Raw content of Bio::EnsEMBL::Variation::DBSQL::VariationAnnotationAdaptor
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# Ensembl module for Bio::EnsEMBL::Variation::DBSQL::VariationAnnotationAdaptor
#
# Copyright (c) 2004 Ensembl
#
# You may distribute this module under the same terms as perl itself
#
#
=head1 NAME
Bio::EnsEMBL::Variation::DBSQL::VariationAnnotationAdaptor
=head1 SYNOPSIS
$vdb = Bio::EnsEMBL::Variation::DBSQL::DBAdaptor->new(...);
$db = Bio::EnsEMBL::DBSQL::DBAdaptor->new(...);
$va = $vdb->get_VariationAdaptor();
$vaa = $vdb->get_VariationAnnotationAdaptor();
# Get a VariationAnotation by its internal identifier
$va = $vaa->fetch_by_dbID(45);
# fetch all annotation for a particular variation
$v = $va->fetch_by_name('rs56');
foreach $va (@{$vaa->fetch_all_by_Variation($v)}) {
print $va->phenotype_name(), $va->phenotype_description(), $va->source_name(), $va->study_type(), $va->local_stable_id(),"\n";
}
=head1 DESCRIPTION
This adaptor provides database connectivity between Variation and VariationAnnotation objects.
=head1 AUTHOR - Yuan Chen
=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::VariationAnnotationAdaptor;
use Bio::EnsEMBL::Variation::Variation;
use Bio::EnsEMBL::Variation::VariationAnnotation;
use Bio::EnsEMBL::Utils::Exception qw(throw warning);
use Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor;
our @ISA = ('Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor');
=head2 fetch_all_by_Variation
Arg [1] : Bio::EnsEMBL:Variation::Variation $var
Example : my @vas = @{$vaa->fetch_all_by_Variation($var)};
Description: Retrieves all variation annotations for a given variation.
Returntype : reference to list Bio::EnsEMBL::Variation::VariationAnnotation
Exceptions : throw on bad argument
Caller : general
Status : At Risk
=cut
sub fetch_all_by_Variation {
my $self = shift;
my $var = shift;
if(!ref($var) || !$var->isa('Bio::EnsEMBL::Variation::Variation')) {
throw('Bio::EnsEMBL::Variation::Variation arg expected');
}
if(!defined($var->dbID())) {
throw("Variation arg must have defined dbID");
}
return $self->generic_fetch("va.variation_id = ".$var->dbID());
}
=head2 fetch_all_by_phenotype_source_name
Arg [1] : string $phenotype_name
Arg [2] : string $source_name (optional)
Example : $vaa = $va_adaptor->fetch_by_phenotype_source_name('BD','EGA');
Description: Retrieves a variation annotation object via its phenotype/source name
Returntype : list of ref of Bio::EnsEMBL::Variation::VariationAnnotation
Exceptions : throw if phenotype name argument is not defined
Caller : general
Status : At Risk
=cut
sub fetch_all_by_pheonotype_name_source_name {
my $self = shift;
my $phenotype_name = shift;
my $source_name = shift;
throw('phenotype_name argument expected') if(!defined($phenotype_name));
my $extra_sql = " AND p.phenotype_name = ? ";
if (defined $source_name ) {
$extra_sql .= qq( AND s.name = ?);
}
return $self->generic_fetch("$extra_sql");
}
=head2 fetch_all_by_phenotype_description_source_name
Arg [1] : string $phenotype_description
Arg [2] : string $source_name (optional)
Example : $vaa = $va_adaptor->fetch_by_phenotype_description_source_name('diabetes','EGA');
Description: Retrieves a variation annotation object via its phenotype description/source name
Returntype : list of ref of Bio::EnsEMBL::Variation::VariationAnnotation
Exceptions : throw if phenotype name argument is not defined
Caller : general
Status : At Risk
=cut
sub fetch_all_by_pheonotype_description_source_name {
my $self = shift;
my $phenotype_description = shift;
my $source_name = shift;
throw('phenotype_description argument expected') if(!defined($phenotype_description));
my $extra_sql = qq( AND p.phenotype_description like '%?%' );
if (defined $source_name ) {
$extra_sql .= qq( AND s.name = ?);
}
return $self->generic_fetch("$extra_sql");
}
# method used by superclass to construct SQL
sub _tables { return (['variation_annotation', 'va'],
[ 'phenotype', 'p'],
[ 'source', 's']);
}
sub _default_where_clause {
my $self = shift;
return 'va.phenotype_id = p.phenotype_id AND va.source_id = s.source_id';
}
sub _columns {
return qw( va.variation_annotation_id va.variation_id p.name p.description
s.name va.study va.study_type va.local_stable_id
va.associated_gene va.associated_variant_risk_allele
va.variation_names va.risk_allele_freq_in_controls va.p_value
);
}
sub _objs_from_sth {
my ($self, $sth) = @_;
my @features;
my ($variation_annotation_id,$var_id,$phenotype_name,$phenotype_description,$source_name,$study,$study_type,$local_stable_id,$associated_gene,$associated_variant_risk_allele,$variation_names,$risk_allele_freq_in_controls,$p_value);
$sth->bind_columns(\$variation_annotation_id,\$var_id,\$phenotype_name,\$phenotype_description,\$source_name,\$study,\$study_type,\$local_stable_id,\$associated_gene,\$associated_variant_risk_allele,\$variation_names,\$risk_allele_freq_in_controls, \$p_value);
while($sth->fetch()) {
push @features, $self->_create_feature_fast('Bio::EnsEMBL::Variation::VariationAnnotation',
{'dbID' => $variation_annotation_id,
'_variation_id' => $var_id,
'phenotype_name' => $phenotype_name,
'phenotype_description' => $phenotype_description,
'source_name' => $source_name,
'study' => $study,
'study_type' => $study_type,
'local_stable_id' => $local_stable_id,
'associated_gene' => $associated_gene,
'associated_variant_risk_allele' => $associated_variant_risk_allele,
'variation_names' => $variation_names,
'risk_allele_freq_in_controls' => $risk_allele_freq_in_controls,
'p_value' => $p_value,
'adaptor' => $self,
});
}
return \@features;
}
1;
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