pyXenium.perturb

pyXenium.perturb is the lightweight SpatialPerturb Bridge surface. It writes handoff specs and stable external CLI commands for running Perturb-seq reference projection with the separately installed SpatialPerturb package.

class SpatialPerturbBridgeConfig(xenium_path, output_dir, prepared_h5ad=None, cache_dir='.spatialperturb-cache', cell_group_path=None, roi_geojson_path=None, sample_name=None, reference_datasets=('gse241115_breast_cropseq',), install_requirement='SpatialPerturb>=0.3')

Bases: object

Configuration for a pyXenium-to-SpatialPerturb handoff specification.

Parameters:

• xenium_path (str | Path)

• output_dir (str | Path)

• prepared_h5ad (str | Path | None)

• cache_dir (str | Path)

• cell_group_path (str | Path | None)

• roi_geojson_path (str | Path | None)

• sample_name (str | None)

• reference_datasets (Sequence[str] | str)

• install_requirement (str)

xenium_path: str | Path

output_dir: str | Path

prepared_h5ad: str | Path | None = None

cache_dir: str | Path = '.spatialperturb-cache'

cell_group_path: str | Path | None = None

roi_geojson_path: str | Path | None = None

sample_name: str | None = None

reference_datasets: Sequence[str] | str = ('gse241115_breast_cropseq',)

install_requirement: str = 'SpatialPerturb>=0.3'

spatialperturb_status()

Return environment status for the optional external SpatialPerturb package.

Return type:

dict[str, Any]

build_spatialperturb_handoff(config)

Build a JSON-serializable handoff spec for the external SpatialPerturb CLI.

Parameters:

config (SpatialPerturbBridgeConfig | Mapping[str, Any])

Return type:

dict[str, Any]

write_spatialperturb_handoff(config, output_path)

Write a SpatialPerturb Bridge handoff spec as JSON and return the spec.

Parameters:

• config (SpatialPerturbBridgeConfig | Mapping[str, Any])

• output_path (str | Path)

Return type:

dict[str, Any]