dae.effect_annotation.effect_checkers package

Submodules

dae.effect_annotation.effect_checkers.coding module

class dae.effect_annotation.effect_checkers.coding.CodingEffectChecker[source]

Bases: EffectChecker

Coding effect checker class.

get_effect(request: PositiveStrandAnnotationRequest | NegativeStrandAnnotationRequest) → AnnotationEffect | None[source]

Return an annotation effect or None.

dae.effect_annotation.effect_checkers.effect_checker module

class dae.effect_annotation.effect_checkers.effect_checker.EffectChecker[source]

Bases: ABC

abstract get_effect(request: PositiveStrandAnnotationRequest | NegativeStrandAnnotationRequest) → AnnotationEffect | None[source]

Return an annotation effect or None.

dae.effect_annotation.effect_checkers.frame_shift module

class dae.effect_annotation.effect_checkers.frame_shift.FrameShiftEffectChecker[source]

Bases: EffectChecker

Frame shift effect checker class.

check_if_new_stop(request: PositiveStrandAnnotationRequest | NegativeStrandAnnotationRequest) → bool[source]

Check for a new stop codon.

check_stop_codon(request: PositiveStrandAnnotationRequest | NegativeStrandAnnotationRequest) → AnnotationEffect | None[source]

Check for stop codon.

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

Create frame-shift annotation effect.

get_effect(request: PositiveStrandAnnotationRequest | NegativeStrandAnnotationRequest) → AnnotationEffect | None[source]

Return an annotation effect or None.

dae.effect_annotation.effect_checkers.intron module

class dae.effect_annotation.effect_checkers.intron.IntronicEffectChecker(splice_site_length: int = 2)[source]

Bases: EffectChecker

Intonic effect checker class.

get_effect(request: PositiveStrandAnnotationRequest | NegativeStrandAnnotationRequest) → AnnotationEffect | None[source]

Return an annotation effect or None.

dae.effect_annotation.effect_checkers.promoter module

class dae.effect_annotation.effect_checkers.promoter.PromoterEffectChecker[source]

Bases: EffectChecker

Promoter effect checker class.

create_effect(transcript_model: TranscriptModel) → AnnotationEffect[source]
create_negative_strand_effect(transcript_model: TranscriptModel, variant: Variant) → AnnotationEffect[source]
create_positive_strand_effect(transcript_model: TranscriptModel, variant: Variant) → AnnotationEffect[source]

Create a positive strand promoter effect.

get_effect(request: PositiveStrandAnnotationRequest | NegativeStrandAnnotationRequest) → AnnotationEffect | None[source]

Return an annotation effect or None.

dae.effect_annotation.effect_checkers.protein_change module

class dae.effect_annotation.effect_checkers.protein_change.ProteinChangeEffectChecker[source]

Bases: EffectChecker

Protein change effect checker.

get_effect(request: PositiveStrandAnnotationRequest | NegativeStrandAnnotationRequest) → AnnotationEffect | None[source]

Return an annotation effect or None.

mutation_type(aaref: list[str | None], aaalt: list[str | None]) → str[source]

Check the mutation type.

dae.effect_annotation.effect_checkers.splice_site module

class dae.effect_annotation.effect_checkers.splice_site.SpliceSiteEffectChecker(splice_site_length: int = 2)[source]

Bases: EffectChecker

Splice site effect checker class.

get_effect(request: PositiveStrandAnnotationRequest | NegativeStrandAnnotationRequest) → AnnotationEffect | None[source]

Return an annotation effect or None.

dae.effect_annotation.effect_checkers.start_loss module

class dae.effect_annotation.effect_checkers.start_loss.StartLossEffectChecker[source]

Bases: EffectChecker

Start loss effect checker class.

get_effect(request: PositiveStrandAnnotationRequest | NegativeStrandAnnotationRequest) → AnnotationEffect | None[source]

Return an annotation effect or None.

dae.effect_annotation.effect_checkers.stop_loss module

class dae.effect_annotation.effect_checkers.stop_loss.StopLossEffectChecker[source]

Bases: EffectChecker

Stop loss effect checker class.

get_effect(request: PositiveStrandAnnotationRequest | NegativeStrandAnnotationRequest) → AnnotationEffect | None[source]

Return an annotation effect or None.

dae.effect_annotation.effect_checkers.utr module

class dae.effect_annotation.effect_checkers.utr.UTREffectChecker[source]

Bases: EffectChecker

UTR effect checker class.

check_stop_codon(request: PositiveStrandAnnotationRequest | NegativeStrandAnnotationRequest) → AnnotationEffect | None[source]

Check for stop codon.

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

Create UTR effect.

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

Create an UTR annotation effect.

get_effect(request: PositiveStrandAnnotationRequest | NegativeStrandAnnotationRequest) → AnnotationEffect | None[source]

Return an annotation effect or None.

Module contents