oaklib.utilities.obograph_utils

Utilities for the OBOGraph Datamodel

See Datamodels

Functions

ancestors_with_stats(graph, curies)	Given an OBO Graph, and a list of start/seed curies, calculate various statistics about each graph node.
as_digraph(graph[, reverse, ...])	Convert to a networkx DiGraph
as_graph(graph[, reverse, filter_reflexive, ...])	Convert to a networkx DiGraph
as_multi_digraph(graph[, reverse, ...])	Convert to a networkx MultiDiGraph
compress_all_graph_ids(graph, converter)
default_stylemap_path()
depth_first_ordering(graph[, predicates])	Return a depth-first ordering of the nodes in the graph.
draw_graph(graph[, seeds, configure, ...])	Generates an image from a graph using graph_to_image then open for display
edges_from_tree(tree[, pred])	Given a parent node and a list of children, return a list of edges
expand_all_graph_ids(graph, converter)
filter_by_predicates(graph, predicates[, ...])	Create a subgraph that has only edges whose predicates are in the predicate list
graph_as_dict(graph)	Serialize a graph to a dict.
graph_id_iterator(graph)	Iterate over the ids in a graph
graph_ids(graph)	Return a set of all ids in a graph
graph_info(graph)
graph_to_d3viz_objects(graph[, predicates, ...])
graph_to_image(graph[, seeds, configure, ...])	Renders a graph to png using obographviz.
graph_to_tree_display(graph[, predicates, ...])	Translate a graph to a textual tree representation
graph_to_tree_structure(graph[, predicates, ...])	Linearizes a graph to a list of trees.
index_graph_edges_by_object(graph)	Returns an index of lists of edges keyed by object id
index_graph_edges_by_predicate(graph)	Returns an index of lists of edges keyed by predicate id
index_graph_edges_by_subject(graph)	Returns an index of lists of edges keyed by subject id
index_graph_edges_by_subject_object(graph)	Returns an index of lists of edges keyed by subject and object
index_graph_nodes(graph)	Returns an index of all nodes key by node id
induce_graph_prefix_map(graph, converter)
load_obograph_document(path)	Load an OBOGraph document from a file
merge_graph_nodes(target, source)	Merge two nodes into a single node
merge_graphs(source, target[, replace])	Merge two graphs into a single graph
mutate_graph_ids(graph, func)	Iterate over the ids in a graph and modify them.
reflexive(edge)
remove_nodes_from_graph(graph, node_ids)	Remove the specified nodes from the graph, and cascade to any edges that reference these nodes
shortest_paths(graph, start_curies[, ...])	Finds all shortest paths from a set of start nodes to a set of end nodes
topological_sort(graph, predicates)	Returns a topological sort of the graph.
tree_node_to_d3viz_object(tree_node[, ...])
trim_graph(graph, seeds[, distance, ...])	Remove all nodes more than a specified distance from a set of seed nodes

Classes

TreeFormatEnum(value)	An enumeration.
TreeNode(*[, id, lbl, meta, children, ...])