def setUp(self): self.workflow = workflow.WorkflowBase() self.workflow.priors_data = self.data.priors_data.copy() self.workflow.gold_standard = self.data.gold_standard.copy() self.workflow.expression_matrix = self.data.expression_matrix.copy() self.workflow.tf_names = self.data.tf_names self.workflow.input_dir = os.path.join(my_dir, "../../data/dream4")
def setUp(self): self.data = workflow.WorkflowBase() self.data.input_dir = os.path.join(my_dir, "../../data/dream4") self.data.get_data() self.beta = [ pd.DataFrame(np.array([[0, 1], [0.5, 0.05]]), index=['gene1', 'gene2'], columns=['tf1', 'tf2']) ] self.beta_resc = [ pd.DataFrame(np.array([[0, 1], [1, 0.05]]), index=['gene1', 'gene2'], columns=['tf1', 'tf2']) ] self.prior = pd.DataFrame([[0, 1], [1, 0]], index=['gene1', 'gene2'], columns=['tf1', 'tf2']) self.gold_standard = pd.DataFrame([[0, 1], [1, 0]], index=['gene1', 'gene2'], columns=['tf1', 'tf2']) self.puppet_workflow = crossvalidation_workflow.create_puppet_workflow( ) self.puppet_workflow = self.puppet_workflow( self.data.expression_matrix, self.data.meta_data, self.data.priors_data, self.data.gold_standard)
def setUp(self): self.workflow = workflow.WorkflowBase() self.workflow.input_dir = os.path.join(my_dir, "../../data/dream4") self.workflow.expression_matrix_file = default.DEFAULT_EXPRESSION_FILE self.workflow.tf_names_file = default.DEFAULT_TFNAMES_FILE self.workflow.meta_data_file = default.DEFAULT_METADATA_FILE self.workflow.priors_file = default.DEFAULT_PRIORS_FILE self.workflow.gold_standard_file = default.DEFAULT_GOLDSTANDARD_FILE
def setUpClass(cls): cls.workflow = workflow.WorkflowBase() cls.workflow.input_dir = os.path.join(my_dir, "../../data/dream4") cls.workflow.expression_matrix_file = "expression.tsv" cls.workflow.meta_data_file = "meta_data.tsv" cls.workflow.tf_names_file = "tf_names.tsv" cls.workflow.priors_file = "gold_standard.tsv" cls.workflow.gold_standard_file = "gold_standard.tsv" cls.workflow.get_data()
def setUp(self): self.workflow = workflow.WorkflowBase() self.workflow.priors_data = self.data.priors_data.copy() self.workflow.gold_standard = self.data.gold_standard.copy() self.workflow.data = self.data.data.copy() self.workflow.tf_names = self.data.tf_names self.workflow.input_dir = os.path.join(my_dir, "../../data/dream4") self.workflow.expression_matrix_file = "expression.tsv" self.workflow.expression_matrix_columns_are_genes = False
def setUpClass(cls): cls.data = workflow.WorkflowBase() cls.data.input_dir = os.path.join(my_dir, "../../data/dream4") cls.data.expression_matrix_file = "expression.tsv" cls.data.meta_data_file = "meta_data.tsv" cls.data.tf_names_file = "tf_names.tsv" cls.data.priors_file = "gold_standard.tsv" cls.data.gold_standard_file = "gold_standard.tsv" cls.data.expression_matrix_columns_are_genes = False cls.data.get_data()
def setUp(self): self.workflow = workflow.WorkflowBase()
def setUp(self): self.workflow = workflow.WorkflowBase() self.workflow.input_dir = os.path.join(my_dir, "../../data/dream4")