use
lib dirname(__FILE__);
my
$dir
= dirname(__FILE__);
my
$config_file_path
=
"$dir/test_config.pl"
;
my
$output_directory
=
"$dir/output/"
;
$tp53_mutation_found
= 0;
my
@trans_files
;
$trans_files
[0] =
"$dir/spt/testing_trans_1.spt"
;
$trans_files
[1] =
"$dir/spt/testing_trans_2.spt"
;
my
@cnv_files
;
$cnv_files
[0] =
"$dir/spc/testing_cnv_1.spc"
;
$cnv_files
[1] =
"$dir/spc/testing_cnv_2.spc"
;
mkdir
(
"$output_directory"
,0770)
unless
(-d
"$output_directory"
);
my
$OS
=
''
;
if
($^O eq
'MSWin32'
){
$OS
=
'.mswin32'
;
}
ok(Shatterproof::load_config_file(
$config_file_path
),
'load_config_file'
);
(
$genome_cnv_data_hash_ref
,
$chromosome_copy_number_count_hash_ref
,
$chromosome_cnv_breakpoints_hash_ref
) = Shatterproof::analyze_cnv_data(
$output_directory
, \
@cnv_files
,
$bin_size
, \
$tp53_mutation_found
);
(
$genome_trans_data_hash_ref
,
$chromosome_translocation_count_hash_ref
,
$genome_trans_breakpoints_hash_ref
) = Shatterproof::analyze_trans_data(
$output_directory
, \
@trans_files
,
$bin_size
, \
$tp53_mutation_found
);
(
$suspect_regions_array_ref
,
$likely_regions_array_ref
,
$genome_cnv_data_windows_hash_ref
,
$genome_trans_data_windows_hash_ref
,
$genome_mutation_data_windows_hash_ref
) = Shatterproof::calculate_chromosome_localization(
$output_directory
,
$genome_cnv_data_hash_ref
,
$genome_trans_data_hash_ref
,
$bin_size
,
$localization_window_size
);
open
(FILE,
"<"
,
"$dir/json/suspect_regions_array_ref.json"
);
my
$test1_json
= JSON::XS::decode_json(<FILE>);
close
(FILE);
cmp_bag(
$suspect_regions_array_ref
,
$test1_json
,
"calculate_chromosome_localization-1"
);
open
(FILE,
"<"
,
"$dir/json/likely_regions_array_ref.json"
);
$test1_json
= JSON::XS::decode_json(<FILE>);
close
(FILE);
cmp_bag(
$likely_regions_array_ref
,
$test1_json
,
"calculate_chromosome_localization-2"
);
open
(FILE,
"<"
,
"$dir/json/genome_cnv_data_windows_hash_ref.json"
);
$test1_json
= JSON::XS::decode_json(<FILE>);
close
(FILE);
cmp_deeply(
$genome_cnv_data_windows_hash_ref
,
$test1_json
,
"calculate_chromosome_localization-3"
);
open
(FILE,
"<"
,
"$dir/json/genome_trans_data_windows_hash_ref.json"
);
$test1_json
= JSON::XS::decode_json(<FILE>);
close
(FILE);
cmp_deeply(
$genome_trans_data_windows_hash_ref
,
$test1_json
,
"calculate_chromosome_localization-4"
);
open
(FILE,
"<"
,
"$dir/json/genome_mutation_data_windows_hash_ref.json"
);
$test1_json
= JSON::XS::decode_json(<FILE>);
close
(FILE);
cmp_deeply(
$genome_mutation_data_windows_hash_ref
,
$test1_json
,
"calculate_chromosome_localization-5"
);
my
$test_file
;
my
$ref_file
;
$test_file
= SPtesting::test_open (
$test_file
,
"$dir/output/mutation_clustering/cnv/chr10_cnv_localization.log"
);
open
(
$ref_file
,
"$dir/ref/chr10_cnv_localization.log.ref"
.
$OS
);
ok(compare(
$test_file
,
$ref_file
)==0,
"calculate_chromosome_localization-6"
);
close
(
$test_file
);
close
(
$ref_file
);
$test_file
= SPtesting::test_open (
$test_file
,
"$dir/output/mutation_clustering/cnv/chr11_cnv_localization.log"
);
open
(
$ref_file
,
"$dir/ref/chr11_cnv_localization.log.ref"
.
$OS
);
ok(compare(
$test_file
,
$ref_file
)==0,
"calculate_chromosome_localization-7"
);
close
(
$test_file
);
close
(
$ref_file
);
$test_file
= SPtesting::test_open (
$test_file
,
"$dir/output/mutation_clustering/cnv/chr1_cnv_localization.log"
);
open
(
$ref_file
,
"$dir/ref/chr1_cnv_localization.log.ref"
.
$OS
);
ok(compare(
$test_file
,
$ref_file
)==0,
"calculate_chromosome_localization-8"
);
close
(
$test_file
);
close
(
$ref_file
);
$test_file
= SPtesting::test_open (
$test_file
,
"$dir/output/mutation_clustering/translocations/chr3_translocation_localization.log"
);
open
(
$ref_file
,
"$dir/ref/chr3_translocation_localization.log.ref"
.
$OS
);
ok(compare(
$test_file
,
$ref_file
)==0,
"calculate_chromosome_localization-9"
);
close
(
$test_file
);
close
(
$ref_file
);
$test_file
= SPtesting::test_open (
$test_file
,
"$dir/output/mutation_clustering/translocations/chr2_translocation_localization.log"
);
open
(
$ref_file
,
"$dir/ref/chr2_translocation_localization.log.ref"
.
$OS
);
ok(compare(
$test_file
,
$ref_file
)==0,
"calculate_chromosome_localization-10"
);
close
(
$test_file
);
close
(
$ref_file
);
$test_file
= SPtesting::test_open (
$test_file
,
"$dir/output/mutation_clustering/translocations/chr21_translocation_localization.log"
);
open
(
$ref_file
,
"$dir/ref/chr21_translocation_localization.log.ref"
.
$OS
);
ok(compare(
$test_file
,
$ref_file
)==0,
"calculate_chromosome_localization-11"
);;
close
(
$test_file
);
close
(
$ref_file
);
$test_file
= SPtesting::test_open (
$test_file
,
"$dir/output/mutation_clustering/all_types/chr4_mutation_localization.log"
);
open
(
$ref_file
,
"$dir/ref/chr4_mutation_localization.log.ref"
.
$OS
);
ok(compare(
$test_file
,
$ref_file
)==0,
"calculate_chromosome_localization-12"
);
close
(
$test_file
);
close
(
$ref_file
);
$test_file
= SPtesting::test_open (
$test_file
,
"$dir/output/mutation_clustering/all_types/chrX_mutation_localization.log"
);
open
(
$ref_file
,
"$dir/ref/chrX_mutation_localization.log.ref"
.
$OS
);
ok(compare(
$test_file
,
$ref_file
)==0,
"calculate_chromosome_localization-13"
);
close
(
$test_file
);
close
(
$ref_file
);
$test_file
= SPtesting::test_open (
$test_file
,
"$dir/output/mutation_clustering/all_types/chrY_mutation_localization.log"
);
open
(
$ref_file
,
"$dir/ref/chrY_mutation_localization.log.ref"
.
$OS
);
ok(compare(
$test_file
,
$ref_file
)==0,
"calculate_chromosome_localization-14"
);
close
(
$test_file
);
close
(
$ref_file
);
remove_tree(
"$dir/output"
);