dae.backends.vcf package

Submodules

dae.backends.vcf.loader module

Defines variant loader classed for VCF variants.

class dae.backends.vcf.loader.SingleVcfLoader(families, vcf_files, genome: dae.genomic_resources.reference_genome.ReferenceGenome, regions=None, params=None, **_kwargs)[source]

Bases: dae.backends.raw.loader.VariantsGenotypesLoader

Defines a variant loader from single VCF file.

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

close()[source]: Close resources used by the loader.

class dae.backends.vcf.loader.VcfFamiliesGenotypes(loader, vcf_variants)[source]

Bases: dae.backends.raw.loader.FamiliesGenotypes

Class for family genotypes build vrom VCF variant.

family_genotype_iterator()[source]

full_families_genotypes()[source]

get_family_best_state(family)[source]

get_family_genotype(family)[source]

class dae.backends.vcf.loader.VcfLoader(families, vcf_files, genome: dae.genomic_resources.reference_genome.ReferenceGenome, regions=None, params=None, **_kwargs)[source]

Bases: dae.backends.raw.loader.VariantsGenotypesLoader

Defines variant loader for VCF variants.

property chromosomes: Return list of all chromosomes from VCF files.

close()[source]: Close resources used by the loader.

classmethod parse_cli_arguments(argv, use_defaults=False)[source]: Parse cli arguments.

reset_regions(regions)[source]

property variants_filenames

Module contents