view release on metacpan or  search on metacpan

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

ACCAGGAGAATACAGTAAACTCTATGAGGCAAGCTATAAACATGTAGCATTGTGATTAGG
GCTGGTTCTCCTTCTAGAGACATGGTAGGATTGCAATTTCATACCATCCTTGAAGTTAGA
GAGAGCCACGTGACTCATTTAGCCAATGAACTGTGAGCAGAATGACATGTCACTTCCAGC
TGAAGCTTTAACAATCTGAGAGACATTCATACATTTTCCATGTGCTGTAGCCTTATACCC
AAAGCCTGGGTCCCAAGTGACCATGACAGGCAGAGCTCCCTGTTGAGCCACAGAGATTTA
GAGAATGGCTGTTAACACAGCATAATCCAGCCCATCCTGACTAATCTGATATTAACATGT
ATAATAAAGAATTCTATCAATGCTGAGGGAAGATGACTAGTTAAGGTCCTAGGTTGCAAG
TCTCAAAACCTCTTCTAAGGATTGTAGACAGGAAATTAAATGACTTCTAGTCCCTAGAGT
TCCCAATCTCCTACCATCCCATCCTAATATGACAGAAGTAATTCCTGAGTTGCTTCTGAA
TCCCAATCTCCTACCATCCCATCCTAATATGACAGAAGTAATTCCTGAGTTGCTTCTGAA
TCCCAATCTCCTACCATCCCATCCTAATATGACAGAAGTAATTCCTGAGTTGCTTCTGAA
ACCAGAGCTTCCCTCAGAACCCTTAGCCTGCCAGATGGCTTCTTGGAGAGCCCTCACTCA
CTTTTCTCCTTCTGCTATTGCTGCTCATTCATTCCAGTTTTTAAAAATTCATCTTTATCC
>Chr5
AGGAACCTCGCTTCTAGAAAAGTCATACAGGTGCTTCCAGGAGGCTACATGGGCACCCAT
ATTTTTCTAGCCACTTTCATTAGACCAATGCAGCAGAGAAGAAAAGCCTCAATAATTATT
ATGACATGGCATGTTAGGATACCAAGTAAATTGCATTTGTAAAATGTGATTTTCTGTTGG
TGTTCACTTCAGCTCTACTGACATTTGGTAAGTATTATTGACTGACTGACTAACTAATGT
GGTCATTAGTCTTCATAAAGAAAGGCTCTCTACAAAAACGGAGGGATGCCCTTTTTCTGG
CATTTAATACGTAAGAAATTGCCTCCAATAGAAACCAGAGTTGCCTGATTACTATCAGCA
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',
		seed           => SEED
	);
	
	my %sg_single_end = (
		%default_attr,
		fastq => App::SimulateReads::Fastq::SingleEnd->new(
			quality_profile   => 'poisson',
			read_size         => QUALITY_SIZE,
			sequencing_error  => 0.1,
			template_id       => 'sr0001 simulation_read length=%r position=%c:%t-%n'
		)
	);

	my %sg_paired_end = (
		%default_attr,
		fastq => App::SimulateReads::Fastq::PairedEnd->new(
			quality_profile   => 'poisson',
			read_size         => QUALITY_SIZE,
			sequencing_error  => 0.1,
			fragment_mean     => 50,
			fragment_stdd     => 10,
			template_id       => 'sr0001 simulation_read length=%r position=%c:%t-%n'
		)
	);

	$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) {
		can_ok $sg, $attr;
		is $sg->$attr, $value, "The value for $attr shold be correct";
	}
}

sub run_simulation : Tests(9) {
	my $test = shift;
	my $output_single_end = OUTPUT_SINGLE_END;
	my $output_paired_end = OUTPUT_PAIRED_END;
	my $output_counts = OUTPUT_COUNTS;

	my $fastq_count = sub {
		my $file = shift;
		my $entries = 0;
		my %chr_acm;
		open my $fh, "<" => $file;
		my $mark = 4;
		my $acm = 0;
		while (<$fh>) {
			chomp;
			if (++$acm == 1) {
				$entries++;
				my @tmp1 = split / /;
				my @tmp2 = split /:/ => $tmp1[-1];
				my @tmp3 = split /=/ => $tmp2[0];
				$chr_acm{$tmp3[1]}++;
			} elsif ($acm == $mark) {
				$acm = 0;
			}
		}
		close $fh;
		return (\%chr_acm, $entries);
	};

	# Testing single-end
	my $sg = $test->default_sg_single_end;
	$sg->run_simulation;