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t/Bio/Tradis/RunTradisBWA.t  view on Meta::CPAN

    $obj = Bio::Tradis::RunTradis->new(
        fastqfile        => $fastqfile,
        reference        => $ref,
        tag              => $tag,
        smalt            => $aligner,
        outfile          => $outfile,
        output_directory => $output_directory,
        _temp_directory  => $temp_directory,
        _stats_handle    => $stats_handle
    ),
    'creating object with gzipped data - Normal files one mismatch'
);

ok( $obj->run_tradis, 'testing complete analysis with gzipped data' );
ok(
    -e "$output_directory/test.plot.AE004091.insert_site_plot.gz",
    'checking plot file existence (gzipped data) - Normal files one mismatch'
);
ok( -e "$output_directory/test.plot.mapped.bam", 'checking mapped bam existence - Normal files one mismatch');
ok( -e "$output_directory/test.plot.mapped.bam.bai", 'checking indexed bam file - Normal files one mismatch');

system("gunzip -c $output_directory/test.plot.AE004091.insert_site_plot.gz > $output_directory/test.plot.unzipped");
system("gunzip -c t/data/RunTradisBWA/expected.plot.gz > $output_directory/expected.plot.unzipped");
compare_ok(
    "$output_directory/test.plot.unzipped",
    "$output_directory/expected.plot.unzipped",
    'checking completed pipeline with gzipped data file contents - Normal files one mismatch'
);

$temp_directory_obj = File::Temp->newdir( CLEANUP => 0,
                                          DIR => $output_directory );
$temp_directory = $temp_directory_obj->dirname();
ok(
    $obj = Bio::Tradis::RunTradis->new(
        fastqfile        => $fastqfile,
        reference        => $ref,
        tag              => $tag,
        smalt            => $aligner,
        outfile          => $outfile,
        output_directory => $output_directory,
        _temp_directory  => $temp_directory,
        _stats_handle    => $stats_handle,
        k                => 10,
      
    ),
    'creating object with custom smalt parameters'
);
# Filtering step
$obj->_filter;
$obj->_remove;
ok( $obj->_map, 'mapping with custom parameters fine' );


# Check die if ref is not found
$temp_directory_obj = File::Temp->newdir( CLEANUP => 0,
                                          DIR => $output_directory );
$temp_directory = $temp_directory_obj->dirname();
ok(
    $obj = Bio::Tradis::RunTradis->new(
        fastqfile        => $fastqfile,
        reference        => "not_really_a_ref.fa",
        tag              => $tag,
        outfile          => $outfile,
        output_directory => $output_directory,
        _temp_directory  => $temp_directory,
        _stats_handle    => $stats_handle,

    ),
    'creating object'
);
throws_ok {$obj->run_tradis} 'Bio::Tradis::Exception::RefNotFound', 'correct error thrown'; 

unlink('t/data/RunTradisBWA/smallref.fa.amb');
unlink('t/data/RunTradisBWA/smallref.fa.ann');
unlink('t/data/RunTradisBWA/smallref.fa.bwt');
unlink('t/data/RunTradisBWA/smallref.fa.pac');
unlink('t/data/RunTradisBWA/smallref.fa.sa');
rmtree($output_directory);
done_testing();