dae.backends.dae package

Submodules

dae.backends.dae.loader module

class dae.backends.dae.loader.DaeTransmittedFamiliesGenotypes(families, family_data)[source]

Bases: dae.backends.raw.loader.FamiliesGenotypes

Tuple of families and family data

family_genotype_iterator()[source]
full_families_genotypes()[source]
get_family_best_state(family)[source]
get_family_genotype(family)[source]
get_family_read_counts(family)[source]
class dae.backends.dae.loader.DaeTransmittedLoader(families, summary_filename, genome, regions=None, params=None, **_kwargs)[source]

Bases: dae.backends.raw.loader.VariantsGenotypesLoader

Loader for dae variants.

close()[source]

Close resources used by the loader.

classmethod parse_cli_arguments(argv, use_defaults=False)[source]

Parse cli arguments.

property variants_filenames
class dae.backends.dae.loader.DenovoFamiliesGenotypes(family, gt, best_state=None)[source]

Bases: dae.backends.raw.loader.FamiliesGenotypes

Tuple of family, genotype, and best_state

family_genotype_iterator()[source]
full_families_genotypes()[source]
get_family_best_state(family)[source]
get_family_genotype(family)[source]
class dae.backends.dae.loader.DenovoLoader(families: dae.pedigrees.family.FamiliesData, denovo_filename: str, genome: dae.genomic_resources.reference_genome.ReferenceGenome, regions: Optional[List[str]] = None, params: Optional[Dict[str, Any]] = None, sort: bool = True)[source]

Bases: dae.backends.raw.loader.VariantsGenotypesLoader

Load denovo variants.

close()[source]

Close resources used by the loader.

classmethod flexible_denovo_load(filepath: str, genome: dae.genomic_resources.reference_genome.ReferenceGenome, families: dae.pedigrees.family.FamiliesData, denovo_location: Optional[str] = None, denovo_variant: Optional[str] = None, denovo_chrom: Optional[str] = None, denovo_pos: Optional[str] = None, denovo_ref: Optional[str] = None, denovo_alt: Optional[str] = None, denovo_person_id: Optional[str] = None, denovo_family_id: Optional[str] = None, denovo_best_state: Optional[str] = None, denovo_genotype: Optional[str] = None, denovo_sep: str = '\t', adjust_chrom_prefix=None, **kwargs) → pandas.core.frame.DataFrame[source]

Load de Novo variants from a file.

Read a text file containing variants in the form of delimiter-separted values and produce a dataframe.

The text file may use different names for the columns containing the relevant data - these are specified with the provided parameters.

Parameters

  • filepath (str) – The path to the DSV file to read.

  • genome – A reference genome object.

  • denovo_location (str) – The label or index of the column containing

the CSHL-style location of the variant.

Parameters

denovo_variant (str) – The label or index of the column containing

the CSHL-style representation of the variant.

Parameters

denovo_chrom (str) – The label or index of the column containing

the chromosome upon which the variant is located.

Parameters

denovo_pos (str) – The label or index of the column containing the

position upon which the variant is located.

Parameters

denovo_ref (str) – The label or index of the column containing the

variant’s reference allele.

Parameters

denovo_alt (str) – The label or index of the column containing the

variant’s alternative allele.

Parameters

denovo_person_id (str) – The label or index of the column

containing either a singular person ID or a comma-separated list of person IDs.

Parameters

denovo_family_id (str) – The label or index of the column

containing a singular family ID.

Parameters

denovo_best_state (str) – The label or index of the column

containing the best state for the variant.

Parameters

families (str) – An instance of the FamiliesData class for the

pedigree of the relevant study.

Returns

Dataframe containing the variants, with the following

header - ‘chrom’, ‘position’, ‘reference’, ‘alternative’, ‘family_id’, ‘genotype’.

Return type

An instance of Pandas’ DataFrame class.

full_variants_iterator()[source]
classmethod parse_cli_arguments(argv, use_defaults=False)[source]

Parse cli arguments.

static produce_genotype(chrom: str, pos: int, genome: dae.genomic_resources.reference_genome.ReferenceGenome, family: dae.pedigrees.family.Family, members_with_variant: List[str]) → numpy.ndarray[source]

Produce genotype.

reset_regions(regions)[source]
static split_location(location)[source]

Module contents