Raw content of Bio::EnsEMBL::Map::DBSQL::QtlAdaptor
<![CDATA[=head1 LICENSE
Copyright (c) 1999-2009 The European Bioinformatics Institute and
Genome Research Limited. All rights reserved.
This software is distributed under a modified Apache license.
For license details, please see
/info/about/code_licence.html
=head1 CONTACT
Please email comments or questions to the public Ensembl
developers list at <ensembl-dev@ebi.ac.uk>.
Questions may also be sent to the Ensembl help desk at
<helpdesk@ensembl.org>.
=cut
=head1 NAME
Bio::EnsEMBL::Map::DBSQL::QtlAdaptor
=head1 SYNOPSIS
=head1 DESCRIPTION
This module is responsible of retrieving QTLs from the database.
=head1 METHODS
=cut
package Bio::EnsEMBL::Map::DBSQL::QtlAdaptor;
use strict;
use Bio::EnsEMBL::Map::Qtl;
use Bio::EnsEMBL::DBSQL::BaseAdaptor;
use vars qw(@ISA);
@ISA = qw(Bio::EnsEMBL::DBSQL::BaseAdaptor);
=head2 fetch_by_dbID
Arg 1 : int $dbID
Example : none
Description: get by database internal identifier
Returntype : Bio::EnsEMBL::Map::Qtl
Exceptions : none
Caller : general
Status : stable
=cut
sub fetch_by_dbID {
my $self = shift;
my $dbID = shift;
return unless $dbID;
my $res = $self->_generic_fetch( [ "q.qtl_id = $dbID" ] );
return $res->[0];
}
=head2 fetch_all
Example : none
Description: get all the qtl's
Returntype : listref Bio::EnsEMBL::Map::Qtl
Exceptions : none
Caller : general
Status : stable
=cut
sub fetch_all {
my $self = shift;
$self->_generic_fetch( [] );
}
=head2 fetch_all_by_trait
Arg [1] : string $trait
The phenotype we are looking for
Example : none
Description: get by phenotype/trait string
Returntype : listref Bio::EnsEMBL::Map::Qtl
Exceptions : none
Caller : general
Status : stable
=cut
sub fetch_all_by_trait {
my $self = shift;
my $trait = shift;
return [] unless $trait;
return $self->_generic_fetch( [ "q.trait = '$trait'" ] );
}
=head2 fetch_all_by_source_database
Arg 1 : string $database_name
Name of the database that provides the Qtl information
Arg [2] : string $database_primary_id
The primary id of the qtl in that database
Example : none
Description: retrieve Qtl by given information
Returntype : listref Bio::EnsEMBL::Map::Qtl
Exceptions : none
Caller : general
Status : stable
=cut
sub fetch_all_by_source_database {
my $self = shift;
my $database_name = shift;
my $database_primary_id = shift;
return [] unless $database_name;
my @conditions;
if( $database_name ) {
push( @conditions, "q.source_database=\"$database_name\"" );
}
if( $database_primary_id ) {
push( @conditions, "q.source_primary_id=\"$database_primary_id\"" );
}
return $self->_generic_fetch( \@conditions );
}
sub _generic_fetch {
my $self = shift;
my $conditions = shift;
my $where = '';
if( @$conditions ) {
$where = "WHERE ".join( " and ", @$conditions );
}
my $query = "SELECT ".
join( ", ", $self->_columns() ).
" FROM qtl q LEFT JOIN qtl_synonym qs ON q.qtl_id = qs.qtl_id ".
$where;
my $sth = $self->prepare( $query );
$sth->execute();
return $self->_obj_from_sth( $sth );
}
sub _columns {
return ( 'q.qtl_id','qs.source_database','qs.source_primary_id',
'q.trait','q.lod_score','q.flank_marker_id_1',
'q.flank_marker_id_2','q.peak_marker_id' );
}
sub _obj_from_sth {
my $self = shift;
my $sth = shift;
my ( $qtl_id, $source_database,
$source_primary_id, $trait, $lod_score, $flank_marker_id_1,
$flank_marker_id_2, $peak_marker_id );
#warning: ordering depends on _columns function implementation
$sth->bind_columns( \$qtl_id,
\$source_database, \$source_primary_id, \$trait,
\$lod_score, \$flank_marker_id_1,
\$flank_marker_id_2, \$peak_marker_id );
my @out = ();
my %already_seen;
while( $sth->fetch()) {
#multiple columns with same qtl are multiple synonyms
if(my $qtl = $already_seen{$qtl_id}) {
$qtl->add_synonym($source_database, $source_primary_id);
next;
}
my $mad = $self->db()->get_MarkerAdaptor();
my $flank_marker_1 = $flank_marker_id_1 ? $mad->fetch_by_dbID( $flank_marker_id_1 ) : undef ;
my $flank_marker_2 = $flank_marker_id_2 ? $mad->fetch_by_dbID( $flank_marker_id_2 ) : undef;
my $peak_marker = $peak_marker_id ? $mad->fetch_by_dbID( $peak_marker_id ) : undef;
my $qtl = Bio::EnsEMBL::Map::Qtl->new
(
$qtl_id,
$self->db->get_QtlAdaptor(),
$flank_marker_1,
$peak_marker,
$flank_marker_2,
$trait,
$lod_score,
{$source_database => $source_primary_id}
);
push @out, $qtl;
$already_seen{$qtl_id} = $qtl;
}
return \@out;
}
=head2 list_traits
Args : none
Example : none
Description: list of all the different traits
Returntype : listref string
Exceptions : none
Caller : general
Status : stable
=cut
sub list_traits {
my $self = shift;
my $sth = $self->prepare( "
SELECT DISTINCT trait
FROM qtl q
" );
my $res = [];
$sth->execute();
push ( @$res ,
map { $_->[0] } @{$sth->fetchall_arrayref()}
);
return $res;
}
1;
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