merges) in _type_by_external_id():
# decrease in time by 35%
$dbea->list_transcript_ids_by_extids('BRCA2');
# decrease in time by 28%
$dbea->list_translation_ids_by_extids('GO:0004835');
# decrease in time by 24%
$dbea->list_gene_ids_by_extids('ARSE');
Also some formatting.
---
modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm | 92 +++++++++++----------
1 file changed, 48 insertions(+), 44 deletions(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm
index c78f95c84e..f3294fd14c 100644
--- a/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm
@@ -45,7 +45,6 @@ use strict;
@ISA = qw( Bio::EnsEMBL::DBSQL::BaseAdaptor );
-
=head2 fetch_by_dbID
Arg [1] : int $dbID
@@ -1020,7 +1019,7 @@ sub list_gene_ids_by_extids {
Arg [1] : string $external_name
Arg [2] : (optional) string $external_db_name
- Example : @tr_ids = $dbea->list_gene_ids_by_extids('BCRA2');
+ Example : @tr_ids = $dbea->list_transcript_ids_by_extids('BCRA2');
Description: Retrieve a list transcript ids by an external identifier that
is linked to any of the genes transcripts, translations or the
gene itself
@@ -1049,7 +1048,7 @@ sub list_transcript_ids_by_extids {
Arg [1] : string $external_name
Arg [2] : (optional) string $external_db_name
- Example : @tr_ids = $dbea->list_gene_ids_by_extids('GO:0004835');
+ Example : @tr_ids = $dbea->list_translation_ids_by_extids('GO:0004835');
Description: Gets a list of translation IDs by external display IDs
Returntype : list of Ints
Exceptions : none
@@ -1141,71 +1140,79 @@ sub _type_by_external_id {
. ' AND xdb.external_db_id = x.external_db_id AND';
}
- my @queries = (
- "SELECT $ID_sql
- FROM $from_sql xref x, object_xref oxr
- WHERE $where_sql x.dbprimary_acc = ? AND
- x.xref_id = oxr.xref_id AND
- oxr.ensembl_object_type= ?",
- "SELECT $ID_sql
- FROM $from_sql xref x, object_xref oxr
- WHERE $where_sql x.display_label = ? AND
- x.xref_id = oxr.xref_id AND
- oxr.ensembl_object_type= ?"
- );
+ my $query1 = qq(
+ SELECT $ID_sql
+ FROM $from_sql
+ xref x,
+ object_xref oxr
+ WHERE $where_sql
+ ( x.dbprimary_acc = ? OR x.display_label = ? )
+ AND x.xref_id = oxr.xref_id
+ AND oxr.ensembl_object_type = ?);
+
+ my $query2;
if ( defined $external_db_name ) {
# If we are given the name of an external database, we need to join
# between the 'xref' and the 'object_xref' tables on 'xref_id'.
- push @queries, "SELECT $ID_sql
+ $query2 = "SELECT $ID_sql
FROM $from_sql xref x, object_xref oxr, external_synonym syn
WHERE $where_sql syn.synonym = ? AND
x.xref_id = oxr.xref_id AND
oxr.ensembl_object_type= ? AND
syn.xref_id = oxr.xref_id";
+
} else {
# If we weren't given an external database name, we can get away
# with less joins here.
- push @queries, "SELECT $ID_sql
+ $query2 = "SELECT $ID_sql
FROM $from_sql object_xref oxr, external_synonym syn
WHERE $where_sql syn.synonym = ? AND
oxr.ensembl_object_type= ? AND
syn.xref_id = oxr.xref_id";
- }
- # Increase speed of query by splitting the OR in query into three
- # separate queries. This is because the 'or' statments render the
- # index useless because MySQL can't use any fields in it.
+ }
my %hash = ();
my @result = ();
- foreach (@queries) {
- my $sth = $self->prepare($_);
- $sth->bind_param( 1, "$name", SQL_VARCHAR );
- $sth->bind_param( 2, $ensType, SQL_VARCHAR );
- $sth->execute();
+ my $sth = $self->prepare($query1);
- while ( my $r = $sth->fetchrow_array() ) {
- if ( !exists $hash{$r} ) {
- $hash{$r} = 1;
- push( @result, $r );
- }
- }
+ $sth->bind_param( 1, "$name", SQL_VARCHAR );
+ $sth->bind_param( 2, "$name", SQL_VARCHAR );
+ $sth->bind_param( 3, $ensType, SQL_VARCHAR );
+ $sth->execute();
+
+ while ( my $r = $sth->fetchrow_array() ) {
+ if ( exists( $hash{$r} ) ) { next }
+ $hash{$r} = 1;
+ push( @result, $r );
+ }
+
+ $sth = $self->prepare($query2);
+
+ $sth->bind_param( 1, "$name", SQL_VARCHAR );
+ $sth->bind_param( 2, $ensType, SQL_VARCHAR );
+ $sth->execute();
+
+ while ( my $r = $sth->fetchrow_array() ) {
+ if ( exists( $hash{$r} ) ) { next }
+ $hash{$r} = 1;
+ push( @result, $r );
}
return @result;
} ## end sub _type_by_external_id
-=head2 _type_by_external_type
+=head2 _type_by_external_db_id
Arg [1] : string $type - external_db type
Arg [2] : string $ensType - ensembl_object_type
Arg [3] : (optional) string $extraType
other object type to be returned
- Example : $self->_type_by_external_id(1030, 'Translation');
+ Example : $self->_type_by_external_db_id(1030, 'Translation');
Description: Gets
Returntype : list of dbIDs (gene_id, transcript_id, etc.)
Exceptions : none
@@ -1265,24 +1272,21 @@ sub _type_by_external_db_id{
WHERE $where_sql x.external_db_id = ? AND
x.xref_id = oxr.xref_id AND oxr.ensembl_object_type= ?";
-# Increase speed of query by splitting the OR in query into three separate
-# queries. This is because the 'or' statments render the index useless
-# because MySQL can't use any fields in the index.
-
my %hash = ();
my @result = ();
-
- my $sth = $self->prepare( $query );
- $sth->bind_param(1, "$external_db_id", SQL_VARCHAR);
- $sth->bind_param(2, $ensType, SQL_VARCHAR);
+ my $sth = $self->prepare($query);
+ $sth->bind_param( 1, "$external_db_id", SQL_VARCHAR );
+ $sth->bind_param( 2, $ensType, SQL_VARCHAR );
$sth->execute();
- while( my $r = $sth->fetchrow_array() ) {
- if( !exists $hash{$r} ) {
+
+ while ( my $r = $sth->fetchrow_array() ) {
+ if ( !exists $hash{$r} ) {
$hash{$r} = 1;
push( @result, $r );
}
}
+
return @result;
}
--
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