Source code for pybel.struct.mutation.deletion.deletion

# -*- coding: utf-8 -*-

"""Functions for deleting nodes and edges in networks."""

from ...filters.edge_filters import filter_edges
from ...filters.edge_predicates import is_associative_relation, not_causal_relation
from ...filters.node_filters import filter_nodes
from ...filters.node_predicates import (
    is_biological_process,
    is_isolated_list_abundance,
    is_pathology,
)
from ...pipeline import in_place_transformation

__all__ = [
    "remove_filtered_edges",
    "remove_filtered_nodes",
    "remove_associations",
    "remove_pathologies",
    "remove_biological_processes",
    "remove_isolated_list_abundances",
    "remove_non_causal_edges",
]


@in_place_transformation
def remove_filtered_edges(graph, edge_predicates=None):
    """Remove edges passing the given edge predicates.

    :param pybel.BELGraph graph: A BEL graph
    :param edge_predicates: A predicate or list of predicates
    :type edge_predicates: None or ((pybel.BELGraph, tuple, tuple, int) -> bool) or iter[(pybel.BELGraph, tuple, tuple, int) -> bool]]
    :return:
    """
    edges = list(filter_edges(graph, edge_predicates=edge_predicates))
    graph.remove_edges_from(edges)


@in_place_transformation
def remove_filtered_nodes(graph, node_predicates=None):
    """Remove nodes passing the given node predicates.

    :param pybel.BELGraph graph: A BEL graph
    :type node_predicates: None or ((pybel.BELGraph, tuple) -> bool) or iter[(pybel.BELGraph, tuple) -> bool)]
    """
    nodes = list(filter_nodes(graph, node_predicates=node_predicates))
    graph.remove_nodes_from(nodes)


@in_place_transformation
def remove_associations(graph):
    """Remove all associative relationships from the graph.

    :param pybel.BELGraph graph: A BEL graph
    """
    remove_filtered_edges(graph, is_associative_relation)


@in_place_transformation
def remove_pathologies(graph):
    """Remove pathology nodes from the graph.

    :param pybel.BELGraph graph: A BEL graph
    """
    remove_filtered_nodes(graph, node_predicates=is_pathology)


@in_place_transformation
def remove_biological_processes(graph):
    """Remove biological process nodes from the graph.

    :param pybel.BELGraph graph: A BEL graph
    """
    remove_filtered_nodes(graph, node_predicates=is_biological_process)


@in_place_transformation
def remove_isolated_list_abundances(graph):
    """Remove isolated list abundances from the graph.

    :param pybel.BELGraph graph: A BEL graph
    """
    remove_filtered_nodes(graph, is_isolated_list_abundance)


@in_place_transformation
def remove_non_causal_edges(graph):
    """Remove non-causal edges from the graph."""
    remove_filtered_edges(graph, not_causal_relation)