Bio::EnsEMBL::ExternalData::Glovar
BaseComposition
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Summary
Bio::EnsEMBL::ExternalData::Glovar::BaseComposition -
This object represents the base composition as provided by Glovar
Package variables
No package variables defined.
Included modules
Inherit
Synopsis
my $base_comp = new Bio::EnsEMBL::ExternalData::Glovar::BaseComposition;
$base_comp->postition('1000');
$base_comp->genomic_base('A');
Description
This module holds data describing the base composition for each base in the
genome that has been covered by the Glovar project.
Methods
Methods description
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 |
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 |
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 |
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 |
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 |
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 |
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 |
Arg[1] : (optional) Int - genomic start position
Example : $base_comp->start('1000');
Description : getter/setter for genomic start position of BaseComposition
object
Return type : Int - genomic start position
Exceptions : none
Caller : general |
Methods code
sub alleles
{ my($self,$arg) = @_;
$self->{'alleles'} = $arg if(defined $arg);
return $self->{'alleles'};} | sub end
{ my ($self,$arg) = @_;
$self->position($arg) if(defined $arg);
return $self->position();} | sub ethnicity
{ my ($self, $arg) = @_;
$self->{'ethnicity'} = $arg if (defined $arg);
return $self->{'ethnicity'};
}
1;} | sub genomic_base
{ my ($self, $arg) = @_;
$self->{'genomic_base'} = $arg if (defined $arg);
return $self->{'genomic_base'};} | 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;} | sub new_fast
{ my $class = shift;
my $hashref = shift;
return bless $hashref, $class;} | sub position
{ my ($self,$arg) = @_;
if(defined $arg){
$self->{'position'} = $arg;
}
return $self->{'position'};} | sub start
{ my ($self,$arg) = @_;
$self->position($arg) if(defined $arg);
return $self->position();} | General documentation
This code is distributed under an Apache style licence:
Please see
/code_licence.html for details