dae.variants_loaders.vcf package

Submodules

dae.variants_loaders.vcf.loader module

Defines variant loader classed for VCF variants.

class dae.variants_loaders.vcf.loader.SingleVcfLoader(families: FamiliesData, vcf_files: list[str], genome: ReferenceGenome, regions: list[str] | None = None, params: dict[str, Any] | None = None, **_kwargs: Any)

Bases: VariantsGenotypesLoader

Defines a variant loader from single VCF file.

property chromosomes: list[str]

Return list of all chromosomes from VCF file(s).

close() → None

Close resources used by the loader.

class dae.variants_loaders.vcf.loader.VcfFamiliesGenotypes(loader: SingleVcfLoader, vcf_variants: list[Optional[pysam.libcbcf.VariantRecord]])

Bases: FamiliesGenotypes

Class for family genotypes build vrom VCF variant.

family_genotype_iterator() → Generator[tuple[dae.pedigrees.family.Family, numpy.ndarray, Optional[numpy.ndarray]], None, None]

class dae.variants_loaders.vcf.loader.VcfLoader(families: FamiliesData, vcf_files: list[str], genome: ReferenceGenome, regions: list[str] | None = None, params: dict[str, Any] | None = None, **kwargs: Any)

Bases: VariantsGenotypesLoader

Defines variant loader for VCF variants.

property chromosomes: list[str]

Return list of all chromosomes from VCF files.

close() → None

Close resources used by the loader.

classmethod parse_cli_arguments(argv: Namespace, use_defaults: bool = False) → tuple[list[str], dict[str, Any]]

Parse cli arguments.

reset_regions(regions: str | list[str] | None) → None

property variants_filenames: list[str]

Module contents