calc.lib.cache.targetgenome
===========================

.. py:module:: calc.lib.cache.targetgenome


Attributes
----------

.. autoapisummary::

   calc.lib.cache.targetgenome.logger


Classes
-------

.. autoapisummary::

   calc.lib.cache.targetgenome.TargetGenome


Module Contents
---------------

.. py:class:: 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)

   .. py:method:: cache_variants(positions: collections.abc.Sequence[tuple[str, int]]) -> None

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



   .. py:property:: cache_dir
      :type: pathlib.Path



   .. py:property:: cached_positions
      :type: polars.DataFrame


      A dataframe of positions previously queried

      Contains two columns: chr_name and chr_pos



   .. py:property:: chrom
      :type: str | None



   .. py:property:: filename
      :type: str



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



   .. py:property:: samples
      :type: list[str]



   .. py:property:: sampleset
      :type: str


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



   .. py:property:: target_path
      :type: pathlib.Path



   .. py:property:: zarr_group
      :type: zarr.Group



.. py:data:: logger