diff variant_effect_predictor/Bio/EnsEMBL/Variation/ReadCoverageCollection.pm @ 0:21066c0abaf5 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/EnsEMBL/Variation/ReadCoverageCollection.pm	Fri Aug 03 10:04:48 2012 -0400
@@ -0,0 +1,338 @@
+=head1 LICENSE
+
+ Copyright (c) 1999-2012 The European Bioinformatics Institute and
+ Genome Research Limited.  All rights reserved.
+
+ This software is distributed under a modified Apache license.
+ For license details, please see
+
+   http://www.ensembl.org/info/about/code_licence.html
+
+=head1 CONTACT
+
+ Please email comments or questions to the public Ensembl
+ developers list at <[e-mail]>.
+
+ Questions may also be sent to the Ensembl help desk at
+ <[e-mail]>.
+
+=cut
+
+# 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 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;