dae.enrichment_tool package

Submodules

dae.enrichment_tool.background module

dae.enrichment_tool.background_facade module

dae.enrichment_tool.event_counters module

class dae.enrichment_tool.event_counters.CounterBase(counter_id: str)[source]

Bases: ABC

Class to represent enrichement events counter object.

event_counts(variant_events: list[dae.enrichment_tool.genotype_helper.VariantEvent], children_by_sex: ChildrenBySex, effect_types: Iterable[str]) → EventCountersResult[source]

Calculate the event counts from the given variant events.

Args:

variant_events (list[VariantEvent]):: A list of variant events.
children_by_sex (dict[str, set[tuple[str, str]]]):: A dictionary mapping sex to a set of child IDs.
effect_types (Iterable[str]):: An iterable of effect types.

Returns:

EventCountersResult: An object containing the event counters.

abstract events(variant_events: list[dae.enrichment_tool.genotype_helper.VariantEvent], children_by_sex: ChildrenBySex, effect_types: Iterable[str]) → EventsResult[source]

select_events_in_person_set(variant_events: list[dae.enrichment_tool.genotype_helper.VariantEvent], persons: set[tuple[str, str]]) → list[dae.enrichment_tool.genotype_helper.VariantEvent][source]: Select variant events that occur in the passed persons.

split_events(variant_events: list[dae.enrichment_tool.genotype_helper.VariantEvent], children_by_sex: ChildrenBySex) → VariantEventsResult[source]

Split the passed variant events based on the children’s sex.

Args:

variant_events (list[VariantEvent]): The list of variant events: to be split.
children_by_sex (dict[str, set[tuple[str, str]]]): A dictionary: containing children grouped by sex.

Returns:

VariantEventsResult: An object containing the split variant events.

class dae.enrichment_tool.event_counters.EnrichmentResult(all: EnrichmentSingleResult, rec: EnrichmentSingleResult, male: EnrichmentSingleResult, female: EnrichmentSingleResult, unspecified: EnrichmentSingleResult, rec_genes: set[str] | None = None)[source]

Bases: object

Represents result of calculating enrichment test.

all: EnrichmentSingleResult

female: EnrichmentSingleResult

male: EnrichmentSingleResult

rec: EnrichmentSingleResult

rec_genes: set[str] | None = None

unspecified: EnrichmentSingleResult

class dae.enrichment_tool.event_counters.EnrichmentSingleResult(name: str, events: int, overlapped: int, expected: float, pvalue: float, overlapped_genes: set[str] | None = None)[source]

Bases: object

Represents result of enrichment tool calculations.

Supported fields are:

name

events – list of events found

overlapped – list of overlapped events

expected – number of expected events

pvalue

class dae.enrichment_tool.event_counters.EventCountersResult(all: int, rec: int, male: int, female: int, unspecified: int, rec_genes: set[str] | None = None)[source]

Bases: object

Represents result of event counting.

all: int

female: int

static from_events_result(events: EventsResult) → EventCountersResult[source]

male: int

rec: int

rec_genes: set[str] | None = None

unspecified: int

class dae.enrichment_tool.event_counters.EventsCounter[source]

Bases: CounterBase

Events counter class.

events(variant_events: list[dae.enrichment_tool.genotype_helper.VariantEvent], children_by_sex: ChildrenBySex, effect_types: Iterable[str]) → EventsResult[source]

class dae.enrichment_tool.event_counters.EventsResult(all: 'list[list[str]]', rec: 'list[list[str]]', male: 'list[list[str]]', female: 'list[list[str]]', unspecified: 'list[list[str]]')[source]

Bases: object

all: list[list[str]]

female: list[list[str]]

male: list[list[str]]

rec: list[list[str]]

unspecified: list[list[str]]

class dae.enrichment_tool.event_counters.GeneEventsCounter[source]

Bases: CounterBase

Counts events in genes.

events(variant_events: list[dae.enrichment_tool.genotype_helper.VariantEvent], children_by_sex: ChildrenBySex, effect_types: Iterable[str]) → EventsResult[source]: Count the events by sex and effect type.

class dae.enrichment_tool.event_counters.VariantEventsResult(all: 'list[VariantEvent]', rec: 'list[VariantEvent]', male: 'list[VariantEvent]', female: 'list[VariantEvent]', unspecified: 'list[VariantEvent]')[source]

Bases: object

all: list[dae.enrichment_tool.genotype_helper.VariantEvent]

female: list[dae.enrichment_tool.genotype_helper.VariantEvent]

male: list[dae.enrichment_tool.genotype_helper.VariantEvent]

rec: list[dae.enrichment_tool.genotype_helper.VariantEvent]

unspecified: list[dae.enrichment_tool.genotype_helper.VariantEvent]

dae.enrichment_tool.event_counters.filter_denovo_one_event_per_family(variant_events: list[dae.enrichment_tool.genotype_helper.VariantEvent], requested_effect_types: Iterable[str]) → list[list[str]][source]

For each variant returns list of affected gene syms.

vs - generator for variants.

This functions receives a generator for variants and transforms each variant into list of gene symbols, that are affected by the variant.

The result is represented as list of lists.

dae.enrichment_tool.event_counters.filter_denovo_one_gene_per_events(variant_events: list[dae.enrichment_tool.genotype_helper.VariantEvent], requested_effect_types: Iterable[str]) → list[list[str]][source]

dae.enrichment_tool.event_counters.filter_denovo_one_gene_per_recurrent_events(variant_events: list[dae.enrichment_tool.genotype_helper.VariantEvent], requsted_effect_types: Iterable[str]) → list[list[str]][source]: Collect only events that occur in more than one family.

dae.enrichment_tool.event_counters.filter_overlapping_events(events: list[list[str]], gene_syms: list[str]) → list[list[str]][source]

dae.enrichment_tool.event_counters.get_sym_2_fn(variant_events: list[dae.enrichment_tool.genotype_helper.VariantEvent], requested_effect_types: Iterable[str]) → dict[str, int][source]: Count the number of requested effect types events in genes.

dae.enrichment_tool.event_counters.overlap_enrichment_result_dict(events_counts: EventsResult, gene_syms: Iterable[str]) → EventsResult[source]: Calculate the overlap between all events and requested gene syms.

dae.enrichment_tool.event_counters.overlap_event_counts(events_counts: EventsResult, gene_syms: Iterable[str]) → EventCountersResult[source]

dae.enrichment_tool.genotype_helper module

class dae.enrichment_tool.genotype_helper.AlleleEvent(persons: set[tuple[str, str]], effect_genes: set[dae.enrichment_tool.genotype_helper.GeneEffect])[source]

Bases: object

effect_genes: set[dae.enrichment_tool.genotype_helper.GeneEffect]

persons: set[tuple[str, str]]

class dae.enrichment_tool.genotype_helper.GeneEffect(gene: str, effect: str)[source]

Bases: object

effect: str

gene: str

class dae.enrichment_tool.genotype_helper.GenotypeHelper(genotype_data: GenotypeData, person_set_collection: PersonSetCollection, effect_types: list[str] | None = None, genes: list[str] | None = None)[source]

Bases: object

Genotype helper for enrichment tools.

static collect_denovo_events(denovo_variants: Iterable[FamilyVariant]) → list[dae.enrichment_tool.genotype_helper.VariantEvent][source]: Collect denovo events.

get_denovo_events() → list[dae.enrichment_tool.genotype_helper.VariantEvent][source]

class dae.enrichment_tool.genotype_helper.VariantEvent(family_id: str, fvuid: str, allele_events: list[dae.enrichment_tool.genotype_helper.AlleleEvent])[source]

Bases: object

allele_events: list[dae.enrichment_tool.genotype_helper.AlleleEvent]

family_id: str

fvuid: str

dae.enrichment_tool package

Submodules

dae.enrichment_tool.background module

dae.enrichment_tool.background_facade module

dae.enrichment_tool.event_counters module

dae.enrichment_tool.genotype_helper module

dae.enrichment_tool.tool module

Module contents