cellink.resources.get_1000genomes

cellink.resources.get_1000genomes(config_path='./cellink/resources/config/1000genomes.yaml', data_home=None, verify_checksum=True, only_download=False, rerun_preprocessing=False, worker_processes=0, max_memory=None, variants_chunk_size=32000, samples_chunk_size=2504)

Download and preprocess the 1000 Genomes Project genotype data.

This function downloads genotype files specified in a YAML configuration, optionally verifies checksums, converts all VCF files across chromosomes to a single Zarr store using vcf2zarr, and loads the result into an AnnData object using cellink.

Parameters:

• config_path (str, default="./cellink/resources/config/1000genomes.yaml") – Path to the YAML configuration file listing remote genotype files.

• data_home (str or None, optional) – Directory where data should be stored. If None, uses the default cellink data directory.

• verify_checksum (bool, default=True) – If True, verifies the checksum of downloaded files.

• only_download (bool, default=False) – If True, only downloads the data without running the data conversion.

• rerun_preprocessing (bool, default=False) – If True, re-runs VCF to Zarr conversion even if output already exists.

• worker_processes (int, default=0) – Number of worker processes for vcf2zarr explode and encode steps. 0 means use a single process (no parallelism).

• max_memory (str or None, optional) – Approximate upper bound on memory usage during the encode step (e.g. “8G”, “32G”). If None and worker_processes > 0, vcf2zarr will use its default memory limit. If worker_processes is 0, this argument is ignored entirely as single-process encoding does not require a memory bound.

• variants_chunk_size (int, default=32000) – Chunk size in the variants dimension for the output Zarr store.

• samples_chunk_size (int, default=2504) – Chunk size in the samples dimension. The 1000 Genomes Project has 2,504 samples, so the default stores all samples in a single chunk.

Return type:

AnnData | None

Returns:

anndata.AnnData Genotype data across all autosomes in a single Zarr-backed AnnData object.

Raises:

• FileNotFoundError – If any required VCF files are missing after download.

• RuntimeError – If vcf2zarr conversion fails, e.g. due to insufficient memory or chunk sizes that exceed array dimensions.