mkt.databases.cli.generate_conservation_data
CLI to build and serialize the KLIFS hierarchical-conservation artifact.
Entry point (generate_conservation_data) that constructs a
mkt.databases.conservation.KLIFSHierarchicalConservation engine over the
shipped DICT_KINASE KLIFS panel, packages its distances + dendrogram +
provenance as a mkt.schema.conservation_schema.KLIFSConservationData, and
serializes it as mkt.schema package data so downstream renderers (e.g. the
plot_dict_kinase figures) can deserialize it rather than recomputing the tree.
Functions
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Generate and serialize the KLIFS conservation-data artifact. |
- mkt.databases.cli.generate_conservation_data.main(metric: ~typing.Annotated[str, <typer.models.OptionInfo object at 0x7754019d5ae0>] = 'blosum', linkage_method: ~typing.Annotated[str, <typer.models.OptionInfo object at 0x7754019d5b70>] = 'average', weighting: ~typing.Annotated[str, <typer.models.OptionInfo object at 0x7754019d5c00>] = 'none', conservation_threshold: ~typing.Annotated[float, <typer.models.OptionInfo object at 0x7754019d5c90>] = 0.8, exclude_pseudokinases: ~typing.Annotated[bool, <typer.models.OptionInfo object at 0x7754019d5d20>] = False, output_dir: ~typing.Annotated[~pathlib.Path | None, <typer.models.OptionInfo object at 0x7754019d5db0>] | None = None, verbose: ~typing.Annotated[bool, <typer.models.OptionInfo object at 0x7754019d5e70>] = False) None[source]
Generate and serialize the KLIFS conservation-data artifact.
- Examples:
# default panel (BLOSUM62 + UPGMA), shipped as package data generate_conservation_data
# percent-identity metric, complete linkage, custom output directory generate_conservation_data –metric identity –linkage-method complete -o ./out