malariagen_data.ag3.Ag3.biallelic_diplotypes

Ag3.biallelic_diplotypes(region: str | Region | Mapping | List[str | Region | Mapping] | Tuple[str | Region | Mapping, ...], sample_sets: Sequence[str] | str | None = None, sample_query: str | None = None, sample_indices: List[int] | None = None, site_mask: str | None = None, site_class: str | None = None, cohort_size: int | None = None, min_cohort_size: int | None = None, max_cohort_size: int | None = None, random_seed: int = 42, min_minor_ac: int | None = None, max_missing_an: int | None = None, n_snps: int | None = None, thin_offset: int = 0, inline_array: bool = True, chunks: str | Tuple[int, ...] | Callable[[Tuple[int, ...]], Tuple[int, ...]] = 'native') → Tuple[ndarray, ndarray]

Load biallelic SNP genotypes.

Parameters

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.

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

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

site_classstr or None, optional

Select sites belonging to one of the following classes: CDS_DEG_4, (4-fold degenerate coding sites), CDS_DEG_2_SIMPLE (2-fold simple degenerate coding sites), CDS_DEG_0 (non-degenerate coding sites), INTRON_SHORT (introns shorter than 100 bp), INTRON_LONG (introns longer than 200 bp), INTRON_SPLICE_5PRIME (intron within 2 bp of 5’ splice site), INTRON_SPLICE_3PRIME (intron within 2 bp of 3’ splice site), UTR_5PRIME (5’ untranslated region), UTR_3PRIME (3’ untranslated region), INTERGENIC (intergenic, more than 10 kbp from a gene).

cohort_sizeint or None, optional

Randomly down-sample to this value if the number of samples in the cohort is greater. Raise an error if the number of samples is less than this value.

min_cohort_sizeint or None, optional

Minimum cohort size. Raise an error if the number of samples is less than this value.

max_cohort_sizeint or None, optional

Randomly down-sample to this value if the number of samples in the cohort is greater.

random_seedint, optional, default: 42

Random seed used for reproducible down-sampling.

min_minor_acint or None, optional

The minimum minor allele count. SNPs with a minor allele count below this value will be excluded.

max_missing_anint or None, optional

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.

n_snpsint or None, optional

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

thin_offsetint, optional, default: 0

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

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

gnndarray

An array of shape (variants, samples) where each value counts the number of alternate alleles per genotype call.

samplesndarray

Sample identifiers.