Raw content of Bio::EnsEMBL::ExternalData::Glovar::BaseComposition
<![CDATA[=head1 NAME
Bio::EnsEMBL::ExternalData::Glovar::BaseComposition -
This object represents the base composition as provided by Glovar
=head1 SYNOPSIS
my $base_comp = new Bio::EnsEMBL::ExternalData::Glovar::BaseComposition;
$base_comp->postition('1000');
$base_comp->genomic_base('A');
=head1 DESCRIPTION
This module holds data describing the base composition for each base in the
genome that has been covered by the Glovar project.
=head1 LICENCE
This code is distributed under an Apache style licence:
Please see /code_licence.html for details
=head1 AUTHOR
Jody Clements <jc3@sanger.ac.uk>
Patrick Meidl <pm2@sanger.ac.uk>
=head1 CONTACT
Post questions to the EnsEMBL development list ensembl-dev@ebi.ac.uk
=cut
package Bio::EnsEMBL::ExternalData::Glovar::BaseComposition;
use strict;
use vars qw(@ISA);
use Bio::EnsEMBL::SimpleFeature;
@ISA = qw(Bio::EnsEMBL::SimpleFeature);
=head2 new
Arg[1] : none
Example : see SYNOPSIS
Description : constructor method for a
Bio::EnsEMBL::ExternalData::Glovar::BaseComposition object
Return type : Bio::EnsEMBL::ExternalData::Glovar::BaseComposition
Exceptions : none
Caller : general
=cut
sub new {
my $invocant = shift;
my $class = ref($invocant) || $invocant;
my $self = {
'position' => 0,
'genomic_base' => 'undef',
'alleles' => {},
'ethnicity' => {},
'_gsf_strand' => 1,
@_,
};
bless $self, $class;
return $self;
}
=head2 new_fast
Arg[1] : hashref - initial object attributes
Example :
my $base_comp = new Bio::EnsEMBL::ExternalData::Glovar::BaseComposition({
'position' => 1,
'genomic_base' => 'A',
'alleles' => {
T => 20,
G => 10,
A => 0,
C => 2
},
'ethnicity' => {
Asian => 9,
Caucasian => 15,
},
'_gsf_strand' => 1,
});
Description : fast constructor method for a
Bio::EnsEMBL::ExternalData::Glovar::BaseComposition object.
Blesses the hashref supplied into your object
Return type : Bio::EnsEMBL::ExternalData::Glovar::BaseComposition
Exceptions : none
Caller : general
=cut
sub new_fast {
my $class = shift;
my $hashref = shift;
return bless $hashref, $class;
}
=head2 position
Arg[1] : (optional) Int - genomic position
Example : $base_comp->position('1000');
Description : getter/setter for genomic position of BaseComposition object
Return type : Int - genomic position
Exceptions : none
Caller : general
=cut
sub position {
my ($self,$arg) = @_;
if(defined $arg){
$self->{'position'} = $arg;
}
return $self->{'position'};
}
=head2 start
Arg[1] : (optional) Int - genomic start position
Example : $base_comp->start('1000');
Description : getter/setter for genomic start position of BaseComposition
object
Return type : Int - genomic start position
Exceptions : none
Caller : general
=cut
sub start {
my ($self,$arg) = @_;
$self->position($arg) if(defined $arg);
return $self->position();
}
=head2 end
Arg[1] : (optional) Int - genomic end position
Example : $base_comp->position('1000');
Description : getter/setter for genomic end position of BaseComposition
object. Identical to start position (since lenght of feature is
always 1)
Return type : Int - genomic end position
Exceptions : none
Caller : general
=cut
sub end {
my ($self,$arg) = @_;
$self->position($arg) if(defined $arg);
return $self->position();
}
=head2 genomic_base
Arg[1] : (optional) String - genomic base
Example : $base_comp->genomic_base('A');
Description : getter/setter for genomic base of the variation (allele in
reference sequence)
Return type : String - genomic base
Exceptions : none
Caller : general
=cut
sub genomic_base {
my ($self, $arg) = @_;
$self->{'genomic_base'} = $arg if (defined $arg);
return $self->{'genomic_base'};
}
=head2 alleles
Arg[1] : (optional) hashref - alleles and their frequencies
Example : $base_comp->alleles({'A'=>3,'C'=>1,'G'=>0,'T'=>10});
Description : getter/setter for allele distribution
Return type : hashref - alleles and their freqencies
Exceptions : none
Caller : general
=cut
sub alleles {
my($self,$arg) = @_;
$self->{'alleles'} = $arg if(defined $arg);
return $self->{'alleles'};
}
=head2 ethnicity
Arg[1] : (optional) hashref - ethnicities and their read frequencies
Example : $base_comp->ethnicity({'Asian'=>2,'Caucasian'=>5});
Description : getter/setter for ethnicity of the reads the variation was
observed
Return type : hashref - ethnicities and their frequencies
Exceptions : none
Caller : general
=cut
sub ethnicity {
my ($self, $arg) = @_;
$self->{'ethnicity'} = $arg if (defined $arg);
return $self->{'ethnicity'};
}
1;
]]>