def test_runs_ericscript_command(self, prepare_data, mock_ft, do_run,
es_config, utils):
ericscript.run(mock.Mock())
do_run.assert_called_once_with(
es_config.get_run_command.return_value,
es_config.info_message,
)
def test_runs_ericscript_command(
self, prepare_data, mock_ft, do_run, es_config, utils):
ericscript.run(mock.Mock())
do_run.assert_called_once_with(
es_config.get_run_command.return_value,
es_config.info_message,
)
def test_gets_ericscript_command(
self, prepare_data, mock_ft, do_run, es_config, utils):
ericscript.run(mock.Mock())
es_config.get_run_command.assert_called_once_with(
mock.ANY,
prepare_data.return_value
)
def test_detect_fusions_with_ericscipt_with_disambiguate(
install_test_files, data_dir, work_dir, setup_logging):
"""Run gene fusion analysis on disambiguated reads with EricScript.
Requires installation of EricScript and its reference data.
"""
sample_config = create_sample_config(data_dir, work_dir, disambiguate=True)
ericscript.run(sample_config)
assert_run_successfully(work_dir=work_dir, data_dir=data_dir)
def test_detect_fusions_with_ericscipt_with_disambiguate(
install_test_files, data_dir, setup_logging):
"""Run gene fusion analysis on disambiguated reads with EricScript.
Requires installation of EricScript and its reference data.
"""
with make_workdir() as work_dir:
sample_config = create_sample_config(
data_dir, work_dir, disambiguate=True)
ericscript.run(sample_config)
assert_run_successfully(work_dir=work_dir, data_dir=data_dir)
def detect_fusions(data):
data = to_single_data(data)
# support the old style of fusion mode calling
if dd.get_fusion_mode(data, False):
data = dd.set_fusion_caller(data, ["oncofuse", "pizzly"])
logger.warning(
"``fusion_mode`` is deprecated in favor of turning on "
"callers with ``fusion_caller``. It will run pizzly and "
"oncofuse for now, but will eventually have support "
"dropped.")
fusion_caller = dd.get_fusion_caller(data, [])
if "oncofuse" in fusion_caller:
oncofuse_file = oncofuse.run(data)
if oncofuse_file:
data = dd.set_oncofuse_file(data, oncofuse_file)
if "pizzly" in fusion_caller:
pizzly_dir = pizzly.run_pizzly(data)
if pizzly_dir:
data = dd.set_pizzly_dir(data, pizzly_dir)
data["fusion"] = {
"fasta":
os.path.join(pizzly_dir,
"%s.fusions.fasta" % dd.get_sample_name(data)),
"json":
os.path.join(pizzly_dir, "%s.json" % dd.get_sample_name(data))
}
if "ericscript" in fusion_caller:
ericscript_dir = ericscript.run(data)
return [[data]]
def detect_fusions(data):
# support the old style of fusion mode calling
if dd.get_fusion_mode(data, False):
data = dd.set_fusion_caller(data, ["oncofuse", "pizzly"])
logger.warning("``fusion_mode`` is deprecated in favor of turning on "
"callers with ``fusion_caller``. It will run pizzly and "
"oncofuse for now, but will eventually have support "
"dropped.")
fusion_caller = dd.get_fusion_caller(data, [])
if "oncofuse" in fusion_caller:
oncofuse_file = oncofuse.run(data)
if oncofuse_file:
data = dd.set_oncofuse_file(data, oncofuse_file)
if "pizzly" in fusion_caller:
pizzly_dir = pizzly.run_pizzly(data)
if pizzly_dir:
data = dd.set_pizzly_dir(data, pizzly_dir)
if "ericscript" in fusion_caller:
ericscript_dir = ericscript.run(data)
return [[data]]
def detect_fusions(data):
data = to_single_data(data)
# support the old style of fusion mode calling
if dd.get_fusion_mode(data, False):
data = dd.set_fusion_caller(data, ["oncofuse", "pizzly"])
logger.warning("``fusion_mode`` is deprecated in favor of turning on "
"callers with ``fusion_caller``. It will run pizzly and "
"oncofuse for now, but will eventually have support "
"dropped.")
fusion_caller = dd.get_fusion_caller(data, [])
if "oncofuse" in fusion_caller:
oncofuse_file = oncofuse.run(data)
if oncofuse_file:
data = dd.set_oncofuse_file(data, oncofuse_file)
if "pizzly" in fusion_caller:
pizzly_dir = pizzly.run_pizzly(data)
if pizzly_dir:
data = dd.set_pizzly_dir(data, pizzly_dir)
data["fusion"] = {"fasta": os.path.join(pizzly_dir, "%s.fusions.fasta" % dd.get_sample_name(data)),
"json": os.path.join(pizzly_dir, "%s.json" % dd.get_sample_name(data))}
if "ericscript" in fusion_caller:
ericscript_dir = ericscript.run(data)
return [[data]]
def test_creates_base_ericscript_output_dir(self, prepare_data, mock_ft,
do_run, es_config, utils):
config = mock.MagicMock()
ericscript.run(config)
utils.safe_makedir.assert_called_once_with(es_config.output_dir)
def test_calls_file_transaction(self, prepare_data, mock_ft, do_run,
es_config, utils):
config = mock.MagicMock()
ericscript.run(config)
mock_ft.assert_called_once_with(config, es_config.sample_out_dir)
def test_gets_ericscript_command(self, prepare_data, mock_ft, do_run,
es_config, utils):
ericscript.run(mock.Mock())
es_config.get_run_command.assert_called_once_with(
mock.ANY, prepare_data.return_value)
def test_returns_sample_config(self, prepare_data, mock_ft, do_run,
es_config, utils):
config = mock.MagicMock()
result = ericscript.run(config)
assert result == config
def test_creates_base_ericscript_output_dir(
self, prepare_data, mock_ft, do_run, es_config, utils):
config = mock.MagicMock()
ericscript.run(config)
utils.safe_makedir.assert_called_once_with(es_config.output_dir)
def test_calls_file_transaction(
self, prepare_data, mock_ft, do_run, es_config, utils):
config = mock.MagicMock()
ericscript.run(config)
mock_ft.assert_called_once_with(config, es_config.sample_out_dir)
def test_returns_sample_config(
self, prepare_data, mock_ft, do_run, es_config, utils):
config = mock.MagicMock()
result = ericscript.run(config)
assert result == config
