anyvar.mapping.protocols

Provide a public interface to mapping models and functions

class anyvar.mapping.protocols.VariantProjectorProtocol(*args, **kwargs)[source]

Protocol for variant projection across the central dogma.

__init__(*args, **kwargs)[source]

project_variations(variation)[source]

Return type:: ProjectionResults

anyvar.mapping.protocols.project_and_register_variations(projector, storage, variation)[source]

Project a variant to other molecule types and store those variants + mappings.

For genomic variants, projects to coding (TRANSCRIBE_TO) and protein (TRANSLATE_TO) representations using cool-seq-tool transcript selection with longest-compatible fallback. For transcript variants, projects directly to the associated protein.

Note: I don’t think this module is the best home for this function.

Parameters:

projector (VariantProjectorProtocol) – variant projector instance
storage (Storage) – Storage instance
variation (Allele) – variation to project

Return type:

ProjectionResults

Returns:

result class containing successfully-generated mappings as well as failures