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")