result module

CharGerResult

class CharGerResult(variant, clinvar=NOTHING, acmg_decisions=NOTHING, charger_decisions=NOTHING)

Bases: object

CharGer classification result of one variant.

Examples

>>> variant = Variant(19, 45855804, 45855804, 'CT', 'C')
>>> result = CharGerResult(variant)
>>> result.acmg_decisions['PVS1'] is None
True

Parameters

• variant (charger.variant.Variant) –

• clinvar (Dict[str, Any]) –

• acmg_decisions (Dict[str, Optional[charger.result.ModuleDecision]]) –

• charger_decisions (Dict[str, Optional[charger.result.ModuleDecision]]) –

Return type

None

variant

The input variant of this result.

clinvar

ClinVar annotation of this variant.

acmg_decisions

The classification decision per ACMG module of this variant.

None if the module is not run. See ModuleDecision for the possible decisions.

charger_decisions

The classification decision of each CharGer module of this variant.

Same usage as acmg_decisions.

Module helper classes

class ModuleDecision(value)

Bases: enum.Enum

The decision of a ACMG or CharGer module of one variant.

Used by CharGerResult.acmg_decisions and CharGerResult.charger_decisions.

Examples

Skip PVS1 classification:

>>> result = CharGerResult(Variant('19', 45855804, 45855804, 'CT', 'C'))
>>> result.acmg_decisions['PVS1'] = ModuleDecision.SKIPPED

PASSED = 1

The variant matched the criteria of the module.

FAILED = 2

The variant didn’t match the criteria of the module.