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)