App-SimulateReads

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t/lib/TestsFor/App/SimulateReads/Fastq.pm  view on Meta::CPAN

use base 'TestsFor';
use autodie;

use constant {
	SEQ_SYS       => 'poisson',
	QUALITY_SIZE  => 10,
};

sub startup : Tests(startup) {
	my $test = shift;
	$test->SUPER::startup;
	my $class = ref $test;
	$class->mk_classdata('default_fastq');
	$class->mk_classdata('default_attr');
	$class->mk_classdata('seq');
	$class->mk_classdata('seq_len');
}

sub setup : Tests(setup) {
	my $test = shift;
	my %child_arg = @_;
	$test->SUPER::setup;

	my %default_attr = (
		quality_profile => SEQ_SYS,
		read_size       => QUALITY_SIZE,
		%child_arg
	);

	$test->default_attr(\%default_attr);
	$test->default_fastq($test->class_to_test->new(%default_attr));

t/lib/TestsFor/App/SimulateReads/Fastq/PairedEnd.pm  view on Meta::CPAN

package TestsFor::App::SimulateReads::Fastq::PairedEnd;
# ABSTRACT: Tests for 'App::SimulateReads::Fastq::PairedEnd' class

use App::SimulateReads::Base 'test';
use base 'TestsFor::App::SimulateReads::Fastq';
use autodie;

sub startup : Tests(startup) {
	my $test = shift;
	$test->SUPER::startup;
}

sub setup : Tests(setup) {
	my $test = shift;

	my %default_attr = (
		sequencing_error => 0.1,
		fragment_mean    => 50,
		fragment_stdd    => 10,
		template_id      => 'sr0001 simulation_read length=%r position=%c:%t-%n'
	);

	$test->SUPER::setup(%default_attr);
}

sub cleanup : Tests(shutdown) {
	my $test = shift;
	$test->SUPER::shutdown;
}

sub constructor : Tests(12) {
	my $test = shift;

	my $class = $test->class_to_test;
	my $fastq = $test->default_fastq;
	my %default_attr = %{ $test->default_attr };

	while (my ($attr, $value) = each %default_attr) {

t/lib/TestsFor/App/SimulateReads/Fastq/SingleEnd.pm  view on Meta::CPAN

package TestsFor::App::SimulateReads::Fastq::SingleEnd;
# ABSTRACT: Tests for 'App::SimulateReads::Fastq::SingleEnd' class

use App::SimulateReads::Base 'test';
use base 'TestsFor::App::SimulateReads::Fastq';
use autodie;

sub startup : Tests(startup) {
	my $test = shift;
	$test->SUPER::startup;
}

sub setup : Tests(setup) {
	my $test = shift;

	my %default_attr = (
		sequencing_error => 0.1,
		template_id      => 'sr0001 simulation_read length=%r position=%c:%t-%n'
	);

	$test->SUPER::setup(%default_attr);
}

sub cleanup : Tests(shutdown) {
	my $test = shift;
	$test->SUPER::shutdown;
}

sub constructor : Tests(8) {
	my $test = shift;

	my $class = $test->class_to_test;
	my $fastq = $test->default_fastq;
	my %default_attr = %{ $test->default_attr };

	while (my ($attr, $value) = each %default_attr) {

t/lib/TestsFor/App/SimulateReads/Quality.pm  view on Meta::CPAN

use autodie;
use base 'TestsFor';

use constant {
	SEQ_SYS       => "poisson", 
	QUALITY_SIZE  => 10
};

sub startup : Tests(startup) {
	my $test = shift;
	$test->SUPER::startup;
	my $class = ref $test;
	$class->mk_classdata('default_quality');
	$class->mk_classdata('default_attr');
}

sub setup : Tests(setup) {
	my $test = shift;
	my %child_arg = @_;
	$test->SUPER::setup;

	my %default_attr = (
		quality_profile => SEQ_SYS,
		read_size       => QUALITY_SIZE,
		%child_arg
	);

	$test->default_attr(\%default_attr);
	$test->default_quality($test->class_to_test->new(%default_attr));
}

t/lib/TestsFor/App/SimulateReads/Read.pm  view on Meta::CPAN

#===============================================================================

package TestsFor::App::SimulateReads::Read;
# ABSTRACT: Tests for 'App::SimulateReads::Read' class

use App::SimulateReads::Base 'test';
use base 'TestsFor';

sub startup : Tests(startup) {
	my $test = shift;
	$test->SUPER::startup;
	my $class = ref $test;
	$class->mk_classdata('default_read');
	$class->mk_classdata('default_attr');
	$class->mk_classdata('seq');
	$class->mk_classdata('seq_len');
}

sub setup : Tests(setup) {
	my $test = shift;
	my %child_arg = @_;
	$test->SUPER::setup;

	my %default_attr = (
		sequencing_error => 0.1,
		read_size        => 10,
		%child_arg
	);

	my $seq = 'TGACCCGCTAACCTCAGTTCTGCAGCAGTAACAACTGCCGTATCTGGACTTTCCTAATACCTCGCATAGTCCGTCCCCTCGCGCGGCAAGAGGTGCGGCG';

	$test->default_attr(\%default_attr);

t/lib/TestsFor/App/SimulateReads/Read/PairedEnd.pm  view on Meta::CPAN

package TestsFor::App::SimulateReads::Read::PairedEnd;
# ABSTRACT: Tests for 'App::SimulateReads::Read::PairedEnd' class

use App::SimulateReads::Base 'test';
use base 'TestsFor::App::SimulateReads::Read';

sub startup : Tests(startup) {
	my $test = shift;
	$test->SUPER::startup;
}

sub setup : Tests(setup) {
	my $test = shift;

	my %default_attr = (
		fragment_mean    => 50,
		fragment_stdd    => 10
	);

	$test->SUPER::setup(%default_attr);
}

sub constructor : Tests(9) {
	my $test = shift;

	my $class = $test->class_to_test;
	my $read = $test->default_read;
	my %default_attr = %{ $test->default_attr };

	while (my ($attr, $value) = each %default_attr) {

t/lib/TestsFor/App/SimulateReads/Read/SingleEnd.pm  view on Meta::CPAN

package TestsFor::App::SimulateReads::Read::SingleEnd;
# ABSTRACT: Tests for 'App::SimulateReads::Read::SingleEnd' class

use App::SimulateReads::Base 'test';
use base 'TestsFor::App::SimulateReads::Read';

sub startup : Tests(startup) {
	my $test = shift;
	$test->SUPER::startup;
}

sub setup : Tests(setup) {
	my $test = shift;
	$test->SUPER::setup;
}

sub gen_read : Tests(51) {
	my $test = shift;

	my $read = $test->default_read;
	my $seq = $test->seq;
	my $seq_len = $test->seq_len;

	throws_ok { ${ $read->gen_read(\$seq, $read->read_size - 1, 1) } }

t/lib/TestsFor/App/SimulateReads/Simulator.pm  view on Meta::CPAN

	GENOME_SIZE       => 2280,
	COVERAGE          => 5,
	PREFIX            => 'ponga',
	OUTPUT_SINGLE_END => 'ponga_R1_001.fastq',
	OUTPUT_PAIRED_END => ['ponga_R1_001.fastq', 'ponga_R2_001.fastq'],
	OUTPUT_COUNTS     => 'ponga_counts.tsv'
};

sub startup : Tests(startup) {
	my $test = shift;
	$test->SUPER::startup;
	my $class = ref $test;
	$class->mk_classdata('default_attr');
	$class->mk_classdata('default_sg_single_end');
	$class->mk_classdata('default_sg_paired_end');

	my $fasta = q{>Chr1
TTACTGCTTTTAACATTACAGTAACTGTTACAGGTTCCAGCAGGCTAACTGGGTGGAAAT
GAGTTTGGTTTCACTTAGTCTCTCTAAAGAGAAAGCAAGTCGGTAGACTAATACCTAATA
AAAGCAAAGCTGCCAACAATTGAAATTGCCTAGGCTGCTCTGTGTGTCCCACATGCATGG
GTGTGGGTGCCAGTGTGTGTGCGTGTGTGCATGCATGTGCATGTGTGTTGGGATAGAGTG

t/lib/TestsFor/App/SimulateReads/Simulator.pm  view on Meta::CPAN

CAGGAGAAATGTATTAATGTGCCTTTCTAGTAACAGGTTTTTAGAAAGTCAAATATAAAC};

	open my $fh, ">" => GENOME;
	print $fh "$fasta\n";
	close $fh;
}

sub setup : Tests(setup) {
	my $test = shift;
	$LOG_VERBOSE = VERBOSE;
	$test->SUPER::setup;

	my %default_attr = (
		prefix         => PREFIX,
		output_gzip    => OUTPUT_GZIP,
		fasta_file     => GENOME,
		coverage       => COVERAGE,
		jobs           => JOBS,
		seqid_weight   => 'length',
		count_loops_by => 'coverage',
		strand_bias    => 'random',

t/lib/TestsFor/App/SimulateReads/Simulator.pm  view on Meta::CPAN

	);

	$test->default_attr(\%default_attr);
	$test->default_sg_single_end($test->class_to_test->new(%sg_single_end));
	$test->default_sg_paired_end($test->class_to_test->new(%sg_paired_end));
}

sub cleanup : Tests(shutdown) {
	my $test = shift;
	unlink GENOME;
	$test->SUPER::shutdown;
}

sub constructor : Tests(18) {
	my $test = shift;

	my $class = $test->class_to_test;
	my $sg = $test->default_sg_single_end;
	my %default_attr = %{ $test->default_attr };

	while (my ($attr, $value) = each %default_attr) {