From dced304cf330f73bd21f22fe6fe5183a54da6f79 Mon Sep 17 00:00:00 2001
From: Andrew Yates <ayates@ebi.ac.uk>
Date: Wed, 21 Mar 2012 16:55:08 +0000
Subject: [PATCH] Do not join to seq_region unless we have to i.e. when we've
got a multispecies DB
---
modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm | 113 +++++++++++++-------
1 file changed, 72 insertions(+), 41 deletions(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm
index 6d2db8c02d..b3ce0e49fd 100644
--- a/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm
@@ -994,9 +994,9 @@ sub exists {
Arg [1] : Bio::EnsEMBL::Gene $gene
(The gene to retrieve DBEntries for)
- Arg [2] : optional external database name
- Arg [3] : optional external_db type
- Example : @db_entries = @{$db_entry_adaptor->fetch_by_Gene($gene)};
+ Arg [2] : optional external database name. SQL wildcards are accepted
+ Arg [3] : optional external_db type. SQL wildcards are accepted
+ Example : @db_entries = @{$db_entry_adaptor->fetch_all_by_Gene($gene)};
Description: This returns a list of DBEntries associated with this gene.
Note that this method was changed in release 15. Previously
it set the DBLinks attribute of the gene passed in to contain
@@ -1020,6 +1020,21 @@ sub fetch_all_by_Gene {
return $self->_fetch_by_object_type($gene->dbID(), 'Gene', $ex_db_reg, $exdb_type);
}
+=head2 fetch_all_by_Operon
+
+ Arg [1] : Bio::EnsEMBL::Operon $operon
+ (The operon to retrieve DBEntries for)
+ Arg [2] : optional external database name. SQL wildcards are accepted
+ Arg [3] : optional external_db type. SQL wildcards are accepted
+ Example : @db_entries = @{$db_entry_adaptor->fetch_all_by_Operon($operon)};
+ Description: This returns a list of DBEntries associated with this operon.
+ Returntype : listref of Bio::EnsEMBL::DBEntries; may be of type IdentityXref if
+ there is mapping data, or OntologyXref if there is linkage data.
+ Exceptions : thows if operon object not passed
+ Caller : general
+
+=cut
+
sub fetch_all_by_Operon {
my ( $self, $gene, $ex_db_reg, $exdb_type ) = @_;
@@ -1034,9 +1049,9 @@ sub fetch_all_by_Operon {
=head2 fetch_all_by_Transcript
Arg [1] : Bio::EnsEMBL::Transcript
- Arg [2] : optional external database name
- Arg [3] : optional external_db type
- Example : @db_entries = @{$db_entry_adaptor->fetch_by_Gene($trans)};
+ Arg [2] : optional external database name. SQL wildcards are accepted
+ Arg [3] : optional external_db type. SQL wildcards are accepted
+ Example : @db_entries = @{$db_entry_adaptor->fetch_all_by_Transcript($trans)};
Description: This returns a list of DBEntries associated with this
transcript. Note that this method was changed in release 15.
Previously it set the DBLinks attribute of the gene passed in
@@ -1045,7 +1060,7 @@ sub fetch_all_by_Operon {
Returntype : listref of Bio::EnsEMBL::DBEntries; may be of type IdentityXref if
there is mapping data, or OntologyXref if there is linkage data.
Exceptions : throes if transcript argument not passed
- Caller : Bio::EnsEMBL::Gene
+ Caller : Bio::EnsEMBL::Transcript
Status : Stable
=cut
@@ -1065,8 +1080,8 @@ sub fetch_all_by_Transcript {
Arg [1] : Bio::EnsEMBL::Translation $trans
(The translation to fetch database entries for)
- Arg [2] : optional external database name
- Arg [3] : optional externaldb type
+ Arg [2] : optional external database name. SQL wildcards are accepted
+ Arg [3] : optional externaldb type. SQL wildcards are accepted
Example : @db_entries = @{$db_entry_adptr->fetch_all_by_Translation($trans)};
Description: Retrieves external database entries for an EnsEMBL translation
Returntype : listref of Bio::EnsEMBL::DBEntries; may be of type IdentityXref if
@@ -1583,33 +1598,47 @@ sub _type_by_external_id {
. 't.is_current = 1 AND ';
}
}
+
+ my $multispecies = $self->db()->is_multispecies();
if ( lc($ensType) eq 'gene' ) {
- $from_sql = 'gene g, seq_region s, coord_system cs, ';
- $where_sql =
- 'g.gene_id = oxr.ensembl_id AND '
- . 'g.is_current = 1 AND '
- . 'g.seq_region_id = s.seq_region_id AND '
- . 's.coord_system_id = cs.coord_system_id AND '
- . 'cs.species_id = ? AND ';
- } elsif ( lc($ensType) eq 'transcript' ) {
- $from_sql = 'transcript t, seq_region s, coord_system cs, ';
- $where_sql =
- 't.transcript_id = oxr.ensembl_id AND '
- . 't.is_current = 1 AND '
- . 't.seq_region_id = s.seq_region_id AND '
- . 's.coord_system_id = cs.coord_system_id AND '
- . 'cs.species_id = ? AND ';
- } elsif ( lc($ensType) eq 'translation' ) {
- $from_sql = 'transcript t, translation tl, '
- . 'seq_region s, coord_system cs, ';
- $where_sql =
- 't.transcript_id = tl.transcript_id AND '
- . 'tl.translation_id = oxr.ensembl_id AND '
- . 't.is_current = 1 AND '
- . 't.seq_region_id = s.seq_region_id AND '
- . 's.coord_system_id = cs.coord_system_id AND '
- . 'cs.species_id = ? AND ';
+ $from_sql = 'gene g, ';
+ $from_sql .= 'seq_region s, coord_system cs, ' if $multispecies;
+
+ $where_sql = 'g.gene_id = oxr.ensembl_id AND g.is_current = 1 AND ';
+ if($multispecies) {
+ $where_sql .= <<'SQL';
+g.seq_region_id = s.seq_region_id AND
+s.coord_system_id = cs.coord_system_id AND
+cs.species_id = ? AND
+SQL
+ }
+ }
+ elsif ( lc($ensType) eq 'transcript' ) {
+ $from_sql = 'transcript t, ';
+ $from_sql .= 'seq_region s, coord_system cs, ' if $multispecies;
+
+ $where_sql = 't.transcript_id = oxr.ensembl_id AND t.is_current = 1 AND ';
+ if($multispecies) {
+ $where_sql .= <<'SQL';
+t.seq_region_id = s.seq_region_id AND
+s.coord_system_id = cs.coord_system_id AND
+cs.species_id = ? AND
+SQL
+ }
+ }
+ elsif ( lc($ensType) eq 'translation' ) {
+ $from_sql = 'translation tl, transcript t, ';
+ $from_sql .= 'seq_region s, coord_system cs, ' if $multispecies;
+
+ $where_sql = 't.transcript_id = tl.transcript_id AND tl.translation_id = oxr.ensembl_id AND t.is_current = 1 AND ';
+ if($multispecies) {
+ $where_sql .= <<'SQL';
+t.seq_region_id = s.seq_region_id AND
+s.coord_system_id = cs.coord_system_id AND
+cs.species_id = ? AND
+SQL
+ }
}
if ( defined($external_db_name) ) {
@@ -1672,19 +1701,21 @@ sub _type_by_external_id {
my $sth = $self->prepare($query1);
- $sth->bind_param( 1, $self->species_id(), SQL_INTEGER );
- $sth->bind_param( 2, $name, SQL_VARCHAR );
- $sth->bind_param( 3, $name, SQL_VARCHAR );
- $sth->bind_param( 4, $ensType, SQL_VARCHAR );
+ my $queryBind = 1;
+ $sth->bind_param( $queryBind++, $self->species_id(), SQL_INTEGER ) if $multispecies;
+ $sth->bind_param( $queryBind++, $name, SQL_VARCHAR );
+ $sth->bind_param( $queryBind++, $name, SQL_VARCHAR );
+ $sth->bind_param( $queryBind++, $ensType, SQL_VARCHAR );
$sth->execute();
my $r;
while ( $r = $sth->fetchrow_array() ) { $result{$r} = 1 }
$sth = $self->prepare($query2);
- $sth->bind_param( 1, $self->species_id(), SQL_INTEGER );
- $sth->bind_param( 2, $name, SQL_VARCHAR );
- $sth->bind_param( 3, $ensType, SQL_VARCHAR );
+ $queryBind = 1;
+ $sth->bind_param( $queryBind++, $self->species_id(), SQL_INTEGER ) if $multispecies;
+ $sth->bind_param( $queryBind++, $name, SQL_VARCHAR );
+ $sth->bind_param( $queryBind++, $ensType, SQL_VARCHAR );
$sth->execute();
while ( $r = $sth->fetchrow_array() ) { $result{$r} = 1 }
--
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