Raw content of Bio::EnsEMBL::Variation::DBSQL::AlleleGroupAdaptor
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# Ensembl module for Bio::EnsEMBL::Variation::DBSQL::AlleleGroupAdaptor
#
# Copyright (c) 2004 Ensembl
#
# You may distribute this module under the same terms as perl itself
#
#
=head1 NAME
Bio::EnsEMBL::Variation::DBSQL::AlleleGroupAdaptor
=head1 SYNOPSIS
$db = Bio::EnsEMBL::Variation::DBSQL::DBAdaptor->new(...);
$aga = $db->get_AlleleGroupAdaptor();
# retrieve an allele group by its name
$ag = $aga->fetch_by_name('ABDR-10');
# retrieve a variation group by its internal identifier
$ag = $aga->fetch_by_dbID(123);
# retrieve all allele groups which are part of the same variation group
@ags = @{$aga->fetch_all_by_VariationGroup($vg)};
=head1 DESCRIPTION
This adaptor provides database connectivity for AlleleGroup objects.
AlleleGroups may be retrieved from the Ensembl variation database by
several means using this module.
=head1 AUTHOR - Graham McVicker
=head1 CONTACT
Post questions to the Ensembl development list ensembl-dev@ebi.ac.uk
=head1 METHODS
=cut
use strict;
use warnings;
package Bio::EnsEMBL::Variation::DBSQL::AlleleGroupAdaptor;
use Bio::EnsEMBL::DBSQL::BaseAdaptor;
use Bio::EnsEMBL::Utils::Exception qw(throw warning);
use Bio::EnsEMBL::Variation::AlleleGroup;
our @ISA = ('Bio::EnsEMBL::DBSQL::BaseAdaptor');
=head2 fetch_by_dbID
Arg [1] : int $dbID
Example : $vg = $vg_adaptor->fetch_by_dbID(5526);
Description: Retrieves a VariationGroup object via its internal identifier.
If no such variation group exists undef is returned.
Returntype : Bio::EnsEMBL::Variation::VariationGroup
Exceptions : throw if dbID arg is not defined
Caller : general
Status : At Risk
=cut
sub fetch_by_dbID {
my $self = shift;
my $dbID = shift;
throw('dbID argument expected') if(!defined($dbID));
# left join allows allele groups without any alleles to be fetched
my $sth = $self->prepare
(q{SELECT ag.allele_group_id, ag.variation_group_id, ag.sample_id,
ag.name, s.name, ag.frequency, aga.allele, aga.variation_id
FROM (allele_group ag, source s)
LEFT JOIN allele_group_allele aga
ON aga.allele_group_id = ag.allele_group_id
WHERE ag.source_id = s.source_id
AND ag.allele_group_id = ?});
$sth->bind_param(1,$dbID,SQL_INTEGER);
$sth->execute();
my $result = $self->_objs_from_sth($sth);
$sth->finish();
return undef if(!@$result);
return $result->[0];
}
=head2 fetch_by_name
Arg [1] : string $name
Example : $vg = $vga->fetch_by_name('PERLEGEN:B000009');
Description: Retrieves a variation group by its name
Returntype : Bio::EnsEMBL::Variation::VariationGroup
Exceptions : throw if name argument is not provided
Caller : general
Status : At Risk
=cut
sub fetch_by_name {
my $self = shift;
my $name = shift;
throw('name argument expected') if(!defined($name));
# left join allows allele groups without any alleles to be fetched
my $sth = $self->prepare
(q{SELECT ag.allele_group_id, ag.variation_group_id, ag.sample_id,
ag.name, s.name, ag.frequency, aga.allele, aga.variation_id
FROM (allele_group ag, source s)
LEFT JOIN allele_group_allele aga
ON aga.allele_group_id = ag.allele_group_id
WHERE ag.source_id = s.source_id
AND ag.name = ?});
$sth->bind_param(1,$name,SQL_VARCHAR);
$sth->execute();
my $result = $self->_objs_from_sth($sth);
$sth->finish();
return undef if(!@$result);
return $result->[0];
}
=head2 fetch_all_by_VariationGroup
Arg [1] : Bio::EnsEMBL::Variation::VariationGroup $vg
Example : @a_grps = @{$a_grp_adp->fetch_all_by_VariationGroup($var_grp)};
Description: Retrieves all allele groups which are part of a VariationGroup
Returntype : Bio::EnsEMBL::Variation::VariationGroup
Exceptions : throw if VariationGroup argument is not provided
Caller : general
Status : At Risk
=cut
sub fetch_all_by_VariationGroup {
my $self = shift;
my $vg = shift;
if(!ref($vg) || !$vg->isa('Bio::EnsEMBL::Variation::VariationGroup')) {
throw('Variation group argument expected');
}
# left join allows allele groups without any alleles to be fetched
my $sth = $self->prepare
(q{SELECT ag.allele_group_id, ag.variation_group_id, ag.sample_id,
ag.name, s.name, ag.frequency, aga.allele, aga.variation_id
FROM (allele_group ag, source s)
LEFT JOIN allele_group_allele aga
ON aga.allele_group_id = ag.allele_group_id
WHERE ag.source_id = s.source_id
AND ag.variation_group_id = ?
ORDER BY ag.allele_group_id});
$sth->bind_param(1,$vg->dbID,SQL_INTEGER);
$sth->execute();
my $result = $self->_objs_from_sth($sth);
$sth->finish();
return $result;
}
sub _objs_from_sth {
my $self = shift;
my $sth = shift;
my ($ag_id, $vg_id, $sample_id, $name, $source, $freq, $allele, $var_id);
$sth->bind_columns(\$ag_id, \$vg_id, \$sample_id, \$name, \$source,
\$freq, \$allele, \$var_id);
my %pop_cache;
my %var_cache;
my %vg_cache;
my $pop_adaptor = $self->db->get_PopulationAdaptor();
my $vg_adaptor = $self->db->get_VariationGroupAdaptor();
my @results;
my ($cur_ag, $cur_ag_id);
# construct all variation groups without their associated variations
while($sth->fetch()) {
if(!defined($cur_ag) || $cur_ag_id != $ag_id) {
# obtain the population for this allele group
my $pop;
if(defined($sample_id)) {
$pop = $pop_cache{$sample_id} ||= $pop_adaptor->fetch_by_dbID($sample_id);
}
# obtain the variation group for this allele group
my $vg;
if(defined($vg_id)) {
$vg = $vg_cache{$vg_id};
if(!$vg) {
$vg = $vg_adaptor->fetch_by_dbID($vg_id);
# cache variations already obtained by variation group to
# save going to DB again
foreach my $v (@{$vg->get_all_Variations()}) {
$var_cache{$v->dbID()} = $v;
}
}
}
# construct this allele group
$cur_ag = Bio::EnsEMBL::Variation::AlleleGroup->new
(-dbID => $ag_id,
-adaptor => $self,
-population => $pop,
-name => $name,
-source => $source,
-variation_group => $vg,
-frequency => $freq);
$cur_ag_id = $ag_id;
push @results, $cur_ag;
}
# add associated alleles and variations to this allele group
if($var_id) {
# all variations should be already obtained by variation group
my $var = $var_cache{$var_id};
if($var) {
$cur_ag->add_Variation($var, $allele);
} else {
warning("AlleleGroup's VariationGroup does not contain variation " .
"$var_id referenced by AlleleGroup.");
}
}
}
return \@results;
}
1;
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