Raw content of Bio::EnsEMBL::Variation::DBSQL::AlleleGroupAdaptor # # 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;