sgkit.io.plink.zarr_to_plink#

sgkit.io.plink.zarr_to_plink(input, *, path=None, bed_path=None, bim_path=None, fam_path=None)#

Convert a Zarr on-disk store to a PLINK file.

Refer to write_plink() for details and limitations.

Deprecated since version 0.11.0: Functions for reading and writing plink are deprecated, please use the bio2zarr and vcztools packages.

Parameters:

input str | Path | MutableMapping[str, bytes]Union[str, Path, MutableMapping[str, bytes]]: Zarr store or path to directory in file system.
path str | Path | NoneUnion[str, Path, None] (default: None): Path to PLINK file set. This should not include a suffix, i.e. if the files are at data.{bed,fam,bim} then only ‘data’ should be provided (suffixes are added internally). Either this path must be provided or all 3 of bed_path, bim_path and fam_path.
bed_path str | Path | NoneUnion[str, Path, None] (default: None): Path to PLINK bed file. This should be a full path including the .bed extension and cannot be specified in conjunction with path.
bim_path str | Path | NoneUnion[str, Path, None] (default: None): Path to PLINK bim file. This should be a full path including the .bim extension and cannot be specified in conjunction with path.
fam_path str | Path | NoneUnion[str, Path, None] (default: None): Path to PLINK fam file. This should be a full path including the .fam extension and cannot be specified in conjunction with path.

Return type:

None