Raw content of Bio::EnsEMBL::Variation::ReadCoverageCollection
<![CDATA[# Ensembl module for Bio::EnsEMBL::Variation::ReadCoverage
#
# Copyright (c) 2008 Ensembl
#
=head1 NAME
Bio::EnsEMBL::Variation::ReadCoverageCollection - A collection of coverage reagion for a read.
=head1 SYNOPSIS
# Read coverage collection feature representing a genomic region covered by a read
$rcc = Bio::EnsEMBL::Variation::ReadCoverageCollection->new
(-start => 100,
-end => 200,
-strand => 1,
-slice => $slice,
-window_start => 1,
-window_end => 1000,
-window_size => 50,
-read_coverage_avg => 100,
-read_coverage_min => 0,
-read_coverage_max => 200,
-sample => $individual);
print $rcc->start(), "-", $rcc->end(), "\n";
=head1 DESCRIPTION
This is a class representing the read coverage collection information
from the ensembl-variation database. A ReadCoverageCollection behaves as any other Ensembl feature collection.
Object for storing read_coverage scores. The scores are averaged (also the minimum and maximum scores) over different window sizes to speed up drawing over large regions. The scores are packed as integer and stored in a string
See B<Bio::EnsEMBL::Feature>.
=head1 AUTHOR
This module was written by 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::ReadCoverageCollection;
use Bio::EnsEMBL::Feature;
use Bio::EnsEMBL::Utils::Exception qw(throw warning);
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
our @ISA = ('Bio::EnsEMBL::Feature');
=head2 new
Arg [-ADAPTOR] :
see superclass constructor
Arg [-START] :
start relative to the slice,see superclass constructor
Arg [-END] :
end relative to the slice,see superclass constructor
Arg [-STRAND] :
1 or -1, same as strand for the slice,see superclass constructor
Arg [-SLICE] :
see superclass constructor
Arg [-SEQ_REGION_START] :
start relative to chromosome,see superclass constructor
Arg [-SEQ_REGION_END] :
end relative to chromosome,see superclass constructor
Arg [-SEQ_REGION_STRAND] :
always 1, see superclass constructor
int Arg [-SCORE_MIN] :
average read_coverage for a window
Arg [-SCORE_AVG] :
minimum read_coverage for a window
Arg [-SCORE_MAX] :
maximum read_coverage for a window
Arg [-SAMPLE_ID] :
int - the individual in which the read_covarage is recorded
Example :
$rc = Bio::EnsEMBL::Variation::ReadCoverage->new
(-start => 100,
-end => 100,
-slice => $slice,
-window_size => 50,
-sample_id => 1);
Description: Constructor. Instantiates a new ReadCoverageCollection object.
Returntype : Bio::EnsEMBL::Variation::ReadCoverageCollection
Exceptions : none
Caller : general
Status : At Risk
=cut
sub new {
my $caller = shift;
my $class = ref($caller) || $caller;
my $self = $class->SUPER::new(@_);
my ($window_size,$window_start,$window_end,$sample_id,$read_coverage_avg,$read_coverage_min,$read_coverage_max,$y_axis_min,$y_axis_max) =
rearrange([qw(WINDOW_SIZE WINDOW_START WINDOW_END SAMPLE_ID READ_COVERAGE_AVG READ_COVERAGE_MIN READ_COVERAGE_MAX Y_AXIS_MIN Y_AXIS_MAX)], @_);
$self->{'window_size'} = $window_size;
$self->{'window_start'} = $window_start;
$self->{'window_end'} = $window_end;
$self->{'sample_id'} = $sample_id;
$self->{'read_coverage_avg'} = $read_coverage_avg;
$self->{'read_coverage_min'} = $read_coverage_min;
$self->{'read_coverage_max'} = $read_coverage_max;
$self->{'y_axis_min'} = $y_axis_min;
$self->{'y_axis_max'} = $y_axis_max;
return $self;
}
=head new_fast
Arg [1] : hash reference $hashref
Example : none
Description: This is an ultra fast constructor which requires knowledge of
the objects internals to be used.
Returntype :
Exceptions : none
Caller :
sub new_fast {
my ($class, $hashref) = @_;
return bless $hashref, $class;
}
=head2 window_size
Arg[1] : int $newval (optional)
The new value to set the window_size attribute to
Example : $window_size = $obj->window_size();
Description : Getter/Setter for the window_size attribute.
the window size this feature has been seen in the genome
ReturnType : int
Exceptions : none
Caller : general
Status : At Risk
=cut
sub window_size{
my $self = shift;
return $self->{'window_size'} = shift if (@_);
return $self->{'window_size'};
}
=head2 window_start
Arg[1] : int $newval (optional)
The new value to set the window_start attribute to
Example : $window_start = $obj->window_start();
Description : Getter/Setter for the window_start attribute.
the window start this feature has been seen in the genome
ReturnType : int
Exceptions : none
Caller : general
Status : At Risk
=cut
sub window_start{
my $self = shift;
return $self->{'window_start'} = shift if (@_);
return $self->{'window_start'};
}
=head2 window_end
Arg[1] : int $newval (optional)
The new value to set the window_end attribute to
Example : $depth = $obj->window_end();
Description : Getter/Setter for the window_end attribute.
the window end this feature has been seen in the genome
ReturnType : int
Exceptions : none
Caller : general
Status : At Risk
=cut
sub window_end{
my $self = shift;
return $self->{'window_end'} = shift if (@_);
return $self->{'window_end'};
}
=head2 read_coverage_avg
Arg[1] : int $newval (optional)
The new value to set the read_coverage_avg attribute to
Example : $avg = $obj->read_coverage_avg();
Description : Getter/Setter for the score_avg attribute.
the average read_coverage this feature has
ReturnType : int
Exceptions : none
Caller : general
Status : At Risk
=cut
sub read_coverage_avg{
my $self = shift;
return $self->{'read_coverage_avg'} = shift if (@_);
return $self->{'read_coverage_avg'};
}
=head2 read_coverage_min
Arg[1] : int $newval (optional)
The new value to set the read_coverage_min attribute to
Example : $min = $obj->read_coverage_min();
Description : Getter/Setter for the score_min attribute.
the minimum read_coverage this feature has
ReturnType : int
Exceptions : none
Caller : general
Status : At Risk
=cut
sub read_coverage_min{
my $self = shift;
return $self->{'read_coverage_min'} = shift if (@_);
return $self->{'read_coverage_min'};
}
=head2 read_coverage_max
Arg[1] : int $newval (optional)
The new value to set the read_coverage_max attribute to
Example : $max = $obj->read_coverage_max();
Description : Getter/Setter for the read_coverage_max attribute.
the maximum read_coverage this feature has
ReturnType : int
Exceptions : none
Caller : general
Status : At Risk
=cut
sub read_coverage_max{
my $self = shift;
return $self->{'read_coverage_max'} = shift if (@_);
return $self->{'read_coverage_max'};
}
=head2 sample_id
Arg[1] : int $newval (optional)
The new value to set the sample_id attribute to
Example : $sample_id = $obj->sample_id();
Description : Getter/Setter for the individual dbId attribute.
the individual dbId this feature has been seen in the genome
ReturnType : int
Exceptions : none
Caller : general
Status : At Risk
=cut
sub sample_id{
my $self = shift;
return $self->{'sample_id'} = shift if (@_);
return $self->{'sample_id'};
}
=head2 y_axis_min
Arg[1] : int $newval (optional)
The new value to set the y_axiss_min attribute to
Example : $y_axis_min = $obj->y_axis_min();
Description : Getter/Setter for the minimum of read_coverage for the collection of feature.
ReturnType : int
Exceptions : none
Caller : general
Status : At Risk
=cut
sub y_axis_min{
my $self = shift;
return $self->{'y_axis_min'} = shift if (@_);
return $self->{'y_axis_min'};
}
=head2 y_axis_max
Arg[1] : int $newval (optional)
The new value to set the y_axiss_max attribute to
Example : $y_axis_max = $obj->y_axis_max();
Description : Getter/Setter for the maximum of read_coverage for the collection of feature.
ReturnType : int
Exceptions : none
Caller : general
Status : At Risk
=cut
sub y_axis_max{
my $self = shift;
return $self->{'y_axis_max'} = shift if (@_);
return $self->{'y_axis_max'};
}
1;
]]>