torchcell.datamodels.schema.MarkerDeletionPerturbation

class MarkerDeletionPerturbation(*, systematic_gene_name: str, perturbed_gene_name: str, gene_namespace: Literal['scerevisiae_s288c_sgd_systematic', 'scerevisiae_cenpk113_7d_locus_tag', 'scerevisiae_peter2018_pangenome_orf', 'ecoli_k12_mg1655_bnumber', 'ecoli_k12_bw25113_locus_tag', 'pputida_kt2440_locus_tag', 'ecoli_b_rel606_locus_tag', 'ecoli_k12_w3110_refseq_locus_tag'] = 'scerevisiae_s288c_sgd_systematic', identifier_mapping: DerivedIdentifierMapping | None = None, provenance: str = 'engineered', state: str = 'absent', mechanism_so_id: str = 'SO:0000159', mechanism_so_name: str = 'deletion', description: str = 'Deletion via KanMX or NatMX gene replacement', perturbation_type: Literal['marker_deletion'] = 'marker_deletion', marker: str, deletion_type: str = 'marker', strain_id: str | None = None)[source]

Bases: DeletionPerturbation, ModelStrict

Gene deletion via a selectable/auxotrophic marker other than KanMX or NatMX.

Some drug-sensitized backgrounds delete a gene with a heterologous auxotrophic cassette – e.g. the Vanacloig 3DeltaAlpha background carries pdr3::KlURA3 and snq2::KlLEU2 (Kluyveromyces lactis URA3 / LEU2 markers). Same AXIS-1 state="absent" and SO deletion mechanism as the marker-specific leaves; marker names the exact cassette so the deletion is not mislabelled KanMX/NatMX.

model_config: ClassVar[ConfigDict] = {'extra': 'forbid', 'frozen': True}: Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].