From e5c2c5168391811cb4c811952676547b6c687bf0 Mon Sep 17 00:00:00 2001
From: Ian Longden <ianl@sanger.ac.uk>
Date: Tue, 8 Nov 2011 16:03:17 +0000
Subject: [PATCH] added fetch_all_by_name which gets all the xrefs that have
the accession, display_label or synonym that is passed to it. external
database source is optional
---
modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm | 126 ++++++++++++++++++++
1 file changed, 126 insertions(+)
diff --git a/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm
index 5a748d1dca..2914260622 100644
--- a/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm
@@ -370,6 +370,132 @@ sub get_all_masters {
}
+=head fetch_all_by_name
+
+ Arg [1] : string $name - The name of the external reference.
+ found in accession, display_label or synonym
+ Arg [2] : (optional) string $dbname - The name of the database which
+ the provided name is for.
+
+ Example : my $xref = @{$dbea->fetch_all_by_name('BRAC2','HGNC')}[0];
+ print $xref->description(), "\n" if($xref);
+ Description: Retrieves list of DBEntrys (xrefs) via a name.
+ The accesion is looked for first then the synonym and finally
+ the display_label.
+ NOTE $dbname this is optional but adding this speeds the
+ process up if you know what you are looking for.
+
+ NOTE: In a multi-species database, this method will
+ return all the entries matching the search criteria, not
+ just the ones associated with the current species.
+ Returntype : Bio::EnsEMBL::DBSQL::DBEntry
+ Exceptions : thrown if arguments are incorrect
+ Caller : general, domainview
+ Status : Stable
+
+=cut
+
+sub fetch_all_by_name {
+ my ( $self, $name, $dbname ) = @_;
+
+ my $sql = (<<SQL);
+ SELECT xref.xref_id, xref.dbprimary_acc, xref.display_label, xref.version,
+ exDB.priority, exDB.db_name, exDB.db_display_name, exDB.db_release,
+ es.synonym, xref.info_type, xref.info_text,
+ exDB.type, exDB.secondary_db_name, exDB.secondary_db_table,
+ xref.description
+ FROM (xref, external_db exDB)
+ LEFT JOIN external_synonym es ON
+ es.xref_id = xref.xref_id
+ WHERE (xref.dbprimary_acc = ? or xref.display_label = ?)
+ AND xref.external_db_id = exDB.external_db_id
+SQL
+
+ if(defined $dbname){
+ $sql .= " AND exDB.db_name = ?";
+ }
+ my $sth = $self->prepare($sql);
+ $sth->bind_param( 1, $name, SQL_VARCHAR );
+ $sth->bind_param( 2, $name, SQL_VARCHAR );
+ if(defined $dbname){
+ $sth->bind_param( 3 , $dbname, SQL_VARCHAR );
+ }
+ $sth->execute();
+
+
+ if ( !$sth->rows() && lc($dbname) eq 'interpro' ) {
+ # This is a minor hack that means that results still come back even
+ # when a mistake was made and no interpro accessions were loaded into
+ # the xref table. This has happened in the past and had the result of
+ # breaking domainview
+
+ $sth->finish();
+ $sth = $self->prepare(
+ "SELECT NULL,
+ i.interpro_ac,
+ i.id,
+ NULL,
+ NULL,
+ 'Interpro',
+ NULL,
+ NULL
+ FROM interpro i
+ WHERE i.interpro_ac = ?" );
+
+ $sth->bind_param( 1, $name, SQL_VARCHAR );
+ $sth->execute();
+ }
+
+ my %exDB;
+ my @exDBlist;
+ my $max_rows = 1000;
+
+ while ( my $rowcache = $sth->fetchall_arrayref( undef, $max_rows ) ) {
+ while ( my $arrayref = shift( @{$rowcache} ) ) {
+ my ( $dbID, $dbprimaryId,
+ $displayid, $version,
+ $priority,
+ $dbname, $db_display_name,
+ $release, $synonym,
+ $info_type, $info_text,
+ $type, $secondary_db_name,
+ $secondary_db_table, $description
+ ) = @$arrayref;
+
+ if ( !defined $exDB{$dbID} ) {
+ my $entrie =
+ Bio::EnsEMBL::DBEntry->new(
+ -adaptor => $self,
+ -dbID => $dbID,
+ -primary_id => $dbprimaryId,
+ -display_id => $displayid,
+ -version => $version,
+ -release => $release,
+ -dbname => $dbname,
+ -priority => $priority,
+ -db_display_name => $db_display_name,
+ -info_type => $info_type,
+ -info_text => $info_text,
+ -type => $type,
+ -secondary_db_name => $secondary_db_name,
+ -secondary_db_table => $secondary_db_table,
+ -description => $description
+ );
+ $exDB{$dbID} = $entrie;
+ push @exDBlist, $entrie;
+ }
+ if ($synonym) { $exDB{$dbID}->add_synonym($synonym) }
+
+ } ## end while ( my $arrayref = shift...
+ } ## end while ( my $rowcache = $sth...
+
+ $sth->finish();
+
+ return \@exDBlist;
+} ## end sub fetch_all_by_name
+
+
+
=head2 fetch_by_db_accession
Arg [1] : string $dbname - The name of the database which the provided
--
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