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