File Coverage

lib/App/SimulateReads/Quality.pm

Criterion	Covered	Total	%
statement	30	44	68.1
branch	3	4	75.0
condition			n/a
subroutine	8	11	72.7
pod	0	2	0.0
total	41	61	67.2

package App::SimulateReads::Quality;
# ABSTRACT: Class to simulate quality entries

use App::SimulateReads::Base 'class';
use App::SimulateReads::Quality::Handle;

our $VERSION = '0.05'; # VERSION

#-------------------------------------------------------------------------------
#  Moose attributes
#-------------------------------------------------------------------------------
has 'quality_profile'    => (is => 'ro', isa => 'My:QualityP', required => 1, coerce => 1);
has 'read_size'          => (is => 'ro', isa => 'My:IntGt0',   required => 1);
has '_quality_by_system' => (
	is         => 'ro',
	isa        => 'My:QualityH',
	builder    => '_build_quality_by_system',
	lazy_build => 1
);
has '_gen_quality'      => (
	is         => 'ro',
	isa        => 'CodeRef',
	builder    => '_build_gen_quality',
	lazy_build => 1
);

sub BUILD {
	my $self = shift;
	## Just to ensure that the lazy attributes are built before &new returns
	$self->_quality_by_system if $self->quality_profile ne 'poisson';
}

#-------------------------------------------------------------------------------
#  Phred score table for poisson distribution simulation
#-------------------------------------------------------------------------------
my @PHRED_SCORE = (
	{
		score  => ['I', 'H', 'G', 'F', 'E', 'D', 'C', 'B', 'A', '@', '?'],
		size   => 11,
		ratio  => 1.5
	},
	{
		score  => ['>', '=', '<', ';', ':', '9', '8', '7', '6', '5'],
		size   => 10,
		ratio  => 2
	},
	{
		score  => ['4', '3', '2', '1', '0', '/', '.', '-', ',', '+'],
		size   => 10,
		ratio  => 2
	},
	{
		score  => ['*', ')', '(', '\'', '&', '%', '$', '#', '"', '!'],
		size   => 10,
		ratio  => 1
	}
);

#===  CLASS METHOD  ============================================================
#        CLASS: Quality
#       METHOD: _build_gen_quality (BUILDER)
#   PARAMETERS: Void
#      RETURNS: $fun CodeRef
#  DESCRIPTION: Dynamic linkage for quality profile generator
#       THROWS: no exceptions
#     COMMENTS: none
#     SEE ALSO: n/a
#===============================================================================
sub _build_gen_quality {
	my $self = shift;
	my $fun;

	given ($self->quality_profile) {
		when ('poisson') {
			$fun = sub { $self->_gen_quality_by_poisson_dist };
		}
		default {
			$fun = sub { $self->_gen_quality_by_system };
		}
	}

	return $fun;
} ## --- end sub _build_gen_quality

#===  CLASS METHOD  ============================================================
#        CLASS: Quality
#       METHOD: _build_quality_by_system (BUILDER)
#   PARAMETERS: Void
#      RETURNS: $quality_by_system My:QualityH
#  DESCRIPTION: Searches into the paths for quality_profile.perldata where is
#               found the quality distribution for a given system
#       THROWS: If quality_profile not found, or a given system is not stored
#               in the database, throws an exception
#     COMMENTS: none
#     SEE ALSO: n/a
#===============================================================================
sub _build_quality_by_system {
	my $self = shift;
	my $db = App::SimulateReads::Quality::Handle->new;
	my ($matrix, $deepth) = $db->retrievedb($self->quality_profile, $self->read_size);
	return { matrix => $matrix, deepth => $deepth };
} ## --- end sub _build_quality_by_system

sub gen_quality {
	my $self = shift;
	my $gen_quality = $self->_gen_quality;
	return $gen_quality->();
} ## --- end sub gen_quality

#===  CLASS METHOD  ============================================================
#        CLASS: Quality
#       METHOD: _gen_quality_by_system (PRIVATE)
#   PARAMETERS: Void
#      RETURNS: \$quality Ref Str
#  DESCRIPTION: Calcultes a quality string by raffle inside a quality matrix -
#               where each position is a vector encoding a distribution. So
#               if the string length is 100 bases, it needs to raffle 100 times.
#               The more present is a given quality, the more chance to be raffled
#               it will be
#       THROWS: no exceptions
#     COMMENTS: none
#     SEE ALSO: n/a
#===============================================================================
sub _gen_quality_by_system {
	my $self = shift;

	my $quality_matrix = $self->_quality_by_system->{matrix};
	my $quality_deepth = $self->_quality_by_system->{deepth};
	my $quality;

	for (my $i = 0; $i < $self->read_size; $i++) {
		$quality .= $quality_matrix->[$i][int(rand($quality_deepth))];
	}

	return \$quality;
} ## --- end sub _gen_quality_by_system

#===  CLASS METHOD  ============================================================
#        CLASS: Quality
#       METHOD: _gen_quality_by_poisson_dist
#   PARAMETERS: Void
#      RETURNS: \$quality Ref Str
#  DESCRIPTION: Calculates quality based in a cumulative poisson distribution
#       THROWS: no exceptions
#     COMMENTS: It uses the @PHRED_SCORE table to simulate a proportion score
#               similar to the poisson distribution
#     SEE ALSO: _poisson_dist
#===============================================================================
sub _gen_quality_by_poisson_dist {
	my $self = shift;
	my $quality;
	return $self->_poisson_dist(\$quality, $self->read_size, scalar @PHRED_SCORE);
} ## --- end sub _gen_quality_by_poisson_dist

#===  CLASS METHOD  ============================================================
#        CLASS: Quality
#       METHOD: _poisson_dist
#   PARAMETERS: $quality_ref Str Ref, $size Int > 0, $countdown Int >= 0
#      RETURNS: $quality_ref Str Ref
#  DESCRIPTION: Recursive routine that generates a quality string based in a
#               uniform random raffle into @PHRED_SCORE partitions. It works as
#               a poisson CDF
#       THROWS: no exceptions
#     COMMENTS: none
#     SEE ALSO: _gen_quality_by_poisson_dist
#===============================================================================
sub _poisson_dist {
	my ($self, $quality_ref, $size, $countdown) = @_;
	return $quality_ref if not $countdown;

	my $ratio = $PHRED_SCORE[4 - $countdown]{ratio};
	my $part = int($size / $ratio) + ($size % $ratio);
	my $score = $PHRED_SCORE[4 - $countdown]{score};
	my $score_size = $PHRED_SCORE[4 - $countdown]{size};

	for (my $i = 0; $i < $part; $i++) {
		$$quality_ref .= $score->[int(rand($score_size))];
	}

	return $self->_poisson_dist($quality_ref, $size - $part, $countdown - 1);
} ## --- end sub _poisson_dist

__END__

=pod

=encoding UTF-8

=head1 NAME

App::SimulateReads::Quality - Class to simulate quality entries

=head1 VERSION

version 0.05

=head1 AUTHOR

Thiago L. A. Miller <[e-mail]>

=head1 COPYRIGHT AND LICENSE

This software is Copyright (c) 2017 by Teaching and Research Institute from Sírio-Libanês Hospital.

This is free software, licensed under:

  The GNU General Public License, Version 3, June 2007

=cut