def test_validate_dir_option_raises_exception_for_non_existing_dir_if_dir_should_exist():
dir_path = None
with temp_dir_created() as dp:
dir_path = dp
with pytest.raises(SchemaError):
validate_dir_option(dir_path, "dummy")
def test_run_in_directory_executes_command_in_directory():
with temp_dir_created() as dirname:
_write_and_run_script(dirname, "pwd > out.txt")
with open(dirname + os.path.sep + 'out.txt') as f:
path = f.readlines()[0].strip()
assert path == dirname
def test_write_flux_simulator_params_files_writes_correct_params_when_paired_ends_are_specified():
with temp_dir_created() as dirname:
_write_flux_simulator_params_files(dirname, paired_end=True)
d = _get_simulation_params_dict(dirname)
assert d["PAIRED_END"] == "YES"
assert d["UNIQUE_IDS"] == "YES"
def test_read_directory_checker_returns_correct_checker_if_directory_shouldnt_exist_and_doesnt_exist():
with utils.temp_dir_created() as temp_dir:
test_options = _get_test_options(temp_dir)
directory_checker = piq._reads_directory_checker(False)
directory_checker(_get_logger(), test_options,
**get_test_qr_options())
def test_run_in_directory_executes_command_in_directory():
with utils.temp_dir_created() as dirname:
_write_and_run_script(dirname, "pwd > out.txt")
with open(dirname + os.path.sep + 'out.txt') as f:
path = f.readlines()[0].strip()
assert path == os.path.realpath(dirname)
def test_validate_dir_option_does_not_raise_exception_for_non_existing_dir_if_dir_should_not_exist(
):
dir_path = None
with temp_dir_created() as dp:
dir_path = dp
validate_dir_option(dir_path, "dummy", should_exist=False)
def test_validate_dir_option_raises_exception_for_non_existing_dir_if_dir_should_exist(
):
dir_path = None
with temp_dir_created() as dp:
dir_path = dp
with pytest.raises(SchemaError):
validate_dir_option(dir_path, "dummy")
def test_read_directory_checker_returns_correct_checker_if_directory_should_exist_and_doesnt_exist():
with utils.temp_dir_created() as temp_dir:
test_options = _get_test_options(temp_dir)
directory_checker = piq._reads_directory_checker(True)
with pytest.raises(SystemExit):
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_validate_dir_option_exception_message_contains_correct_info():
dir_path = None
with temp_dir_created() as dp:
dir_path = dp
msg = "dummy"
with pytest.raises(SchemaError) as exc_info:
validate_dir_option(dir_path, msg)
check_exception_message(exc_info, msg, dir_path)
def test_validate_dir_option_exception_message_contains_correct_info():
dir_path = None
with temp_dir_created() as dp:
dir_path = dp
msg = "dummy"
with pytest.raises(SchemaError) as exc_info:
validate_dir_option(dir_path, msg)
check_exception_message(exc_info, msg, dir_path)
def test_write_flux_simulator_params_files_writes_correct_common_params():
with temp_dir_created() as dirname:
_write_flux_simulator_params_files(dirname)
for d in [_get_expression_params_dict(dirname),
_get_simulation_params_dict(dirname)]:
assert d["REF_FILE_NAME"] == TRANSCRIPT_GTF_FILE
assert d["GEN_DIR"] == GENOME_FASTA_DIR
assert d["NB_MOLECULES"] == str(NUM_MOLECULES)
assert d["POLYA_SCALE"] == "NaN"
assert d["POLYA_SHAPE"] == "NaN"
def test_write_flux_simulator_params_files_writes_correct_simulation_params():
with temp_dir_created() as dirname:
_write_flux_simulator_params_files(dirname)
d = _get_simulation_params_dict(dirname)
assert d["SEQ_FILE_NAME"] == fs.SIMULATED_READS_PREFIX + ".bed"
assert d["PRO_FILE_NAME"] == fs.EXPRESSION_PROFILE_FILE
assert d["FASTA"] == "YES"
assert d["READ_NUMBER"] == fs.READ_NUMBER_PLACEHOLDER
assert d["READ_LENGTH"] == str(READ_LENGTH)
assert d["PCR_DISTRIBUTION"] == "none"
assert "PAIRED_END" not in d
assert "UNIQUE_IDS" not in d
assert "ERR_FILE" not in d
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_write_flux_simulator_params_files_writes_correct_simulation_params():
with temp_dir_created() as dirname:
_write_flux_simulator_params_files(dirname)
spd = _get_simulation_params_dict(dirname)
assert spd["SEQ_FILE_NAME"] == \
"main_" + fs.SIMULATED_READS_PREFIX + ".bed"
assert spd["PRO_FILE_NAME"] == \
fs.get_expression_profile_file(fs.MAIN_TRANSCRIPTS)
assert spd["FASTA"] == "YES"
assert spd["READ_NUMBER"] == fs.READ_NUMBER_PLACEHOLDER
assert spd["READ_LENGTH"] == str(READ_LENGTH)
assert spd["PCR_DISTRIBUTION"] == "none"
assert "PAIRED_END" not in spd
assert "UNIQUE_IDS" not in spd
assert "ERR_FILE" not in spd
def test_run_in_directory_include_command_line_args():
with utils.temp_dir_created() as dirname:
ps.run_in_directory(dirname, "touch", [SCRIPT_NAME])
time.sleep(0.1)
assert os.path.exists(dirname + os.path.sep + SCRIPT_NAME)
def test_validate_dir_option_does_not_raise_exception_for_existing_dir_if_dir_should_exist(
):
with temp_dir_created() as dir_path:
validate_dir_option(dir_path, "dummy")
def test_run_in_directory_include_command_line_args():
with temp_dir_created() as dirname:
ps.run_in_directory(dirname, "touch", [SCRIPT_NAME])
time.sleep(0.1)
assert os.path.exists(dirname + os.path.sep + SCRIPT_NAME)
def test_validate_dir_option_raises_exception_for_existing_dir_if_dir_should_not_exist():
with temp_dir_created() as dir_path:
with pytest.raises(SchemaError):
validate_dir_option(dir_path, "dummy", should_exist=False)
def test_validate_dir_option_does_not_raise_exception_for_non_existing_dir_if_dir_should_not_exist():
dir_path = None
with temp_dir_created() as dp:
dir_path = dp
validate_dir_option(dir_path, "dummy", should_exist=False)
def test_write_flux_simulator_params_files_writes_simulation_params_file():
with temp_dir_created() as dirname:
_write_flux_simulator_params_files(dirname)
assert os.path.exists(_get_simulation_params_file(dirname))
def test_validate_dir_option_raises_exception_for_existing_dir_if_dir_should_not_exist(
):
with temp_dir_created() as dir_path:
with pytest.raises(SchemaError):
validate_dir_option(dir_path, "dummy", should_exist=False)
def test_validate_dir_option_does_not_raise_exception_for_existing_dir_if_dir_should_exist():
with temp_dir_created() as dir_path:
validate_dir_option(dir_path, "dummy")
