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t/Microarray-File-Data-BlueFuse.t  view on Meta::CPAN

#! /usr/bin/perl -w

use strict;

use FindBin;
use Test::More tests=>7;
use Test::Group;
use Test::Differences;
use Test::Deep;

BEGIN {
	use_ok('Microarray::File::Data::BlueFuse');
}

my ($oFile,$oSpot);

my $file = $FindBin::Bin.'/../test_files/bluefuse_output.xls';
begin_skipping_tests "The test-file 'bluefuse_output.xls' could not be found" unless (-e $file);  

test "Object creation" => sub {
	ok($oFile = bluefuse_file->new($file),'object creation');
	isa_ok($oFile,'bluefuse_file','bluefuse_file object');
};

test "Header information" => sub {
	is($oFile->analysis_software,'BlueFuse for Microarrays v3.5(6446)','analysis_software');
	is($oFile->build,'6446','build');
	is($oFile->date,'9/26/2007','date');
	is($oFile->experiment,'new scanner Male vs Female');
	is($oFile->channel1_image_file,'C:\Documents and Settings\Tanya Lebi\Desktop\UCL\2007-09-26_12006_532.tif','channel1_image_file');
	is($oFile->channel2_image_file,'C:\Documents and Settings\Tanya Lebi\Desktop\UCL\2007-09-26_12006_635.tif','channel2_image_file');
	is($oFile->frame_ch1,'1','frame_ch1');
	is($oFile->frame_ch2,'1','frame_ch2');
	is($oFile->gal_file,'C:\Documents and Settings\Tanya Lebi\Desktop\12.gal','gal_file');
	is($oFile->clone_file,'C:\Documents and Settings\Tanya Lebi\Desktop\ParaffinArrays.cfg','clone_file');
	is($oFile->clone_text,'Generated for demo purposes GRS 29/01/07','clone_text');
	is($oFile->replicate_field,'Name','replicate_field');
	test "Confidence flag range" => sub {
		my $hFlags = $oFile->confidence_flag_range;
		eq_or_diff $hFlags,{A=>['0.90','1.00'],B=>['0.70','0.90'],C=>['0.30','0.70'],D=>['0.10','0.30'],E=>['0.00','0.10']},'confidence_flag_range hashref';
		my @aFlags = $oFile->confidence_flag_range;
		eq_or_diff \@aFlags,[('0.00','0.10','0.30','0.70','0.90','1.00')],'confidence_flag_range list';
		my @aRangeA = $oFile->confidence_flag_range('A');
		eq_or_diff \@aRangeA,[('0.90','1.00')],'confidence_flag_range list A';
		my @aRangeB = $oFile->confidence_flag_range('B');
		eq_or_diff \@aRangeB,[('0.70','0.90')],'confidence_flag_range list B';
		my @aRangeC = $oFile->confidence_flag_range('C');
		eq_or_diff \@aRangeC,[('0.30','0.70')],'confidence_flag_range list C';
		my @aRangeD = $oFile->confidence_flag_range('D');
		eq_or_diff \@aRangeD,[('0.10','0.30')],'confidence_flag_range list D';
		my @aRangeE = $oFile->confidence_flag_range('E');
		eq_or_diff \@aRangeE,[('0.00','0.10')],'confidence_flag_range list E';
		my $aRangeA = $oFile->confidence_flag_range('A');
		eq_or_diff $aRangeA,['0.90','1.00'],'confidence_flag_range arrayref A';
		my $aRangeB = $oFile->confidence_flag_range('B');
		eq_or_diff $aRangeB,['0.70','0.90'],'confidence_flag_range arrayref B';
		my $aRangeC = $oFile->confidence_flag_range('C');
		eq_or_diff $aRangeC,['0.30','0.70'],'confidence_flag_range arrayref C';
		my $aRangeD = $oFile->confidence_flag_range('D');
		eq_or_diff $aRangeD,['0.10','0.30'],'confidence_flag_range arrayref D';
		my $aRangeE = $oFile->confidence_flag_range('E');
		eq_or_diff $aRangeE,['0.00','0.10'],'confidence_flag_range arrayref E';
	};
};
test "Array QC" => sub {
	test "Confidence flag percen" => sub {
		my $hFlags = $oFile->confidence_flag_percen;
		eq_or_diff $hFlags,{A=>59.28,B=>18.28,C=>8.44,D=>1.25,E=>12.74},'confidence_flag_percen hashref';