calc.lib.cache.targetgenome

Attributes

logger

Classes

TargetGenome

Module Contents

class calc.lib.cache.targetgenome.TargetGenome(*, target_path: pgscatalog.calc.lib.types.Pathish, target_index_path: pgscatalog.calc.lib.types.Pathish | None, cache_dir: pgscatalog.calc.lib.types.Pathish, sampleset: str, chrom: str | None = None, threads: int = 2, sample_file: pgscatalog.calc.lib.types.Pathish | None = None)

cache_variants(positions: collections.abc.Sequence[tuple[str, int]]) → None

Query an indexed target genome and store variants in a zarr array

property cache_dir: pathlib.Path

property cached_positions: polars.DataFrame

A dataframe of positions previously queried

Contains two columns: chr_name and chr_pos

property chrom: str | None

property filename: str

property filetype: calc.lib.cache.genomefiletypes.GenomeFileType

property samples: list[str]

property sampleset: str

A human label for a (set of) target genomes, e.g. UKBiobank

property target_path: pathlib.Path

property zarr_group: zarr.Group

calc.lib.cache.targetgenome.logger