def remove_pathologies(graph): """Remove pathology nodes :param pybel.BELGraph graph: A BEL graph """ nodes = get_nodes(graph, function_inclusion_filter_builder(PATHOLOGY)) graph.remove_nodes_from(nodes)
def remove_biological_processes(graph): """Remove biological process nodes :param pybel.BELGraph graph: A BEL graph """ nodes = get_nodes(graph, function_inclusion_filter_builder(BIOPROCESS)) graph.remove_nodes_from(nodes)
def get_translocated(graph): """Gets all nodes that are translocated :param pybel.BELGraph graph: A BEL graph :return: A set of nodes that are translocated :rtype: set[tuple] """ return get_nodes(graph, is_translocated)
def get_activities(graph): """Gets all nodes that have molecular activities :param pybel.BELGraph graph: A BEL graph :return: A set of nodes that have molecular activities :rtype: set[tuple] """ return get_nodes(graph, has_activity)
def get_degradations(graph): """Gets all nodes that are degraded :param pybel.BELGraph graph: A BEL graph :return: A set of nodes that are degraded :rtype: set[tuple] """ return get_nodes(graph, is_degraded)
def test_concatenate_multiple_node_filters(self): def even(_, node) -> bool: return node % 2 == 0 def big(_, node) -> bool: return node > 3 nodes = get_nodes(self.universe, [even, big]) self.assertEqual({4, 6, 8}, nodes) self.assertEqual(3, count_passed_node_filter(self.universe, [even, big]))
def collapse_to_protein_interactions(graph): """Collapses to a graph made of only causal gene/protein edges :param pybel.BELGraph graph: A BEL Graph """ collapse_by_central_dogma_to_genes(graph) remove_filtered_edges(graph, invert_edge_filter(has_polarity)) filtered_graph = graph.subgraph( get_nodes(graph, node_predicates=function_inclusion_filter_builder(GENE))) return filtered_graph
def test_concatenate_single_node_filter(self): nodes = get_nodes(self.universe, [true_node_predicate]) self.assertEqual(self.all_universe_nodes, nodes)
def test_missing_node_filter(self): nodes = get_nodes(self.universe, concatenate_node_predicates([])) self.assertEqual(self.all_universe_nodes, nodes)
def test_keep_node_permissive(self): nodes = get_nodes(self.universe, true_node_predicate) self.assertEqual(self.all_universe_nodes, nodes)
def test_no_node_filter_argument(self): nodes = get_nodes(self.universe, []) self.assertEqual(self.all_universe_nodes, nodes)
def test_concatenate_single_node_filter(self): nodes = get_nodes(self.universe, [keep_node_permissive]) self.assertEqual(self.all_universe_nodes, nodes)