dae.common_reports package

Submodules

dae.common_reports.common_report module

class dae.common_reports.common_report.CommonReport(data: dict[str, Any])

Bases: object

Class representing a common report JSON.

static load(report_filename: str) → CommonReport | None

Load a common report from a file.

If file does not exists returns None.

save(report_filename: str) → None

Save common report into a file.

to_dict(*, full: bool = False) → dict[str, Any]

dae.common_reports.denovo_report module

class dae.common_reports.denovo_report.DenovoReport(json: dict[str, Any])

Bases: object

Class representing a denovo report JSON.

static from_genotype_study(genotype_data: Any, person_set_collections: list[PersonSetCollection]) → DenovoReport

Create a denovo report JSON from a genotype data study.

is_empty() → bool

to_dict() → dict[str, Any]

class dae.common_reports.denovo_report.DenovoReportTable(json: dict[str, Any])

Bases: object

Class representing a denovo report table JSON.

static from_variants(denovo_variants: Iterable[FamilyVariant], effect_groups: list[str], effect_types: list[str], person_set_collection: PersonSetCollection) → DenovoReportTable

Construct a denovo report table from variants.

is_empty() → bool

Return whether the table does not have a single counted variant.

to_dict() → dict[str, Any]

class dae.common_reports.denovo_report.EffectCell(person_set: PersonSet, effect: str)

Bases: object

Class representing a cell in the denovo report table.

property column_name: str

count_variant(family_variant: FamilyVariant, family_allele: FamilyAllele) → None

Count given variant in the cell data.

is_empty() → bool

property number_of_children_with_event: int

property number_of_observed_events: int

property observed_rate_per_child: int | float

property percent_of_children_with_events: int | float

to_dict() → dict[str, int | float | str]

class dae.common_reports.denovo_report.EffectRow(effect: str, person_sets: list[PersonSet])

Bases: object

Class representing a row in the denovo report table.

count_variant(fv: FamilyVariant) → None

get_empty() → list[bool]

is_row_empty() → bool

remove_elements(indexes: list[int]) → None

to_dict() → dict[str, Any]

dae.common_reports.family_counter module

class dae.common_reports.family_counter.FamiliesGroupCounters(json: dict[str, Any])

Bases: object

Class representing families group counters JSON.

static from_families(families: FamiliesData, person_set_collection: PersonSetCollection, *, draw_all_families: bool) → FamiliesGroupCounters

Create families group counters from a dict of families.

to_dict(*, full: bool = False) → dict[str, Any]

class dae.common_reports.family_counter.FamilyCounter(json: dict[str, Any])

Bases: object

Class representing a family counter JSON.

property family: dict[str, Any]

static from_family(family: Family, pedigree: list, label: int | None = None) → FamilyCounter

to_dict(*, full: bool = False) → dict[str, Any]

Transform counter to dict.

dae.common_reports.family_counter.get_family_pedigree(family: Family, person_set_collection: PersonSetCollection) → list

dae.common_reports.family_counter.get_family_type(family: Family, person_to_set: dict) → tuple

Transform a family into a tuple of strings describing members.

dae.common_reports.family_report module

Provides family report class.

class dae.common_reports.family_report.FamiliesReport(json: dict[str, Any])

Bases: object

Class representing a family report JSON.

static from_families_data(families: FamiliesData, person_set_collections: Iterable[PersonSetCollection], *, draw_all_families: bool = True) → FamiliesReport

Create a family report from families data.

static from_study(study: Any, person_set_collections: Iterable[PersonSetCollection]) → FamiliesReport

Create a family report from a genotype study.

to_dict(*, full: bool = False) → list[dict[str, Any]]

dae.common_reports.people_counter module

class dae.common_reports.people_counter.PeopleCounter(json: dict[str, int | str])

Bases: object

Class representing a people counter JSON.

static from_person_set(person_set: PersonSet) → PeopleCounter

Build people counter JSON from person set.

is_empty() → bool

is_empty_field(field: str) → bool

Return whether a given field has not counted a single variant.

to_dict(rows: list) → dict[str, int | str]

class dae.common_reports.people_counter.PeopleCounters(json: dict[str, Any])

Bases: object

Class representing people counters JSON.

static from_person_set_collection(person_set_collection: PersonSetCollection) → PeopleCounters

Create people counters JSON from dict of families.

to_dict() → dict[str, Any]

class dae.common_reports.people_counter.PeopleReport(json: list[dict[str, Any]])

Bases: object

Class representing people report JSON.

static from_person_set_collections(person_set_collections: list[PersonSetCollection]) → PeopleReport

Create people report from list of person set collections.

to_dict() → list[dict[str, Any]]

Module contents