dae.variants_loaders.vcf package

Subpackages

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[Region] | None = None, params: dict[str, Any] | None = None, **_kwargs: Any)[source]

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[source]

Close resources used by the loader.

class dae.variants_loaders.vcf.loader.VcfFamiliesGenotypes(loader: SingleVcfLoader, all_genotypes: dict[str, tuple[int, ...]])[source]

Bases: FamiliesGenotypes

Class for family genotypes build vrom VCF variant.

family_genotype_iterator() → Generator[tuple[Family, ndarray, ndarray | None], None, None][source]
class dae.variants_loaders.vcf.loader.VcfLoader(families: FamiliesData, vcf_files: list[str], genome: ReferenceGenome, regions: list[Region] | None = None, params: dict[str, Any] | None = None, **kwargs: Any)[source]

Bases: VariantsGenotypesLoader

Defines variant loader for VCF variants.

property chromosomes: list[str]

Return list of all chromosomes from VCF files.

close() → None[source]

Close resources used by the loader.

init_vcf_loaders() → None[source]

Initialize VCF loaders.

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

Parse cli arguments.

reset_regions(regions: list[Region] | Sequence[Region | None] | None) → None[source]
property variants_filenames: list[str]
dae.variants_loaders.vcf.loader.vcffile_chromosomes(filename: str) → list[str][source]

Return list of all chromosomes from VCF file.

dae.variants_loaders.vcf.serializer module

class dae.variants_loaders.vcf.serializer.VcfSerializer(families: FamiliesData, genome: ReferenceGenome, output_path: Path | str | None, header: list[str] | None = None)[source]

Bases: object

Stores a sequence of alleles in a VCF file.

close() → None[source]
open() → VcfSerializer[source]
serialize(full_variants: Iterable[tuple[SummaryVariant, list[FamilyVariant]]]) → None[source]

Serialize a sequence of alleles to a VCF file.

Module contents