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 tovictim (
BaseEntity
) – The BEL node to collapse into the surviving node
- Return type
- 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
- pybel.struct.mutation.collapse.collapse_all_variants(graph)[source]¶
Collapse all genes’, RNAs’, miRNAs’, and proteins’ variants to their parents.
- Parameters
graph (pybel.BELGraph) – A BEL Graph
- Return type
- pybel.struct.mutation.collapse.surviors_are_inconsistent(survivor_mapping)[source]¶
Check that there’s no transitive shit going on.
- Return type
- pybel.struct.mutation.collapse.collapse_to_genes(graph)[source]¶
Collapse all protein, RNA, and miRNA nodes to their corresponding gene nodes.
- Parameters
graph (pybel.BELGraph) – A BEL graph