gain.effect_annotation.effect_checkers package

Submodules

gain.effect_annotation.effect_checkers.coding module

class CodingEffectChecker

Bases: EffectChecker

Coding effect checker class.

get_effect(request: PositiveStrandAnnotationRequest | NegativeStrandAnnotationRequest) → AnnotationEffect | None

Return an annotation effect or None.

gain.effect_annotation.effect_checkers.effect_checker module

class EffectChecker

Bases: ABC

abstractmethod get_effect(request: PositiveStrandAnnotationRequest | NegativeStrandAnnotationRequest) → AnnotationEffect | None

Return an annotation effect or None.

gain.effect_annotation.effect_checkers.frame_shift module

class FrameShiftEffectChecker

Bases: EffectChecker

Frame shift effect checker class.

check_if_new_stop(request: PositiveStrandAnnotationRequest | NegativeStrandAnnotationRequest) → bool

Check for a new stop codon.

check_stop_codon(request: PositiveStrandAnnotationRequest | NegativeStrandAnnotationRequest) → AnnotationEffect | None

Check for stop codon.

create_effect(request: PositiveStrandAnnotationRequest | NegativeStrandAnnotationRequest, change_length: int) → AnnotationEffect | None

Create frame-shift annotation effect.

get_effect(request: PositiveStrandAnnotationRequest | NegativeStrandAnnotationRequest) → AnnotationEffect | None

Return an annotation effect or None.

gain.effect_annotation.effect_checkers.intron module

class IntronicEffectChecker(splice_site_length: int = 2)

Bases: EffectChecker

Intonic effect checker class.

get_effect(request: PositiveStrandAnnotationRequest | NegativeStrandAnnotationRequest) → AnnotationEffect | None

Return an annotation effect or None.

gain.effect_annotation.effect_checkers.promoter module

class PromoterEffectChecker

Bases: EffectChecker

Promoter effect checker class.

The promoter is the window of promoter_len bases upstream of the first exon. The near base of the variant must lie in the window. A near base at distance promoter_len is inside, and at distance promoter_len + 1 it is outside. The distance of the base next to the exon is 1. A variant with any base inside an exon has no promoter effect.

create_effect(transcript_model: TranscriptModel) → AnnotationEffect

create_negative_strand_effect(transcript_model: TranscriptModel, variant: Variant) → AnnotationEffect

create_positive_strand_effect(transcript_model: TranscriptModel, variant: Variant) → AnnotationEffect

Create a positive strand promoter effect.

get_effect(request: PositiveStrandAnnotationRequest | NegativeStrandAnnotationRequest) → AnnotationEffect | None

Return a promoter effect or None.

gain.effect_annotation.effect_checkers.protein_change module

class ProteinChangeEffectChecker

Bases: EffectChecker

Protein change effect checker.

get_effect(request: PositiveStrandAnnotationRequest | NegativeStrandAnnotationRequest) → AnnotationEffect | None

Return an annotation effect or None.

mutation_type(aaref: list[str], aaalt: list[str]) → str

Check the mutation type.

gain.effect_annotation.effect_checkers.splice_site module

class SpliceSiteEffectChecker(splice_site_length: int = 2)

Bases: EffectChecker

Splice site effect checker class.

get_effect(request: PositiveStrandAnnotationRequest | NegativeStrandAnnotationRequest) → AnnotationEffect | None

Return an annotation effect or None.

gain.effect_annotation.effect_checkers.start_loss module

class StartLossEffectChecker

Bases: EffectChecker

Start loss effect checker class.

get_effect(request: PositiveStrandAnnotationRequest | NegativeStrandAnnotationRequest) → AnnotationEffect | None

Return an annotation effect or None.

gain.effect_annotation.effect_checkers.stop_loss module

class StopLossEffectChecker

Bases: EffectChecker

Stop loss effect checker class.

get_effect(request: PositiveStrandAnnotationRequest | NegativeStrandAnnotationRequest) → AnnotationEffect | None

Return an annotation effect or None.

gain.effect_annotation.effect_checkers.utr module

class UTREffectChecker

Bases: EffectChecker

UTR effect checker class.

check_stop_codon(request: PositiveStrandAnnotationRequest | NegativeStrandAnnotationRequest) → AnnotationEffect | None

Check for stop codon.

create_effect(request: PositiveStrandAnnotationRequest | NegativeStrandAnnotationRequest, strand: str) → AnnotationEffect | None

Create UTR effect.

create_utr_effect(request: PositiveStrandAnnotationRequest | NegativeStrandAnnotationRequest, strand: str) → AnnotationEffect

Create an UTR annotation effect.

get_effect(request: PositiveStrandAnnotationRequest | NegativeStrandAnnotationRequest) → AnnotationEffect | None

Return an annotation effect or None.

Module contents