def test_bbsr(self):
self.workflow = create_puppet_workflow(base_class="tfa",
regression_class="bbsr")
self.workflow = self.workflow(self.data, self.prior,
self.gold_standard)
self.workflow.tf_names = self.tf_names
self.workflow.run()
self.assertEqual(self.workflow.results.score, 1)
def test_base(self):
self.workflow = create_puppet_workflow(
base_class=tfa_workflow.TFAWorkFlow)
self.workflow = self.workflow(self.data, self.prior,
self.gold_standard)
self.workflow.tf_names = self.tf_names
with self.assertRaises(NotImplementedError):
self.workflow.run()
def setUp(self):
self.expr = TestDataSingleCellLike.expression_matrix.transpose()
self.meta = TestDataSingleCellLike.meta_data
self.prior = TestDataSingleCellLike.priors_data
self.gold_standard = self.prior.copy()
self.gene_list = TestDataSingleCellLike.gene_metadata
self.tf_names = TestDataSingleCellLike.tf_names
self.workflow = create_puppet_workflow(base_class=SingleCellWorkflow)(
self.expr.transpose(), self.meta, self.prior, self.gold_standard)
def test_stars(self):
self.workflow = create_puppet_workflow(base_class="tfa",
regression_class="stars")
self.workflow = self.workflow(self.data, self.prior,
self.gold_standard)
self.workflow.set_regression_parameters(num_subsamples=5)
self.workflow.tf_names = self.tf_names
self.workflow.run()
self.assertAlmostEqual(self.workflow.results.score, 0.32222, places=4)
def test_bbsr(self):
self.workflow = create_puppet_workflow(base_class="tfa",
regression_class="bbsr")
self.workflow = self.workflow(self.expr, self.meta, self.prior,
self.gold_standard)
self.workflow.gene_list = self.gene_list
self.workflow.tf_names = self.tf_names
self.workflow.meta_data_file = None
self.workflow.read_metadata()
self.workflow.run()
self.assertEqual(self.workflow.results.score, 1)
def test_base(self):
self.workflow = create_puppet_workflow(
base_class=tfa_workflow.TFAWorkFlow)
self.workflow = self.workflow(self.expr, self.meta, self.prior,
self.gold_standard)
self.workflow.gene_list = self.gene_list
self.workflow.tf_names = self.tf_names
self.workflow.meta_data_file = None
self.workflow.read_metadata()
with self.assertRaises(NotImplementedError):
self.workflow.run()
def test_elasticnet(self):
self.workflow = create_puppet_workflow(base_class="tfa",
regression_class="elasticnet")
self.workflow = self.workflow(self.data, self.prior,
self.gold_standard)
self.workflow.tf_names = self.tf_names
with warnings.catch_warnings():
warnings.simplefilter("ignore")
self.workflow.run()
self.assertEqual(self.workflow.results.score, 1)
def test_sklearn(self):
self.workflow = create_puppet_workflow(base_class="tfa",
regression_class="sklearn")
self.workflow = self.workflow(self.data, self.prior,
self.gold_standard)
self.workflow.tf_names = self.tf_names
with self.assertRaises(ValueError):
self.workflow.set_regression_parameters(model=42)
with self.assertRaises(ValueError):
self.workflow.set_regression_parameters(model=LinearRegression())
self.workflow.set_regression_parameters(model=LinearRegression)
with warnings.catch_warnings():
warnings.simplefilter("ignore")
self.workflow.run()
self.assertEqual(self.workflow.results.score, 1)