diff --git a/modules/Bio/EnsEMBL/DBSQL/ChromosomeAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/ChromosomeAdaptor.pm
index 6124168814100d0a576d2324f9bbc38c50941cb3..d55aed74081f4ed54cfb77bba65909bff8af8afa 100644
--- a/modules/Bio/EnsEMBL/DBSQL/ChromosomeAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/ChromosomeAdaptor.pm
@@ -80,6 +80,7 @@ sub fetch_by_dbID {
unless(defined $self->{'_chr_cache'} ) {
$self->{'_chr_cache'} = {};
+ $self->{'_chr_name_cache'} = {};
}
#
@@ -90,8 +91,8 @@ sub fetch_by_dbID {
my $sth = $self->prepare( "SELECT name, known_genes, unknown_genes,
snps, length
FROM chromosome
- WHERE chromosome_id = $id" );
- $sth->execute();
+ WHERE chromosome_id = ?" );
+ $sth->execute( $id );
my($name, $known_genes, $unknown_genes, $snps, $length);
$sth->bind_columns(\$name,\$known_genes,\$unknown_genes,\$snps,\$length);
@@ -108,14 +109,16 @@ sub fetch_by_dbID {
}
$chr = new Bio::EnsEMBL::Chromosome( -adaptor => $self,
+ -dbID => $id,
-chr_name => $name,
- -chromosome_id => $id,
-known_genes => $known_genes,
-unknown_genes => $unknown_genes,
-snps => $snps,
'-length' => $length );
$self->{'_chr_cache'}->{$id} = $chr;
+ $self->{'_chr_name_cache'}->{$name} = $chr;
+
}
return $chr;
@@ -137,15 +140,46 @@ sub fetch_by_dbID {
sub fetch_by_chr_name{
my ($self,$chr_name) = @_;
- #Convert the name to the dbID
- my $dbID = $self->get_dbID_by_chr_name($chr_name);
+ my $chr = ();
- unless(defined $dbID) {
- $self->warn("chromosome with name $chr_name not in database");
- return undef;
- }
-
- return $self->fetch_by_dbID($dbID);
+ unless(defined $chr_name) {
+ $self->throw("Chromosome name argument required\n");
+ }
+
+ unless(defined $self->{'_chr_cache'} ) {
+ $self->{'_chr_cache'} = {};
+ $self->{'_chr_name_cache'} = {};
+ }
+
+ #
+ # If there is not already a cached version of this chromosome pull it
+ # from the database and add it to the cache.
+ #
+ unless($chr = $self->{'_chr_name_cache'}->{$chr_name}) {
+ my $sth = $self->prepare( "SELECT chromosome_id, known_genes, unknown_genes,
+ snps, length
+ FROM chromosome
+ WHERE name = ?" );
+ $sth->execute( $chr_name );
+
+ my($dbID, $known_genes, $unknown_genes, $snps, $length);
+ $sth->bind_columns(\$dbID,\$known_genes,\$unknown_genes,\$snps,\$length);
+ $sth->fetch();
+
+ $chr = new Bio::EnsEMBL::Chromosome( -adaptor => $self,
+ -dbID => $dbID,
+ -chr_name => $chr_name,
+ -known_genes => $known_genes,
+ -unknown_genes => $unknown_genes,
+ -snps => $snps,
+ '-length' => $length );
+
+ $self->{'_chr_cache'}->{$dbID} = $chr;
+ $self->{'_chr_name_cache'}->{$chr_name} = $chr;
+
+ }
+
+ return $chr;
}
@@ -179,13 +213,14 @@ sub fetch_all {
my $chr = new Bio::EnsEMBL::Chromosome( -adaptor => $self,
-chr_name => $name,
- -chromosome_id => $chromosome_id,
+ -dbID => $chromosome_id,
-known_genes => $known_genes,
-unknown_genes => $unknown_genes,
-snps => $snps,
'-length' => $length );
$self->{'_chr_cache'}->{$chromosome_id} = $chr;
+ $self->{'_chr_name_cache'}->{$name} = $chr;
push @chrs, $chr;
}
diff --git a/modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm
index da8183d11c127069ffddbf240ac2c034fff8d9bc..2ff40d556051a3e87f5f8eedfaa53b28af7d0f6e 100755
--- a/modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm
@@ -734,7 +734,6 @@ sub assembly_type{
$obj->{'assembly'} = $value;
}
if (! defined $obj->{'assembly'}) {
- print STDERR "DBAdaptor.pm: using default assembly type\n";
my $ass;
eval {
$ass = $obj->get_MetaContainer()->get_default_assembly();
diff --git a/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
index 0e337428946f34620b57e6a9cd8b27c768dce7d5..a76e21ef527fdd5843217cdb788bada3dfb743e5 100644
--- a/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
@@ -123,6 +123,8 @@ sub list_stable_geneIds {
Arg [1] : int $geneId
the unique internal database id of the Gene to be retrieved
+ Arg [2] : int $chromosomal_coordinates (optional)
+ if defined, try to return chromosomal coordinates.
Example : $gene = $gene_adaptor->fetch_by_dbID
Description: Retrieves a gene object from the database using its unique
internal identifier.
@@ -133,7 +135,7 @@ sub list_stable_geneIds {
=cut
sub fetch_by_dbID {
- my ( $self, $geneId ) = @_;
+ my ( $self, $geneId, $chr_coordinates ) = @_;
my $exonAdaptor = $self->db->get_ExonAdaptor();
my @exons = @{$exonAdaptor->fetch_all_by_gene_id( $geneId )};
@@ -223,6 +225,18 @@ sub fetch_by_dbID {
$gene->add_Transcript( $transcript );
}
+ # if chromosomal coordinates are needed, transform with empty slice
+
+ if( defined $chr_coordinates ) {
+ my $sa = $self->db->get_SliceAdaptor();
+ my $empty_slice = Bio::EnsEMBL::Slice->new
+ (
+ -empty => 1,
+ -adaptor => $sa
+ );
+ $gene->transform( $empty_slice );
+ }
+
return $gene;
}
diff --git a/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
index 63bdfc2876c20d70d7487b445dd2d9d706603846..d90ace976fc1bac6298274085712d44a41ddce7d 100644
--- a/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
@@ -106,7 +106,7 @@ sub fetch_by_chr_start_end {
-chr_start => $start,
-chr_end => $end,
-assembly_type => $type,
- -adaptor => $self->db->get_SliceAdaptor()
+ -adaptor => $self
);
return $slice;
@@ -177,8 +177,14 @@ sub fetch_by_fpc_name {
my $slice;
- $slice = new Bio::EnsEMBL::Slice($chr,$slice_start,$slice_end,
- $strand,$type);
+ $slice = new Bio::EnsEMBL::Slice
+ (
+ -chr_name => $chr,
+ -chr_start =>$slice_start,
+ -chr_end => $slice_end,
+ -strand => $strand,
+ -assembly_type => $type
+ );
return $slice;
}
@@ -394,7 +400,18 @@ sub fetch_by_chr_name{
my $chromosome = $ca->fetch_by_chr_name($chr_name);
my $chr_end = $chromosome->length();
- return $self->fetch_by_chr_start_end($chr_name, $chr_start, $chr_end);
+ my $type = $self->db->assembly_type();
+
+ my $slice = Bio::EnsEMBL::Slice->new
+ (
+ -chr_name => $chr_name,
+ -chr_start => 1,
+ -chr_end => $chr_end,
+ -assembly_type => $type,
+ -adaptor => $self
+ );
+
+ return $slice;
}