malariagen_data.af1.Af1.is_accessible

Af1.is_accessible(region: str | Region | Mapping, site_mask: str = 'default', inline_array: bool = True, chunks: str | Tuple[int, ...] | Callable[[Tuple[int, ...]], Tuple[int, ...]] = 'native') → ndarray

Compute genome accessibility array.

Parameters

regionstr or Region or Mapping

Region of the reference genome. Can be a contig name, region string (formatted like “{contig}:{start}-{end}”), or identifier of a genome feature such as a gene or transcript.

site_maskstr, optional, default: ‘default’

Which site filters mask to apply. See the site_mask_ids property for available values.

inline_arraybool, optional, default: True

Passed through to dask from_array().

chunksstr or tuple of int or Callable[[typing.Tuple[int, …]], tuple of int], optional, default: ‘native’

If ‘auto’ let dask decide chunk size. If ‘native’ use native zarr chunks. Also, can be a target size, e.g., ‘200 MiB’, or a tuple of integers.

Returns

ndarray

An array of boolean values identifying accessible genome sites.