torchcell.data.DCellGraphProcessor

class DCellGraphProcessor[source]

Bases: GraphProcessor

Graph processor for DCell model that applies perturbations directly to the gene ontology graph.

This processor updates the gene ontology node states based on perturbations rather than deleting nodes from the graph before conversion.

process(cell_graph: HeteroData, phenotype_info: list[Phenotype | FitnessPhenotype | GeneInteractionPhenotype | GeneEssentialityPhenotype | GradedGeneEssentialityPhenotype | SyntheticLethalityPhenotype | SyntheticRescuePhenotype | CalMorphPhenotype | MicroarrayExpressionPhenotype | MicroarrayExpressionScorePhenotype | MicroarrayExpressionRatioPhenotype | InductionTimecourseExpressionPhenotype | RNASeqExpressionPhenotype | PseudobulkExpressionPhenotype | VisualScorePhenotype | MetabolitePhenotype | ProteinAbundancePhenotype | ProteinFoldChangePhenotype | EnvironmentResponsePhenotype | ProductTiterPhenotype | ProteinTurnoverPhenotype | ProteinSynthesisRatePhenotype | PhosphositeIntensityPhenotype | FluxPhenotype | PromoterActivityPhenotype | PooledSortSeqExpressionPhenotype | BiosensorFluorescencePhenotype | MorphologyPhenotype | MrnaNumberFractionPhenotype | FitnessContrastPhenotype | SingleCellExpressionPhenotype | LifeCyclePhenotype | GenomeArchitecturePhenotype], data: list[dict[str, Experiment | FitnessExperiment | GeneInteractionExperiment | GeneEssentialityExperiment | SyntheticLethalityExperiment | SyntheticRescueExperiment | CalMorphExperiment | MicroarrayExpressionExperiment | MicroarrayExpressionScoreExperiment | MicroarrayExpressionRatioExperiment | InductionTimecourseExpressionExperiment | RNASeqExpressionExperiment | PseudobulkExpressionExperiment | VisualScoreExperiment | MetaboliteExperiment | ProteinAbundanceExperiment | ProteinFoldChangeExperiment | EnvironmentResponseExperiment | StrainEnvironmentResponseExperiment | SegregantGrowthExperiment | SegregantPerturbationExperiment | ProductTiterExperiment | ProteinTurnoverExperiment | ProteinSynthesisRateExperiment | FluxExperiment | PromoterActivityExperiment | PooledSortSeqExpressionExperiment | BiosensorFluorescenceExperiment | GradedGeneEssentialityExperiment | PhosphositeIntensityExperiment | MorphologyExperiment | MrnaNumberFractionExperiment | FitnessContrastExperiment | SegregantExpressionExperiment | LifeCycleExperiment | PseudobulkUmiCountExperiment | GenomeArchitectureExperiment | ExperimentReference | FitnessExperimentReference | GeneInteractionExperimentReference | GeneEssentialityExperimentReference | SyntheticLethalityExperimentReference | SyntheticRescueExperimentReference | CalMorphExperimentReference | MicroarrayExpressionExperimentReference | MicroarrayExpressionScoreExperimentReference | MicroarrayExpressionRatioExperimentReference | InductionTimecourseExpressionExperimentReference | RNASeqExpressionExperimentReference | PseudobulkExpressionExperimentReference | VisualScoreExperimentReference | MetaboliteExperimentReference | ProteinAbundanceExperimentReference | ProteinFoldChangeExperimentReference | EnvironmentResponseExperimentReference | StrainEnvironmentResponseExperimentReference | SegregantGrowthExperimentReference | SegregantPerturbationExperimentReference | ProductTiterExperimentReference | ProteinTurnoverExperimentReference | ProteinSynthesisRateExperimentReference | FluxExperimentReference | PromoterActivityExperimentReference | PooledSortSeqExpressionExperimentReference | BiosensorFluorescenceExperimentReference | GradedGeneEssentialityExperimentReference | PhosphositeIntensityExperimentReference | MorphologyExperimentReference | MrnaNumberFractionExperimentReference | FitnessContrastExperimentReference | SegregantExpressionExperimentReference | LifeCycleExperimentReference | PseudobulkUmiCountExperimentReference | GenomeArchitectureExperimentReference]]) → HeteroData[source]: Apply perturbations to the gene ontology graph and attach phenotypes.