malariagen_data.ag3.Ag3.snp_allele_counts

Ag3.snp_allele_counts(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, inline_array: bool = True, chunks: str | Tuple[int, ...] | Callable[[Tuple[int, ...]], Tuple[int, ...]] = 'native') → ndarray

Compute SNP allele counts. This returns the number of times each SNP allele was observed in the selected samples.

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.

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

ndarray

A numpy array of shape (n_variants, 4), where the first column has the reference allele (0) counts, the second column has the first alternate allele (1) counts, the third column has the second alternate allele (2) counts, and the fourth column has the third alternate allele (3) counts.

Notes

This computation may take some time to run, depending on your computing environment. Results of this computation will be cached and re-used if the results_cache parameter was set when instantiating the class.