diff --git a/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm
index b4151091e79d8c281043fd67a0b404d008ced2ca..fda73e61bf2d4ad4d33a19e36fa7878c032463ff 100644
--- a/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm
@@ -305,6 +305,46 @@ sub store {
+
+=head2 exists
+
+ Arg [1] : Bio::EnsEMBL::DBEntry $dbe
+ Example : if($dbID = $db_entry_adaptor->exists($dbe)) { do stuff; }
+ Description: Returns the db id of this DBEntry if it exists in this database
+ otherwise returns undef. Exists is defined as an entry with
+ the same external_db and display_id
+ Returntype : int
+ Exceptions : thrown on incorrect args
+ Caller : GeneAdaptor::store, TranscriptAdaptor::store
+
+=cut
+
+sub exists {
+ my $self = shift;
+ my $dbe = shift;
+
+ unless($dbe && ref $dbe && $dbe->isa('Bio::EnsEMBL::DBEntry')) {
+ $self->throw("arg must be a Bio::EnsEMBL::DBEntry not [$dbe]");
+ }
+
+ my $sth = $self->prepare('SELECT x.xref_id
+ FROM xref x, external_db xdb
+ WHERE x.external_db_id = xdb.external_db_id
+ AND x.display_label = ?
+ AND xdb.db_name = ?');
+
+ $sth->execute($dbe->display_id, $dbe->external_db);
+
+ my ($dbID) = $sth->fetchrow_array;
+
+ $sth->finish;
+
+ return $dbID;
+}
+
+
+
+
=head2 fetch_all_by_Gene
Arg [1] : Bio::EnsEMBL::Gene $gene
diff --git a/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
index 312c82ce45ce0718d0640fd96ab51e2c5b21a915..99041ae0ba52778e90f049b2b9abd4ea18c8cb5b 100644
--- a/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
@@ -745,12 +745,27 @@ sub store {
}
+ #
+ # store the dbentries associated with this gene
+ #
my $dbEntryAdaptor = $self->db->get_DBEntryAdaptor();
foreach my $dbl ( @{$gene->get_all_DBLinks} ) {
$dbEntryAdaptor->store( $dbl, $gene_dbID, "Gene" );
}
+ #
+ # Update the genes display xref if it is set
+ #
+ my $display_xref = $gene->display_xref;
+ if($display_xref) {
+ if(my $dbe_id = $dbEntryAdaptor->exists($display_xref)) {
+ my $dispxref_sth = $self->prepare('UPDATE gene SET display_xref_id = ?
+ WHERE gene_id = ?');
+ $dispxref_sth->execute($dbe_id, $gene_dbID);
+ }
+ }
+
# write exons transcripts and exon_transcript table
@@ -912,68 +927,30 @@ sub deleteObj {
}
-=head2 get_external_name
-
- Arg [1] : int $dbID
- the database identifier of the gene whose external name is
- sought
- Example : $external_name = $gene_adaptor->get_external_name(42);
- Description: Retrieves the external name for a gene. This is implemented
- by joining across the xref and gene tables, using the
- display_xref_id column.
- Returntype : string
- Exceptions : thrown if $dbId arg is not defined
- Caller : general
-
-=cut
-
-sub get_external_name {
- my ($self, $dbID) = @_;
-
- if( !defined $dbID ) {
- $self->throw("Must call with a dbID");
- }
-
- my $sth = $self->prepare("SELECT x.display_label
- FROM gene g,
- xref x
- WHERE g.gene_id = ?
- AND g.display_xref_id = x.xref_id
- ");
- $sth->execute($dbID);
-
- my ($xref) = $sth->fetchrow_array();
- if( !defined $xref ) {
- return undef;
- }
-
- return $xref;
-}
-
+
-=head2 get_external_dbname
+=head2 get_display_xref
- Arg [1] : int $dbID
- the database identifier of the gene for which the name of
- external db from which its external name is derived.
- Example : $external_dbname = $gene_adaptor->get_external_dbname(42);
- Description: Retrieves the external db name for a gene from which its external
- name is derived.. This is implemented by joining across the xref,
- gene and external_db tables, using the display_xref_id column.
- Returntype : string
+ Arg [1] : Bio::EnsEMBL::Gene $gene
+ retrieve display_xref for this gene
+ Example : none
+ Description: Retrieves the display_xref for a gene.
+ Returntype : Bio::EnsEMBL::DBEntry
Exceptions : thrown if $dbId arg is not defined
Caller : general
=cut
-sub get_external_dbname {
- my ($self, $dbID) = @_;
+sub get_display_xref {
+ my ($self, $gene ) = @_;
- if( !defined $dbID ) {
- $self->throw("Must call with a dbID");
+ if( !defined $gene ) {
+ $self->throw("Must call with a Gene object");
}
- my $sth = $self->prepare("SELECT e.db_name
+ my $sth = $self->prepare("SELECT e.db_name,
+ x.display_label,
+ x.xref_id
FROM gene g,
xref x,
external_db e
@@ -981,49 +958,22 @@ sub get_external_dbname {
AND g.display_xref_id = x.xref_id
AND x.external_db_id = e.external_db_id
");
- $sth->execute($dbID);
-
- my ($db_name) = $sth->fetchrow_array();
- if( !defined $db_name ) {
- return undef;
- }
-
- return $db_name;
-}
-
-
-=head2 get_display_xref_id
-
- Arg [1] : int $dbID
- the database identifier of the gene for which the name of
- external db from which its external name is derived.
- Example : $external_dbname = $gene_adaptor->get_display_xref_id(42);
- Description: Retrieves the display_xref_id for a gene.
- Returntype : int
- Exceptions : thrown if $dbId arg is not defined
- Caller : general
-
-=cut
-
-sub get_display_xref_id {
- my ($self, $dbID) = @_;
-
- if( !defined $dbID ) {
- $self->throw("Must call with a dbID");
- }
+ $sth->execute( $gene->dbID );
- my $sth = $self->prepare("SELECT display_xref_id
- FROM gene
- WHERE gene_id = ?
- ");
- $sth->execute($dbID);
- my ($xref_id) = $sth->fetchrow_array();
+ my ($db_name, $display_label, $xref_id ) = $sth->fetchrow_array();
if( !defined $xref_id ) {
return undef;
}
-
- return $xref_id;
+ my $db_entry = Bio::EnsEMBL::DBEntry->new
+ (
+ -dbid => $xref_id,
+ -adaptor => $self->db->get_DBEntryAdaptor(),
+ -dbname => $db_name,
+ -display_id => $display_label
+ );
+
+ return $db_entry;
}
@@ -1048,40 +998,30 @@ sub update {
my $update = 0;
if( !defined $gene || !ref $gene || !$gene->isa('Bio::EnsEMBL::Gene') ) {
- $self->throw("Must update a gene object, not a $gene");
+ $self->throw("Must update a gene object, not a $gene");
}
- my $sth = $self->prepare("SELECT type, analysis_id, transcript_count, display_xref_id
- FROM gene
- WHERE gene_id = ?
- ");
-
- $sth->execute($gene->dbID);
-
- if ( my ($type, $analysis, $transcripts, $dxref_id) = $sth->fetchrow_array() ){
-
- if ( $dxref_id != $gene->display_xref ) { $update = 1; }
- elsif ( $type ne $gene->type ) { $update = 1; }
- elsif ( $analysis != $gene->analysis->dbID ) { $update = 1; }
- elsif ( $transcripts != scalar(@{$gene->get_all_Transcripts})) {
- $self->warn("Trying to update the number of transcripts on a stored gene. Not yet implemented.");
- }
+ my $xref_id;
+ if($gene->display_xref && $gene->display_xref->dbID) {
+ $xref_id = $gene->display_xref->dbID;
+ } else {
+ $xref_id = 0;
+ }
- if ( $update ) {
+ my $tcount = scalar @{$gene->get_all_Transcripts};
- $sth = $self->prepare("UPDATE gene
- SET type = ?,
- analysis_id = ?,
- display_xref_id = ?
- WHERE gene_id = ?
- ");
+ $sth = $self->prepare("UPDATE gene
+ SET type = ?,
+ analysis_id = ?,
+ display_xref_id = ?,
+ transcript_count = ?
+ WHERE gene_id = ?");
- $sth->execute($gene->type, $gene->analysis->dbID, $gene->display_xref, $gene->dbID);
- }
- }
- else {
- $self->warn("Trying to update a gene that is not in the database. Try store\'ing first.");
- }
+ $sth->execute($gene->type,
+ $gene->analysis->dbID,
+ $xref_id,
+ $tcout,
+ $gene->dbID);
}
diff --git a/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm
index 59170946761f26af3f02455e49ab291683c587da..f9cadca79279514e567a4e2e37881b2fadf7a549 100644
--- a/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm
@@ -202,13 +202,13 @@ sub store {
# ok - now load this line in
my $tst = $self->prepare("
insert into transcript ( gene_id, translation_id, exon_count, display_xref_id )
- values ( ?, ?, ?, ?)
+ values ( ?, ?, ?, 0)
");
if( defined $translation ) {
- $tst->execute( $gene_dbID, $translation->dbID(), $exon_count, $xref_id );
+ $tst->execute( $gene_dbID, $translation->dbID(), $exon_count );
} else {
- $tst->execute( $gene_dbID, 0, $exon_count, $xref_id );
+ $tst->execute( $gene_dbID, 0, $exon_count );
}
my $transc_dbID = $tst->{'mysql_insertid'};
@@ -218,8 +218,23 @@ sub store {
foreach my $dbl ( @{$transcript->get_all_DBLinks} ) {
$dbEntryAdaptor->store( $dbl, $transc_dbID, "Transcript" );
+
}
+ #
+ # Update transcript to point to display xref if it is set
+ #
+ if(my $dxref = $transcript->display_xref) {
+ if(my $dxref_id = $dbEntryAdaptor->exists($dxref)) {
+ $self->prepare( "update transcript set display_xref_id = ".
+ $dxref_id . " where transcript_id = ".$transc_dbID);
+ $self->execute();
+ $dxref->dbID($dxref_id);
+ $dxref->adaptor($dbEntryAdaptor);
+ }
+ }
+
+
my $etst = $self->prepare("insert into exon_transcript (exon_id,transcript_id,rank) values (?,?,?)");
my $rank = 1;
foreach my $exon ( @{$transcript->get_all_Exons} ) {
@@ -374,68 +389,31 @@ sub remove {
-=head2 get_external_name
- Arg [1] : int $dbID
- the database identifier of the transcript whose external name
- is sought
- Example : $external_name = $transcript_adaptor->get_external_name(42);
- Description: Retrieves the external name for a transcript. This is implemented
- by joining across the xref and transcript tables, using the
- display_xref_id column.
- Returntype : string
- Exceptions : thrown if $dbId arg is not defined
- Caller : general
-=cut
-
-sub get_external_name {
- my ($self, $dbID) = @_;
-
- if( !defined $dbID ) {
- $self->throw("Must call with a dbID");
- }
-
- my $sth = $self->prepare("SELECT x.display_label
- FROM transcript t,
- xref x
- WHERE t.transcript_id = ?
- AND t.display_xref_id = x.xref_id
- ");
- $sth->execute($dbID);
-
- my ($xref) = $sth->fetchrow_array();
- if( !defined $xref ) {
- return undef;
- }
-
- return $xref;
-}
-
-
-=head2 get_external_dbname
+=head2 get_display_xref
Arg [1] : int $dbID
- the database identifier of the transcript for which the name of
- external db from which its external name is derived.
- Example : $external_dbname = $transcript_adaptor->get_external_dbname(42);
- Description: Retrieves the external db name for a transcript from which its external
- name is derived.. This is implemented by joining across the xref,
- transcript and external_db tables, using the display_xref_id column.
- Returntype : string
+ the database identifier of the transcript for which the name
+ of external db from which its external name is derived.
+ Example : $external_dbname = $transcript_adaptor->get_display_xref_id(42);
+ Description: Retrieves the display_xref_id for a transcript.
+ Returntype : int
Exceptions : thrown if $dbId arg is not defined
Caller : general
=cut
-sub get_external_dbname {
- my ($self, $dbID) = @_;
+sub get_display_xref {
+ my ($self, $transcript) = @_;
- if( !defined $dbID ) {
- $self->throw("Must call with a dbID");
+ if( !defined $transcript ) {
+ $self->throw("Must call with a Transcript object");
}
- my $sth = $self->prepare("SELECT e.db_name
+ my $sth = $self->prepare("SELECT e.db_name,
+ x.display_label,
+ x.xref_id
FROM transcript t,
xref x,
external_db e
@@ -443,49 +421,23 @@ sub get_external_dbname {
AND t.display_xref_id = x.xref_id
AND x.external_db_id = e.external_db_id
");
- $sth->execute($dbID);
-
- my ($db_name) = $sth->fetchrow_array();
- if( !defined $db_name ) {
- return undef;
- }
-
- return $db_name;
-}
-
-
-=head2 get_display_xref_id
-
- Arg [1] : int $dbID
- the database identifier of the transcript for which the name
- of external db from which its external name is derived.
- Example : $external_dbname = $transcript_adaptor->get_display_xref_id(42);
- Description: Retrieves the display_xref_id for a transcript.
- Returntype : int
- Exceptions : thrown if $dbId arg is not defined
- Caller : general
-
-=cut
-
-sub get_display_xref_id {
- my ($self, $dbID) = @_;
-
- if( !defined $dbID ) {
- $self->throw("Must call with a dbID");
- }
+ $sth->execute( $transcript->dbID );
- my $sth = $self->prepare("SELECT display_xref_id
- FROM transcript
- WHERE transcript_id = ?
- ");
- $sth->execute($dbID);
- my ($xref_id) = $sth->fetchrow_array();
+ my ($db_name, $display_label, $xref_id ) = $sth->fetchrow_array();
if( !defined $xref_id ) {
return undef;
}
- return $xref_id;
+ my $db_entry = Bio::EnsEMBL::DBEntry->new
+ (
+ -dbid => $xref_id,
+ -adaptor => $self->db->get_DBEntryAdaptor(),
+ -dbname => $db_name,
+ -display_id => $display_label
+ );
+
+ return $db_entry;
}
@@ -512,33 +464,24 @@ sub update {
$self->throw("Must update a transcript object, not a $transcript");
}
- my $sth = $self->prepare("SELECT exon_count, display_xref_id
- FROM transcript
- WHERE transcript_id = ?
- ");
-
- $sth->execute($transcript->dbID);
-
- if ( my ($exons, $dxref_id) = $sth->fetchrow_array() ){
-
- if ( $exons != scalar(@{$transcript->get_all_Exons})) {
- $self->warn("Trying to update the number of exons on a stored transcript. Not yet implemented.");
- }
-
- if ( $dxref_id != $transcript->display_xref ) {
+ my $sth = $self->prepare("UPDATE transcript
+ SET display_xref_id = ?,
+ exon_count = ?
+ WHERE transcript_id = ?
+ ");
- $sth = $self->prepare("UPDATE transcript
- SET display_xref_id = ?
- WHERE transcript_id = ?
- ");
+ my $display_xref = $transcript->display_xref();
+ my $display_xref_id;
- $sth->execute($transcript->display_xref, $transcript->dbID);
- }
- }
- else {
- $self->warn("Trying to update a transcript that is not in the database. Try store\'ing first.");
+ if( defined $display_xref && $display_xref->dbID() ) {
+ $display_xref_id = $display_xref->dbID();
+ } else {
+ $display_xref_id = 0;
}
-}
+
+ my $exon_count = scalar( @{$transcript->get_all_Exons()} );
+ $sth->execute( $display_xref_id, $exon_count, $transcript->dbID() );
+ }
diff --git a/modules/Bio/EnsEMBL/Gene.pm b/modules/Bio/EnsEMBL/Gene.pm
index b24b00be9b1ddae209d9453639775ff76c93c017..a4501e917ea70282ae1611d8bf400b6783fd6672 100755
--- a/modules/Bio/EnsEMBL/Gene.pm
+++ b/modules/Bio/EnsEMBL/Gene.pm
@@ -391,16 +391,20 @@ sub external_name {
my ($self, $ext_name) = @_;
if(defined $ext_name) {
- $self->{'_ext_name'} = $ext_name;
+ return ( $self->{'_ext_name'} = $ext_name );
}
if( exists $self->{'_ext_name'} ) {
return $self->{'_ext_name'};
}
- $self->{'_ext_name'} = $self->adaptor->get_external_name($self->dbID);
- return $self->{'_ext_name'};
+ my $display_xref = $self->display_xref();
+ if( defined $display_xref ) {
+ return $display_xref->display_id()
+ } else {
+ return undef;
+ }
}
@@ -417,19 +421,23 @@ sub external_name {
=cut
sub external_db {
- my ($self, $ext_dbname) = @_;
+ my ( $self, $ext_dbname ) = @_;
if(defined $ext_dbname) {
- $self->{'_ext_dbname'} = $ext_dbname;
+ return ( $self->{'_ext_dbname'} = $ext_dbname );
}
if( exists $self->{'_ext_dbname'} ) {
return $self->{'_ext_dbname'};
}
- $self->{'_ext_dbname'} = $self->adaptor->get_external_dbname($self->dbID);
- return $self->{'_ext_dbname'};
+ my $display_xref = $self->display_xref();
+ if( defined $display_xref ) {
+ return $display_xref->dbname()
+ } else {
+ return undef;
+ }
}
@@ -925,20 +933,16 @@ sub species {
=cut
-sub display_xref{
-
- my ($self,$value) = @_;
-
- if( defined $value ) {
- $self->{'display_xref'} = $value;
- return;
- }
+sub display_xref {
- if( exists $self->{'display_xref'} ) {
+ my $self = shift;
+ if( @_ ) {
+ $self->{'display_xref'} = shift;
+ } elsif( exists $self->{'display_xref'} ) {
return $self->{'display_xref'};
- }
-
- $self->{'display_xref'} = $self->adaptor->get_display_xref_id($self->dbID);
+ } elsif ( defined $self->adaptor() ) {
+ $self->{'display_xref'} = $self->adaptor->get_display_xref( $self );
+ }
return $self->{'display_xref'};
}
diff --git a/modules/Bio/EnsEMBL/Transcript.pm b/modules/Bio/EnsEMBL/Transcript.pm
index 67addd815a314b7cacd9b4a5bf05999374d7db19..7c37d21bc22a02eb17399dfd3d5381d24e8403aa 100755
--- a/modules/Bio/EnsEMBL/Transcript.pm
+++ b/modules/Bio/EnsEMBL/Transcript.pm
@@ -163,19 +163,23 @@ sub dbID {
=cut
sub external_db {
- my ($self, $ext_dbname) = @_;
+ my ( $self, $ext_dbname ) = @_;
if(defined $ext_dbname) {
- $self->{'_ext_dbname'} = $ext_dbname;
+ return ( $self->{'_ext_dbname'} = $ext_dbname );
}
if( exists $self->{'_ext_dbname'} ) {
return $self->{'_ext_dbname'};
}
- $self->{'_ext_dbname'} = $self->adaptor->get_external_dbname($self->dbID);
- return $self->{'_ext_dbname'};
+ my $display_xref = $self->display_xref();
+ if( defined $display_xref ) {
+ return $display_xref->dbname()
+ } else {
+ return undef;
+ }
}
@@ -190,20 +194,25 @@ sub external_db {
=cut
+
sub external_name {
my ($self, $ext_name) = @_;
if(defined $ext_name) {
- $self->{'_ext_name'} = $ext_name;
+ return ( $self->{'_ext_name'} = $ext_name );
}
if( exists $self->{'_ext_name'} ) {
return $self->{'_ext_name'};
}
- $self->{'_ext_name'} = $self->adaptor->get_external_name($self->dbID);
- return $self->{'_ext_name'};
+ my $display_xref = $self->display_xref();
+ if( defined $display_xref ) {
+ return $display_xref->display_id()
+ } else {
+ return undef;
+ }
}
@@ -250,26 +259,23 @@ sub adaptor {
=cut
-sub display_xref{
-
- my ($self,$value) = @_;
-
- if( defined $value ) {
- $self->{'display_xref'} = $value;
- return;
- }
+sub display_xref {
- if( exists $self->{'display_xref'} ) {
+ my $self = shift;
+ if( @_ ) {
+ $self->{'display_xref'} = shift;
+ } elsif( exists $self->{'display_xref'} ) {
return $self->{'display_xref'};
- }
-
- $self->{'display_xref'} = $self->adaptor->get_display_xref_id($self->dbID);
+ } elsif ( defined $self->adaptor() ) {
+ $self->{'display_xref'} = $self->adaptor->get_display_xref( $self );
+ }
return $self->{'display_xref'};
}
+
=head2 _translation_id
Title : _translation_id
diff --git a/modules/t/gene.t b/modules/t/gene.t
index 1f6503e2b263c0900fa08af0dc2a324c2a09acf1..5bd25a826972b8e6c8335fe3a20083373d3a192c 100644
--- a/modules/t/gene.t
+++ b/modules/t/gene.t
@@ -62,7 +62,7 @@ debug( "Gene external dbname: " . $gene->external_db );
ok( $gene->external_db eq "SPTREMBL");
debug( "Gene display xref id: " . $gene->display_xref );
-ok( $gene->display_xref == 128324);
+ok( $gene->display_xref->dbID() == 128324);
# test the getters and setters
@@ -385,14 +385,16 @@ $gene = $ga->fetch_by_stable_id( "ENSG00000171456" );
$ga->update($gene);
my $newgene = $ga->fetch_by_stable_id( "ENSG00000171456" );
-ok ( $newgene->display_xref == 128324 );
+ok ( $newgene->display_xref->dbID() == 128324 );
ok ( $newgene->type eq 'ensembl' );
# now change the original gene and update it
-$gene->display_xref(42);
+my $dbEntryAdaptor= $db->get_DBEntryAdaptor();
+
+$gene->display_xref( $dbEntryAdaptor->fetch_by_dbID( 614 ));
$gene->type('dummy');
$ga->update($gene);
$newgene = $ga->fetch_by_stable_id( "ENSG00000171456" );
-ok ( $newgene->display_xref == 42 );
+ok ( $newgene->display_xref->dbID() == 614 );
ok ( $newgene->type eq 'dummy' );
diff --git a/modules/t/transcript.t b/modules/t/transcript.t
index abcd1c5c537a10a7b51f30f240469351e90a9c4e..e4debf3f43ad65f060fb04e62a6f77ec0da66967 100644
--- a/modules/t/transcript.t
+++ b/modules/t/transcript.t
@@ -80,8 +80,8 @@ ok ( $tr->external_name eq "MAPRE1");
debug ( "External transcript dbname: " . $tr->external_db );
ok ( $tr->external_db eq 'HUGO' );
-debug ( "Display_xref_id: " . $tr->display_xref );
-ok ( $tr->display_xref == 97759 );
+debug ( "Display_xref_id: " . $tr->display_xref->dbID() );
+ok ( $tr->display_xref->dbID() == 97759 );
ok( test_getter_setter( $tr, "display_xref", 42 ));
ok( test_getter_setter( $tr, "dbID", 100000 ));
@@ -175,13 +175,14 @@ $tr = $ta->fetch_by_stable_id( "ENST00000217347" );
$ta->update($tr);
my $up_tr = $ta->fetch_by_stable_id( "ENST00000217347" );
-ok ( $up_tr->display_xref == 97759 );
+ok ( $up_tr->display_xref->dbID() == 97759 );
+my $dbentryAdaptor = $db->get_DBEntryAdaptor();
-$tr->display_xref(42);
+$tr->display_xref($dbentryAdaptor->fetch_by_dbID( 614 ));
$ta->update($tr);
$up_tr = $ta->fetch_by_stable_id( "ENST00000217347" );
-ok ( $up_tr->display_xref == 42 );
+ok ( $up_tr->display_xref->dbID() == 614 );