def setUp(self):
super(SetUpSparseDataMTL, self).setUp()
self._task_objects = [
TaskDataStub(sparse=True),
TaskDataStub(sparse=True)
]
self._task_objects[0].tasks_from_metadata = False
self._task_objects[1].tasks_from_metadata = False
def test_result_processor_perfect(self):
self.workflow._task_objects = [TaskDataStub()]
self.workflow._load_tasks()
beta1 = pd.DataFrame(np.array([[0, 1], [0, 1], [1, 0], [0.5, 0]]),
["gene1", "gene2", "gene4", "gene6"],
["gene3", "gene6"])
beta2 = pd.DataFrame(np.array([[0, 1], [0, 1], [1, 0], [0.5, 0]]),
["gene1", "gene2", "gene4", "gene6"],
["gene3", "gene6"])
beta3 = pd.DataFrame(np.array([[0, 1], [0, 1], [1, 0], [0.5, 0.2]]),
["gene1", "gene2", "gene4", "gene6"],
["gene3", "gene6"])
rb1 = pd.DataFrame(np.array([[0, 1], [0, 1], [1, 0], [0.25, 0]]),
["gene1", "gene2", "gene4", "gene6"],
["gene3", "gene6"])
rb2 = pd.DataFrame(np.array([[0, 1], [0, 1], [1, 0], [1, 0]]),
["gene1", "gene2", "gene4", "gene6"],
["gene3", "gene6"])
rb3 = pd.DataFrame(np.array([[0, 1], [0, 1], [1, 0], [0.5, 0.5]]),
["gene1", "gene2", "gene4", "gene6"],
["gene3", "gene6"])
self.workflow.startup_finish()
self.workflow.emit_results(
[[beta1, beta1], [beta2, beta2], [beta3, beta3]],
[[rb1, rb1], [rb2, rb2], [rb3, rb3]], self.workflow.gold_standard,
self.workflow.priors_data)
self.assertAlmostEqual(self.workflow.results.score, 1)
def test_num_props(self):
self.assertIsNone(self.workflow._num_obs)
self.assertIsNone(self.workflow._num_tfs)
self.assertIsNone(self.workflow._num_genes)
task_obs = TaskDataStub.expression_matrix.shape[1]
task_tfs = TaskDataStub.priors_data.shape[1]
task_genes = TaskDataStub.expression_matrix.shape[0]
self.workflow._task_objects = [
TaskDataStub(), TaskDataStub(),
TaskDataStub()
]
self.assertEqual(self.workflow._num_obs, task_obs * 3)
self.assertEqual(self.workflow._num_genes, task_genes)
self.assertEqual(self.workflow._num_tfs, task_tfs)
def test_align_task_priors(self):
self.workflow.set_crossvalidation_parameters(
split_gold_standard_for_crossvalidation=True, cv_split_ratio=0.2)
self.workflow._process_default_priors()
gs_genes = self.workflow.gold_standard.shape[0]
self.workflow._task_objects = [
copy.deepcopy(TaskDataStub()),
copy.deepcopy(TaskDataStub()),
copy.deepcopy(TaskDataStub())
]
self.assertTupleEqual(self.workflow._task_objects[0].priors_data.shape,
TaskDataStub.priors_data.shape)
self.workflow._process_task_priors()
expect_size = 2
prior_sizes = list(
map(lambda x: x.priors_data.shape[0], self.workflow._task_objects))
self.assertListEqual([expect_size] * 3, prior_sizes)
def test_taskdata_processing(self):
self.workflow._task_objects = [TaskDataStub()]
# Test the TaskData processing
self.assertEqual(len(self.workflow._task_objects), 1)
self.workflow._load_tasks()
self.assertEqual(len(self.workflow._task_objects), 3)
# Test processing the TaskData objects into data structures in MultitaskLearningWorkflow
self.assertEqual(self.workflow._n_tasks, 3)
self.assertEqual(
list(
map(lambda x: x.expression_matrix.shape,
self.workflow._task_objects)), [(6, 2), (6, 4), (6, 4)])
self.assertEqual(
list(map(lambda x: x.meta_data.shape,
self.workflow._task_objects)), [(2, 2), (4, 2), (4, 2)])
def test_task_processing(self):
self.workflow._task_objects = [TaskDataStub()]
self.workflow._load_tasks()
self.workflow.startup_finish()
self.assertEqual(self.workflow._regulators.tolist(),
["gene3", "gene6"])
self.assertEqual(self.workflow._targets.tolist(),
["gene1", "gene2", "gene4", "gene6"])
self.assertEqual(len(self.workflow._task_design), 3)
self.assertEqual(len(self.workflow._task_response), 3)
self.assertEqual(len(self.workflow._task_bootstraps), 3)
pdt.assert_frame_equal(self.workflow._task_design[0].to_df(),
pd.DataFrame([[16., 5.], [15., 15.]],
index=["gene3", "gene6"],
columns=["0", "6"]).T,
check_dtype=False)
pdt.assert_frame_equal(self.workflow._task_response[0].to_df(),
pd.DataFrame(
[[2, 3], [28, 27], [16, 5], [3, 4]],
index=["gene1", "gene2", "gene4", "gene6"],
columns=["0", "6"]).T,
check_dtype=False)
def setUp(self):
super(SetUpDenseDataMTL, self).setUp()
self._task_objects = [TaskDataStub(), TaskDataStub()]
self._task_objects[0].tasks_from_metadata = False
self._task_objects[1].tasks_from_metadata = False
def setUp(self):
super(TestMultitaskFactory, self).setUp()
self._task_objects = [TaskDataStub(), TaskDataStub()]
self._task_objects[0].tasks_from_metadata = False
self._task_objects[1].tasks_from_metadata = False