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)
