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

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

use App::Sandy::Base 'test';
use App::Sandy::PieceTable;
use App::Sandy::RNG;
#use Data::Dumper;
use base 'TestsFor';

use constant {
	SEED => 17
};

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');
	$class->mk_classdata('table');
	$class->mk_classdata('table_seq');
	$class->mk_classdata('slice_len');
	$class->mk_classdata('rng');
}

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

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

	my $seq = 'TGACCCGCTAACCTCAGTTCTGCAGCAGTAACAACTGCCGTATCTGGACTTTCCTAATACCTCGCATAGTCCGTCCCCTCGCGCGGCAAGAGGTGCGGCG';
	my $table_seq = "A large span of text";

	$test->default_attr(\%default_attr);
	$test->default_read($test->class_to_test->new(%default_attr));
	$test->seq($seq);
	$test->seq_len(length $seq);
	$test->slice_len(10);
	$test->table(App::Sandy::PieceTable->new(orig => \$table_seq));
	$test->rng(App::Sandy::RNG->new(SEED));
}

sub constructor : Tests(4) {
	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) {
		can_ok $read, $attr;
		is $read->$attr, $value,"The value for $attr shold be correct";
	}
}

sub subseq_seq : Test(5) {
	my $test = shift;

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

	my ($read_seq1_ref, $pos1) = $read->subseq(\$seq, $seq_len, $slice_len, 0);

	is length($$read_seq1_ref), 10,
		"Setting a slice_len ($slice_len) should return a seq ($slice_len) in subseq";

	ok index($seq, $$read_seq1_ref) >= 0,
		"Read sequence must be inside seq in subseq";

	my ($read_seq2_ref, $pos2) = $read->subseq_rand(\$seq, $seq_len, $slice_len, $rng);

	is length($$read_seq2_ref), 10,
		"Setting a slice_len ($slice_len) should return a seq ($slice_len) in subseq_rand";

	ok index($seq, $$read_seq2_ref) >= 0,
		"Read sequence must be inside seq in subseq";

	my ($read_seq3_ref, $pos3) = $read->subseq_rand(\$seq, $seq_len, $slice_len, $rng);
	is index($seq, $$read_seq3_ref), $pos3,
		"Position returned in subseq_rand ($pos3) should be equal to postion in index";
}