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 build_and_save(study: GenotypeData, force: bool = False) → CommonReport | None

Build a common report for a study, saves it and returns the report.

If the common reports are disabled for the study, the function skips building the report and returns None.

If the report already exists the default behavior is to skip building the report. You can force building the report by passing force=True to the function.

static build_report(genotype_data_study: GenotypeData) → CommonReport

Generate common report JSON from genotpye data study.

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: GenotypeData, 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_genotype_study(genotype_data_study: GenotypeData, 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, Union[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, Union[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[dae.person_sets.PersonSetCollection]) → PeopleReport

Create people report from list of person set collections.

to_dict() → list[dict[str, Any]]

Module contents