malariagen_data.af1.Af1.haplotype_pairwise_distances

Af1.haplotype_pairwise_distances(region: str | Region | Mapping | List[str | Region | Mapping] | Tuple[str | Region | Mapping, ...], analysis: str = 'default', sample_sets: Sequence[str] | str | None = None, sample_query: str | None = None, cohort_size: int | None = None, random_seed: int = 42) → Tuple[ndarray, ndarray, int]

Compute pairwise distances between haplotypes.

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.

analysisstr, optional, default: ‘default’

Which haplotype phasing analysis to use. See the phasing_analysis_ids property for available values.

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.

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.

random_seedint, optional, default: 42

Random seed used for reproducible down-sampling.

Returns

distndarray

Pairwise distance.

phased_samplesndarray

Sample identifiers for haplotypes.

n_snpsint

Number of SNPs used.