Raw content of Bio::EnsEMBL::ExternalData::Disease::DBHandler
<![CDATA[#
# BioPerl module for Bio::EnsEMBL::ExternalData::Disease::DBHandler
#
# Written by Arek Kasprzyk <arek@ebi.ac.uk>
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::EnsEMBL::ExternalData::Disease::DBHandler
=head1 SYNOPSIS
my $diseasedb = new Bio::EnsEMBL::ExternalData::Disease::DBHandler(
-user => 'ensembl',
-dbname => 'disease',
-host=>'sol28.ebi.ac.uk',
-port=>'3307',
-ensdb=>$ensembldb,
my @diseases=$diseasedb->diseases_on_chromosome(22);
my @diseases=$diseasedb->diseases_without_genes;
my @diseases=$diseasedb->all_diseases;
my $disease =$diseasedb->disease_by_name("DiGeorge syndrome (2)");
my @diseases=$diseasedb->diseases_like("corneal");
=head1 DESCRIPTION
This object represents a disease database consisting of disease phenotype descriptions,
chromosomal locations and/or associated genes from OMIM morbid map and
Mitelman Catalogoue of Chromosome Abnormalities.
In additon, when database representations of ensembl and map databases are set,
it will provide a 'translation' of OMIM and Mitelman genes to ensembl gene predictions
and their localization in local and global coordinates.
=head1 AUTHOR - Arek Kasprzyk
Email arek@ebi.ac.uk
Describe contact details here
=head1 APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
=cut
package Bio::EnsEMBL::ExternalData::Disease::DBHandler;
use strict;
use DBI;
use Bio::EnsEMBL::Gene;
use Bio::EnsEMBL::Root;
use Bio::EnsEMBL::ExternalData::Disease::Disease;
use Bio::EnsEMBL::ExternalData::Disease::DiseaseLocation;
use vars qw(@ISA);
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
@ISA = qw(Bio::EnsEMBL::Root);
sub new
{
my($class,@args) = @_;
my $self = bless {}, $class;
my ($db,$host,$port,$driver,$user,$password,$debug,$ensdb) =
rearrange([qw(DBNAME
HOST
PORT
DRIVER
USER
PASS
DEBUG
ENSDB
)],@args);
$driver ||= 'mysql';
$host ||= 'localhost';
$port ||= 3306;
$db ||= 'disease';
$user ||= 'ensembl';
$ensdb && $self->_ensdb($ensdb);
my $dsn = "DBI:$driver:database=$db;host=$host;port=$port";
if( $debug && $debug > 10 ) {
$self->_db_handle("dummy dbh handle in debug mode $debug");
} else {
my $dbh = DBI->connect("$dsn","$user",$password,{RaiseError => 1});
$dbh || $self->throw("Could not connect to database $db user $user using [$dsn] as a locator");
$self->_db_handle($dbh);
}
return $self;
}
=head2 add_db_adaptor
Arg [1] : Bio::EnsEMBL::DBSQL::DBAdaptor object
Function : Registers core database with this adaptor
Returntype: Bio::EnsEMBL::DBSQL::DBAdaptor object
Exceptions: none
Caller : EnsEMBL::DB::Core
Example :
=cut
sub add_db_adaptor {
my $self = shift;
my $ensdb = shift || $self->throw("Need an ensembl DB adaptor");
return $self->_ensdb($ensdb);
}
=head2 disease by name
Title : disease_by_name
Usage : my $disease=$diseasedb->disease_by_name("DiGeorge syndrome (2)");
Function: gets disease by name
Example :
Returns : Bio::EnsEMBL::ExternalData::Disease::Disease object
Args :
=cut
sub disease_by_name
{
my ($self,$disease_name)=@_;
my $query_string= "select d.disease,g.id,g.gene_symbol,g.omim_id,g.start_cyto,g.end_cyto,
g.chromosome from disease as d,gene as g where d.id = g.id
and d.disease='$disease_name'";
return $self->_get_disease_objects($query_string);
}
=head2 disease by omim id
Title : disease_by_omim_id
Usage : my $disease=$diseasedb->disease_by_omim_id("201810");
Function: gets disease by omim id
Example :
Returns : Bio::EnsEMBL::ExternalData::Disease::Disease object
Args :
=cut
sub disease_by_omim_id
{
my ($self,$omim_id)=@_;
my $query_string= "select d.disease,g.id,g.gene_symbol,g.omim_id,g.start_cyto,g.end_cyto,
g.chromosome from disease as d,gene as g where d.id = g.id
and g.omim_id='$omim_id'";
return $self->_get_disease_objects($query_string);
}
=head2 disease by ensembl gene
Title : disease_by_ensembl_gene
Usage : my @diseases=$diseasedb->disease_by_ensembl_gene($gene);
Function: gets disease (if any) for an EnsEMBL Gene object
Returns : A list of Bio::EnsEMBL::ExternalData::Disease::Disease object or 0 if none
Args : Bio::EnsEMBL::Gene object
=cut
sub disease_name_by_ensembl_gene
{
my ($self,$gene) = @_;
$self->throw("$gene is not a Bio::EnsEMBL::Gene object!") unless
$gene->isa('Bio::EnsEMBL::Gene');
my $DBlinks = ( $gene->get_all_DBLinks || [] );
my @genes = ( map { $_->display_id, @{$_->get_all_synonyms || [] } }
grep { $_->database eq 'HUGO' } @$DBlinks );
return 0 unless @genes;
my $query_string = "select distinct d.disease, g.omim_id
from disease as d,gene as g
where d.id = g.id and g.gene_symbol in (".
join(',' , map {$self->_db_handle->quote($_)} @genes) .
") order by d.disease";
return $self->_get_disease_objects($query_string);
}
=head2 all diseases
Title : all_diseases
Usage : my @diseases=$diseasedb->all_diseases[(30,10)];
Function: gets all diseases from the database, with optional offset,limit
Example :
Returns : an array of Bio::EnsEMBL::ExternalData::Disease::Disease objects
Args :
=cut
sub all_diseases
{
my ($self,$offset,$count)=@_;
my $query_string='';
if (defined $offset){
$offset='limit '.$offset;
if($count){$count=','.$count;}
my $get_disease_ids_sql="SELECT distinct d.id
FROM disease AS d,gene AS g
WHERE d.id = g.id $offset $count;";
my $sth=$self->_db_handle->prepare($get_disease_ids_sql);
$sth->execute;
my @ids;
while ( my $rowhash = $sth->fetchrow_hashref){
push @ids, $rowhash->{'id'};
}
if (scalar @ids){
my $id_string=join(',',@ids);
$query_string= "SELECT d.disease,
g.id,
g.gene_symbol,
g.omim_id,
g.start_cyto,
g.end_cyto,
g.chromosome
FROM disease AS d,gene AS g
WHERE g.id=d.id
AND d.id IN ($id_string)";
}
else {
# no matches for this query, so:
return ();
}
}
else {
$query_string='SELECT d.disease,
g.id,
g.gene_symbol,
g.omim_id,
g.start_cyto,
g.end_cyto,
g.chromosome
FROM disease AS d,gene AS g
WHERE d.id = g.id';
}
return $self->_get_disease_objects($query_string);
}
=head2 all disease names
Title : all_disease_names
Usage : my @diseases=$diseasedb->all_disease_names(90,2);
Function: gets all disease names from the database limites by offset and count
Example :
Returns : an array of disease names (strings)
Args :
=cut
sub all_disease_names
{
my ($self,$offset,$count)=@_;
if ($offset||$offset == 0){$offset='limit '.$offset;}
if($count){$count=','.$count;}
my $query_string="select disease from disease $offset $count;";
$self->_get_disease_names($query_string);
}
=head2 all disease count
Title : all_disease_count
Usage : my $count=$diseasedb->all_disease_count;
Function: number of diseases
Example :
Returns : a number of diseases
Args :
=cut
sub all_disease_count
{
my ($self)=@_;
my $query_string="SELECT disease FROM disease;";
$self->_get_count($query_string);
}
=head2 diseases on chromosome
Title : diseases_on_chromosome
Usage : my @diseases=$diseasedb->diseases_on_chromosome(22,90,30);
Function: gets all diseases for a given chromosome limited by offset and count
Example :
Returns : an array of Bio::EnsEMBL::ExternalData::Disease::Disease objects
Args :
=cut
sub diseases_on_chromosome
{
my ($self,$chromosome_no,$offset,$count)=@_;
my $query_string='';
$chromosome_no || $self->throw("I need a chromosome");
# If we've got limits, then do a limited query, otherwise, do a full query
# There was a bug, $offset||$offset == 0, fixed.
if (defined $offset){
$offset='limit '.$offset;
if($count){$count=','.$count;}
my $get_disease_ids_sql="SELECT distinct d.id
FROM disease AS d,gene AS g
WHERE d.id = g.id
AND g.chromosome='$chromosome_no'
$offset $count;";
my $sth=$self->_db_handle->prepare($get_disease_ids_sql);
$sth->execute;
my @ids;
while ( my $rowhash = $sth->fetchrow_hashref){
push @ids, $rowhash->{'id'};
}
if (scalar @ids){
my $id_string=join(',',@ids);
$query_string= "SELECT d.disease,
g.id,
g.gene_symbol,
g.omim_id,
g.start_cyto,
g.end_cyto,
g.chromosome
FROM disease AS d,gene AS g
WHERE g.id=d.id
AND d.id IN ($id_string)";
}
else {
return ();
}
}
else {
$query_string= "SELECT d.disease,
g.id,
g.gene_symbol,
g.omim_id,
g.start_cyto,
g.end_cyto,
g.chromosome
FROM disease AS d,gene AS g
WHERE g.id=d.id
AND g.chromosome='$chromosome_no'";
}
return $self->_get_disease_objects($query_string);
}
=head2 disease names on chromosome
Title : diseases_names_on_chromosome
Usage : my @diseases=$diseasedb->disease_name_on_chromosome(90,2);
Function: gets all disease names per chromosome limited by offset and count
Example :
Returns : an array of disease names (strings)
Args :
=cut
sub disease_names_on_chromosome
{
my ($self,$chromosome_no,$offset,$count)=@_;
$chromosome_no || $self->throw("I need a chromosome");
if ($offset||$offset == 0){$offset='limit '.$offset;}
if($count){$count=','.$count;}
my $query_string="SELECT distinct g.id, d.disease
FROM disease AS d,gene AS g
WHERE d.id = g.id
AND g.chromosome='$chromosome_no' $offset $count;";
$self->_get_disease_names($query_string);
}
=head2 diseases on chromosome count
Title : disease on chromosome count
Usage : my $count=$diseasedb->diseases_on_chromosome_count(3);
Function: number of diseases
Example :
Returns : a number of diseases
Args :
=cut
sub diseases_on_chromosome_count
{
my ($self,$chromosome)=@_;
$chromosome || $self->throw("I need a chromosome");
my $query_string= "SELECT distinct g.id, d.disease
FROM disease AS d,gene AS g
WHERE d.id = g.id
AND g.chromosome='$chromosome'";
$self->_get_count($query_string);
}
=head2 diseases with genes
Title : diseases_with_genes
Usage : my @diseases=$diseasedb->diseases_with_genes;
Function: gets all diseases associated with genes
Example :
Returns : an array of Bio::EnsEMBL::ExternalData::Disease::Disease objects
Args :
=cut
sub diseases_with_genes
{
my ($self)=@_;
my $query_string= "select d.disease,g.id,g.gene_symbol,g.omim_id,g.start_cyto,g.end_cyto,
g.chromosome from disease as d,gene as g where d.id = g.id
and g.gene_symbol IS NOT NULL";
return $self->_get_disease_objects($query_string);
}
=head2 disease names with genes
Title : disease_names_with_genes
Usage : my @diseases=$diseasedb->disease_names_with_genes(90,3);
Function: gets all diseases associated with genes limited by offset and count
Example :
Returns : an array of disease names
Args :
=cut
sub disease_names_with_genes
{
my ($self,$offset,$count)=@_;
if ($offset||$offset == 0){$offset='limit '.$offset;}
if($count){$count=','.$count;}
my $query_string= "select d.disease from disease as d,gene as g where d.id = g.id
and g.gene_symbol IS NOT NULL $offset $count";
$self->_get_disease_names($query_string);
}
=head2 diseases with genes count
Title : disease with genes count
Usage : my $count=$diseasedb->diseases_with_genes_count(3);
Function: number of diseases with genes
Example :
Returns : a number of diseases with genes
Args :
=cut
sub diseases_with_genes_count
{
my ($self)=@_;
my $query_string= "select disease from disease as d,gene as g where d.id = g.id
and g.gene_symbol IS NOT NULL;";
$self->_get_count($query_string);
}
=head2 diseases without genes
Title : diseases_without_genes
Usage : my @diseases=$diseasedb->diseases_without_genes;
Function: gets all diseases which have no gene info in the database
Example :
Returns : an array of Bio::EnsEMBL::ExternalData::Disease::Disease objects
Args :
=cut
sub diseases_without_genes
{
my ($self)=@_;
my $query_string= "select d.disease,g.id,g.gene_symbol,g.omim_id,g.start_cyto,g.end_cyto,
g.chromosome from disease as d,gene as g where d.id = g.id
and g.gene_symbol IS NULL";
return $self->_get_disease_objects($query_string);
}
=head2 disease names without genes
Title : disease_names_without_genes
Usage : my @diseases=$diseasedb->disease_names_without_genes(90,3);
Function: gets all diseases associated with genes limited by offset and count
Example :
Returns : an array of disease names
Args :
=cut
sub disease_names_without_genes
{
my ($self,$offset,$count)=@_;
if ($offset||$offset == 0){$offset='limit '.$offset;}
if($count){$count=','.$count;}
my $query_string= "select d.disease from disease as d,gene as g where d.id = g.id
and g.gene_symbol IS NULL $offset,$count";
$self->_get_disease_names($query_string);
}
=head2 diseases without genes count
Title : disease without genes count
Usage : my $count=$diseasedb->diseases_without_genes_count(3);
Function: number of diseases without genes
Example :
Returns : a number of diseases without genes
Args :
=cut
sub diseases_without_genes_count
{
my ($self)=@_;
my $query_string= "select disease from disease as d,gene as g where d.id = g.id
and g.gene_symbol IS NULL;";
$self->_get_count($query_string);
}
=head2 diseases like
Title : diseases_like
Usage : my @diseases=$diseasedb->diseases_like("leukemia");
Function: gets diseases with a name containing given string
Example :
Returns : an array of Bio::EnsEMBL::ExternalData::Disease::Disease objects
Args :
=cut
sub diseases_like
{
my ($self,$disease)=@_;
$disease || $self->throw("I need disease name");
my $query_string="select d.disease,g.id,g.gene_symbol,g.omim_id,g.start_cyto,g.end_cyto,
g.chromosome from disease as d,gene as g where d.id = g.id and d.disease like '%$disease%'";
return $self->_get_disease_objects($query_string);
}
=head2 disease names like
Title : disease_names_like
Usage : my @diseases=$diseasedb->disease_names_like("leukemia",3,2);
Function: gets diseases names with a name containing given string
Example :
Returns : an array of disease names
Args :
=cut
sub disease_names_like
{
my ($self,$disease,$offset,$count)=@_;
$disease || $self->throw("I need disease name");
if ($offset||$offset == 0){$offset='limit '.$offset;}
if($count){$count=','.$count;}
my $query_string="select d.disease from disease as d,gene as g
where d.id = g.id and d.disease like '%$disease%' $offset $count";
return $self->_get_disease_names($query_string);
}
=head2 disease name like count
Title : disease name like count
Usage : my $count=$diseasedb->disease_names_like_count(3);
Function: number of diseases matching given string
Example :
Returns : a number of diseases matching given string
Args :
=cut
sub disease_names_like_count
{
my ($self,$disease)=@_;
$disease || $self->throw("I need disease name");
my $query_string= "select disease from disease as d,gene as g
where d.id = g.id and d.disease like '%$disease%'";
$self->_get_count($query_string);
}
sub _get_disease_objects
{
my ($self,$query_string)=@_;
my $sth=$self->_db_handle->prepare($query_string);
$sth->execute;
my $id;
my @diseases;
my $disease;
while ( my $rowhash = $sth->fetchrow_hashref)
{
if (!defined($id) or $id != $rowhash->{'id'})
{
$disease=new Bio::EnsEMBL::ExternalData::Disease::Disease;
$disease->name($rowhash->{'disease'});
push @diseases,$disease;
}
my $location=new Bio::EnsEMBL::ExternalData::Disease::DiseaseLocation(
-db_id=>$rowhash->{'omim_id'},
-cyto_start=>$rowhash->{'start_cyto'},
-cyto_end=>$rowhash->{'end_cyto'},
-external_gene=>$rowhash->{'gene_symbol'},
-chromosome=>$rowhash->{'chromosome'});
if (defined $rowhash->{'gene_symbol'}){$location->has_gene(1);}
$id=$rowhash->{'id'};
$disease->add_Location($location);
}
if (defined $self->_ensdb){@diseases=$self->_link2ensembl(@diseases);}
return @diseases;
}
sub _get_disease_names
{
my ($self,$query_string)=@_;
my $sth=$self->_db_handle->prepare($query_string);
$sth->execute;
my @diseases;
while ( my $rowhash = $sth->fetchrow_hashref)
{
push @diseases,$rowhash->{'disease'};
}
return @diseases;
}
sub _get_count
{
my ($self,$query_string)=@_;
my $sth=$self->_db_handle->prepare($query_string);
$sth->execute;
my @diseases;
while ( my $rowhash = $sth->fetchrow_hashref)
{
push @diseases,$rowhash->{'disease'};
}
scalar @diseases;
}
sub _link2ensembl {
my ($self,@diseases)=@_;
foreach my $dis (@diseases){
foreach my $location($dis->each_Location){
eval {
# my $ensembl_gene = $self->_ensdb->get_GeneAdaptor->fetch_by_maximum_DBLink($location->external_gene);
my $ensembl_gene = $self->_ensdb->get_GeneAdaptor->fetch_all_by_external_name($location->external_gene);
$location->ensembl_gene($ensembl_gene);
};
if ($@){print STDERR "problems with ensembl genes\n$@\n";}
}
}
return @diseases;
}
sub _db_handle
{
my ($self,$value) = @_;
if( defined $value) {$self->{'_db_handle'} = $value;}
return $self->{'_db_handle'};
}
sub _prepare
{
my ($self,$string) = @_;
if( ! $string ) {$self->throw("Attempting to prepare an empty SQL query!");}
my( $sth );
eval {$sth = $self->_db_handle->prepare($string);};
$self->throw("Error preparing $string\n$@") if $@;
return $sth;
}
sub _ensdb
{
my ($self,$value) = @_;
if( defined $value) {$self->{'_ensdb'} = $value;}
return $self->{'_ensdb'};
}
]]>