Raw content of Bio::EnsEMBL::Variation::VariationAnnotation
<![CDATA[# Ensembl module for Bio::EnsEMBL::Variation::VariationAnnotation
#
# Copyright (c) 2004 Ensembl
#
=head1 NAME
Bio::EnsEMBL::Variation::VariationAnnotation - A genotype phenotype annotation for a nucleotide variation.
=head1 SYNOPSIS
# Variation Annotation is associated with a variation object
$va = Bio::EnsEMBL::Variation::VariationAnnotation->new
(_variation_id => 8,
-phenotype_name => 'BD',
-phenotype_description => 'Bipolar Disorder',
-source_name => 'EGA',
-study_type => 'GWAS',
-local_stable_id => 'EGAS00000000001',
-study => 'pubmed/17293876',
-associated_gene => 'HHEX',
-associated_variant_risk_allele => 'rs13266634-C',
-variation_names => 'rs13266634',
-risk_allele_freq_in_controls => '0.3',
-p_value => '6.00E-08',
-variation => $v);
...
print $va->phenotype_name(),'-',$va->phenotype_description,"\n";
print "From source ",$va->source_name,'-',$va->local_stable_id,"\n";
print " With study_type ", $va->study_type(),"\n";
...
# Get the Variation object which this annotation represents
# If not already retrieved from the DB, this will be
# transparently lazy-loaded
my $v = $va->variation();
=head1 DESCRIPTION
This is a class representing the genotype-phenotype annotation of a variation
from the ensembl-variation database. The actual variation information is
represented by an associated Bio::EnsEMBL::Variation::Variation object.
=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::VariationAnnotation;
use Bio::EnsEMBL::Utils::Exception qw(throw warning);
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
use Bio::EnsEMBL::Variation::Variation;
use Bio::EnsEMBL::Storable;
use vars qw(@ISA);
@ISA = qw(Bio::EnsEMBL::Storable);
=head2 new
Arg [-dbID] :
int - unique internal identifier for variation_annotation
Arg [-ADAPTOR] :
Bio::EnsEMBL::Variation::DBSQL::VariationAnnotationAdaptor
Arg [-PHENOTYPE_NAME] :
string - name of the phenotype
Arg [-PHENOTYPE_DESCRIPTION] :
string - description of the phenotype
Arg [-SOURCE_NAME] :
string - name of the source
Arg [-VARIATION_NAMES] :
string - name of the associated variations
Arg [-VARIATION] :
int - the variation object associated with this annotation.
Arg [_VARIATION_ID] :
int _ the internal id of the variation object associated with this
identifier. This may be provided instead of a variation object so that
the variation may be lazy-loaded from the database on demand.
Arg [-STUDY] :
string - the pubmed/ids or project/study names
Arg [-ASSOCIATED_GENE] :
string - the gene names associated with this annotation/variant.
Arg [-ASSOCIATED_VARIANT_RISK_ALLELE] :
string - the variants-risk alleles associated with this annotation.
Arg [-RISK_ALLELE_FREQ_IN_CONTROLS] :
string - the risk allele frequency in controls associated with this annotation.
Arg [-VARIATION] :
string - the p_value associated with this annotation.
Example :
$va = Bio::EnsEMBL::Variation::VariationAnnotation->new
(-phenotype_name => 'BD',
-phenotype_description => 'Bipolar Disorder',
-souce_name => 'EGA',
-variation_names => 'rs123',
-local_stable_id => 'EGAS00000000001',
_variation_id => 10,
-study => 'pubmed/17293876',
-associated_gene => 'HHEX',
-associated_variant_risk_allele => 'rs13266634-C',
-risk_allele_freq_in_controls => '0.3',
-p_value => '6.00E-08',
-variation => $v);
Description: Constructor. Instantiates a new VariationAnnotation object.
Returntype : Bio::EnsEMBL::Variation::VariationAnnotation
Exceptions : none
Caller : general
Status : At Risk
=cut
sub new {
my $caller = shift;
my $class = ref($caller) || $caller;
my $self = $class->SUPER::new(@_);
my ($dbID,$adaptor,$phenotype_name,$phenotype_description,$source_name,$study_type,$local_stable_id,$variation_id,$variation_names,$variation,$study,$associated_gene,$associated_variant_risk_allele,$risk_allele_freq_in_controls,$p_value) =
rearrange([qw(dbID ADAPTOR PHENOTYPE_NAME PHENOTYPE_DESCRIPTION SOURCE_NAME
STUDY_TYPE LOCAL_STABLE_ID _VARIATION_ID VARIATION_NAMES VARIATION
STUDY ASSOCIATED_GENE ASSOCIATED_VARIANT_RISK_ALLELE
RISK_ALLELE_FREQ_IN_CONTROLS P_VALUE)],@_);
$self->{'dbID'} = $dbID;
$self->{'adaptor'} = $adaptor;
$self->{'phenotype_name'} = $phenotype_name;
$self->{'phenotype_description'} = $phenotype_description;
$self->{'local_stable_id'} = $local_stable_id;
$self->{'variation'} = $variation;
$self->{'_variation_id'} = $variation_id;
$self->{'source_name'} = $source_name;
$self->{'variation_names'} = $variation_names;
$self->{'study_type'} = $study_type;
$self->{'study'} = $study;
$self->{'associated_gene'} = $associated_gene;
$self->{'associated_variant_risk_allele'} = $associated_variant_risk_allele;
$self->{'risk_allele_freq_in_controls'} = $risk_allele_freq_in_controls;
$self->{'p_value'} = $p_value;
return $self;
}
sub new_fast {
my $class = shift;
my $hashref = shift;
return bless $hashref, $class;
}
=head2 phenotype_name
Arg [1] : string phenotype_name (optional)
The new value to set the phenotype_name attribute to
Example : $phenotype_name = $obj->phenotype_name()
Description: Getter/Setter for the phenotype_name attribute.
Returntype : string
Exceptions : none
Caller : general
Status : Stable
=cut
sub phenotype_name{
my $self = shift;
return $self->{'phenotype_name'} = shift if(@_);
return $self->{'phenotype_name'};
}
=head2 phenotype_description
Arg [1] : string phenotype_description (optional)
The new value to set the phenotype_description attribute to
Example : $phenotype_description = $obj->phenotype_description()
Description: Getter/Setter for the phenotype_description attribute.
Returntype : string
Exceptions : none
Caller : general
Status : At Risk
=cut
sub phenotype_description{
my $self = shift;
return $self->{'phenotype_description'} = shift if(@_);
return $self->{'phenotype_description'};
}
=head2 source_name
Arg [1] : string source_name (optional)
The new value to set the source_name attribute to
Example : $source_name = $obj->source_name()
Description: Getter/Setter for the source_name attribute.
Returntype : string
Exceptions : none
Caller : general
Status : At Risk
=cut
sub source_name{
my $self = shift;
return $self->{'source_name'} = shift if(@_);
return $self->{'source_name'};
}
=head2 study_type
Arg [1] : string study_type (optional)
The new value to set the study_type attribute to
Example : $study_type = $obj->study_type()
Description: Getter/Setter for the study_type attribute.
Returntype : string
Exceptions : none
Caller : general
Status : At Risk
=cut
sub study_type{
my $self = shift;
return $self->{'study_type'} = shift if(@_);
return $self->{'study_type'};
}
=head2 local_stable_id
Arg [1] : string local_stable_id (optional)
The new value to set the local_stable_id attribute to
Example : $local_stable_id = $obj->local_stable_id()
Description: Getter/Setter for the local_stable_id attribute.
Returntype : string
Exceptions : none
Caller : general
Status : At Risk
=cut
sub local_stable_id{
my $self = shift;
return $self->{'local_stable_id'} = shift if(@_);
return $self->{'local_stable_id'};
}
=head2 variation
Arg [1] : (optional) Bio::EnsEMBL::Variation::Variation $variation
Example : $v = $va->variation();
Description: Getter/Setter for the variation associated with this annotation.
If not set, and this VariationAnnotation has an associated adaptor
an attempt will be made to lazy-load the variation from the
database.
Returntype : Bio::EnsEMBL::Variation::Variation
Exceptions : throw on incorrect argument
Caller : general
Status : Stable
=cut
sub variation {
my $self = shift;
if(@_) {
if(!ref($_[0]) || !$_[0]->isa('Bio::EnsEMBL::Variation::Variation')) {
throw("Bio::EnsEMBL::Variation::Variation argument expected");
}
$self->{'variation'} = shift;
}
elsif(!defined($self->{'variation'}) && $self->{'adaptor'} &&
defined($self->{'_variation_id'})) {
# lazy-load from database on demand
my $va = $self->{'adaptor'}->db()->get_VariationAdaptor();
$self->{'variation'} = $va->fetch_by_dbID($self->{'_variation_id'});
}
return $self->{'variation'};
}
=head2 variation_names
Arg [1] : string $newval (optional)
The new value to set the variation_names attribute to
Example : $variation_names = $obj->variation_names()
Description: Getter/Setter for the variation_names attribute. This is the
names of the variation associated with this study.
Returntype : string
Exceptions : none
Caller : general
Status : At Risk
=cut
sub variation_names{
my $self = shift;
return $self->{'variation_names'} = shift if(@_);
return $self->{'variation_names'};
}
=head2 study
Arg [1] : string $newval (optional)
The new value to set the study attribute to
Example : $variation_names = $obj->study()
Description: Getter/Setter for the study attribute. This is the
pubmed/id or project name associated with this study.
Returntype : string
Exceptions : none
Caller : general
Status : At Risk
=cut
sub study{
my $self = shift;
return $self->{'study'} = shift if(@_);
return $self->{'study'};
}
=head2 associated_gene
Arg [1] : string $newval (optional)
The new value to set the associated_gene attribute to
Example : $associated_gene = $obj->associated_gene()
Description: Getter/Setter for the associated_gene attribute. This is the
gene names associated with this study.
Returntype : string
Exceptions : none
Caller : general
Status : At Risk
=cut
sub associated_gene{
my $self = shift;
return $self->{'associated_gene'} = shift if(@_);
return $self->{'associated_gene'};
}
=head2 associated_variant_risk_allele
Arg [1] : string $newval (optional)
The new value to set the associated_variant_risk_allele attribute to
Example : $associated_variant_risk_allele = $obj->associated_variant_risk_allele()
Description: Getter/Setter for the associated_variant_risk_allele attribute. This is the
associated_variant_risk_allele associated with this study.
Returntype : string
Exceptions : none
Caller : general
Status : At Risk
=cut
sub associated_variant_risk_allele{
my $self = shift;
return $self->{'associated_variant_risk_allele'} = shift if(@_);
return $self->{'associated_variant_risk_allele'};
}
=head2 risk_allele_freq_in_controls
Arg [1] : string $newval (optional)
The new value to set the risk_allele_freq_in_controls attribute to
Example : $risk_allele_freq_in_controls = $obj->risk_allele_freq_in_controls()
Description: Getter/Setter for the risk_allele_freq_in_controls attribute. This is the
risk_allele_freq_in_controls associated with this study.
Returntype : string
Exceptions : none
Caller : general
Status : At Risk
=cut
sub risk_allele_freq_in_controls{
my $self = shift;
return $self->{'risk_allele_freq_in_controls'} = shift if(@_);
return $self->{'risk_allele_freq_in_controls'};
}
=head2 p_value
Arg [1] : string $newval (optional)
The new value to set the p_value attribute to
Example : $p_value = $obj->p_value()
Description: Getter/Setter for the p_value attribute. This is the
p_value associated with this study.
Returntype : string
Exceptions : none
Caller : general
Status : At Risk
=cut
sub p_value{
my $self = shift;
return $self->{'p_value'} = shift if(@_);
return $self->{'p_value'};
}
1;
]]>