def test_get_options_dir_returns_correct_path_for_run_directory():
output_dir = "dummy"
quant_method = "quant"
assert piq._get_options_dir(
True, _get_test_options(output_dir),
**get_test_qr_options(quant_method=quant_method)) == \
output_dir + os.path.sep + quant_method + "_30x_50b_pe_no_bias"
def test_read_directory_checker_returns_correct_checker_if_directory_should_exist_and_does_exist():
with utils.temp_dir_created() as temp_dir:
test_options = _get_test_options(temp_dir)
options_dir = piq._get_options_dir(
False, test_options, **get_test_qr_options())
os.mkdir(options_dir)
directory_checker = piq._reads_directory_checker(True)
directory_checker(_get_logger(), test_options, **get_test_qr_options())
def test_prepare_quantification_creates_correct_file():
with utils.temp_dir_created() as dir_path:
options = _get_test_options(dir_path)
qr_options = get_test_qr_options(quant_method=quant._Cufflinks())
piq._prepare_quantification(
_get_logger(), options, **qr_options)
quant_dir = piq._get_options_dir(True, options, **qr_options)
_check_file_exists(quant_dir, "run_quantification.sh")
def test_prepare_read_simulation_creates_correct_files():
with utils.temp_dir_created() as dir_path:
options = _get_test_options(dir_path)
qr_options = get_test_qr_options()
piq._prepare_read_simulation(_get_logger(), options, **qr_options)
reads_dir = piq._get_options_dir(False, options, **qr_options)
_check_file_exists(reads_dir, "run_simulation.sh")
_check_file_exists(reads_dir, "flux_simulator_main_expression.par")
_check_file_exists(reads_dir, "flux_simulator_main_simulation.par")
def test_create_reads_executes_run_simulation_script():
with utils.temp_dir_created() as dir_path:
options = _get_test_options(dir_path)
qr_options = get_test_qr_options()
reads_dir = piq._get_options_dir(False, options, **qr_options)
os.mkdir(reads_dir)
test_filename = "test"
utils.write_executable_script(
reads_dir, "run_simulation.sh", "touch " + test_filename)
piq._create_reads(_get_logger(), options, **qr_options)
time.sleep(0.1)
assert os.path.exists(reads_dir + os.path.sep + test_filename)
def test_get_options_dir_returns_correct_path_for_reads_directory():
output_dir = "dummy"
assert piq._get_options_dir(
False, _get_test_options(output_dir),
**get_test_qr_options(quant_method="quant")) == \
output_dir + os.path.sep + "30x_50b_pe_no_bias"