Collapse¶

Functions for collapsing nodes.

pybel.struct.mutation.collapse.collapse_pair(graph, survivor, victim)[source]¶

Rewire all edges from the synonymous node to the survivor node, then deletes the synonymous node.

Does not keep edges between the two nodes.

Parameters

graph (pybel.BELGraph) – A BEL graph
survivor (BaseEntity) – The BEL node to collapse all edges on the synonym to
victim (BaseEntity) – The BEL node to collapse into the surviving node

Return type

None

pybel.struct.mutation.collapse.collapse_nodes(graph, survivor_mapping)[source]¶

Collapse all nodes in values to the key nodes, in place.

Parameters

graph (pybel.BELGraph) – A BEL graph
survivor_mapping (Mapping[BaseEntity, Set[BaseEntity]]) – A dictionary with survivors as their keys, and iterables of the corresponding victims as values.

Return type

None

pybel.struct.mutation.collapse.collapse_all_variants(graph)[source]¶

Collapse all genes’, RNAs’, miRNAs’, and proteins’ variants to their parents.

pybel.struct.mutation.collapse.surviors_are_inconsistent(survivor_mapping)[source]¶

Check that there’s no transitive shit going on.

pybel.struct.mutation.collapse.collapse_to_genes(graph)[source]¶

Collapse all protein, RNA, and miRNA nodes to their corresponding gene nodes.