malariagen_data.ag3.Ag3.biallelic_snps_to_plink

Ag3.biallelic_snps_to_plink(output_dir: str, region: str | Region | Mapping | List[str | Region | Mapping] | Tuple[str | Region | Mapping, ...], n_snps: int, overwrite: bool = False, thin_offset: int = 0, sample_sets: Sequence[str] | str | None = None, sample_query: str | None = None, sample_indices: List[int] | None = None, site_mask: str | None = 'default', min_minor_ac: int | float | None = 2, max_missing_an: int | float | None = 0, random_seed: int = 42, inline_array: bool = True, chunks: int | str | Tuple[int | str, ...] | Callable[[Tuple[int, ...]], int | str | Tuple[int | str, ...]] = 'native')

Write Anopheles biallelic SNP data to the Plink binary file format.

This function writes biallelic SNPs to the Plink binary file format. It enables subsetting to specific regions (region), selecting specific sample sets, or lists of samples, randomly downsampling sites, and specifying filters based on missing data and minimum minor allele count (see the docs for biallelic_snp_calls for more information). The overwrite parameter, set to true, will enable overwrite of data with the same SNP selection parameter values.

Parameters

output_dirstr

A string indicating the desired output file location.

regionstr or Region or Mapping or list of str or Region or Mapping or tuple of str 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. Can also be a sequence (e.g., list) of regions.

n_snpsint

The desired number of SNPs to use when running the analysis. SNPs will be evenly thinned to approximately this number.

overwritebool, optional, default: False

A boolean indicating whether a previously written file with the same name ought to be overwritten. Default is False.

thin_offsetint, optional, default: 0

Starting index for SNP thinning. Change this to repeat the analysis using a different set of SNPs.

sample_setssequence of str or str or None, optional

List of sample sets and/or releases. Can also be a single sample set or release.

sample_querystr or None, optional

A pandas query string to be evaluated against the sample metadata, to select samples to be included in the returned data.

sample_indiceslist of int or None, optional

Advanced usage parameter. A list of indices of samples to select, corresponding to the order in which the samples are found within the sample metadata. Either provide this parameter or sample_query, not both.

site_maskstr or None, optional, default: ‘default’

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

min_minor_acint or float or None, optional, default: 2

The minimum minor allele count. SNPs with a minor allele count below this value will be excluded. Can also be a float, which will be interpreted as a fraction.

max_missing_anint or float or None, optional, default: 0

The maximum number of missing allele calls to accept. SNPs with more than this value will be excluded. Set to 0 to require no missing calls. Can also be a float, which will be interpreted as a fraction.

random_seedint, optional, default: 42

Random seed used for reproducible down-sampling.

inline_arraybool, optional, default: True

Passed through to dask from_array().

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

Define how input data being read from zarr should be divided into chunks for a dask computation. If ‘native’, use underlying zarr chunks. If a string specifying a target memory size, e.g., ‘300 MiB’, resize chunks in arrays with more than one dimension to match this size. If ‘auto’, let dask decide chunk size. If ‘ndauto’, let dask decide chunk size but only for arrays with more than one dimension. If ‘ndauto0’, as ‘ndauto’ but only vary the first chunk dimension. If ‘ndauto1’, as ‘ndauto’ but only vary the second chunk dimension. If ‘ndauto01’, as ‘ndauto’ but only vary the first and second chunk dimensions. Also, can be a tuple of integers, or a callable which accepts the native chunks as a single argument and returns a valid dask chunks value.

Returns

Base path to files containing binary Plink output files. Append .bed, .bim or .fam to obtain paths for the binary genotype table file, variant information file and sample information file respectively.

Notes

This computation may take some time to run, depending on your computing environment. Unless the overwrite parameter is set to True, results will be returned from a previous computation, if available.