Index

A

absentOrNone() (in module dragonn.synthetic.util) AbstractApplySingleMutationFromSet (class in dragonn.synthetic.synthetic) AbstractBackgroundGenerator (class in dragonn.synthetic.synthetic) AbstractEmbeddable (class in dragonn.synthetic.synthetic) AbstractEmbeddableGenerator (class in dragonn.synthetic.synthetic) AbstractEmbedder (class in dragonn.synthetic.synthetic) AbstractLoadedMotifs (class in dragonn.synthetic.synthetic) AbstractPositionGenerator (class in dragonn.synthetic.synthetic) AbstractPriorEmbeddedThings (class in dragonn.synthetic.synthetic) AbstractQuantityGenerator (class in dragonn.synthetic.synthetic) AbstractSequenceSetGenerator (class in dragonn.synthetic.synthetic) AbstractSetOfMutations (class in dragonn.synthetic.synthetic) AbstractSingleSequenceGenerator (class in dragonn.synthetic.synthetic) AbstractSubstringGenerator (class in dragonn.synthetic.synthetic) AbstractTransformation (class in dragonn.synthetic.synthetic) add_letter_to_axis() (in module dragonn.plot) add_letters_to_axis() (in module dragonn.plot) addArguments() (in module dragonn.synthetic.util) addAttribute() (dragonn.synthetic.util.Entity method) addDictionary() (in module dragonn.synthetic.util) addEmbedding() (dragonn.synthetic.synthetic.AbstractPriorEmbeddedThings method) (dragonn.synthetic.synthetic.PriorEmbeddedThings_numpyArrayBacked method) AdditionalInfo (class in dragonn.synthetic.synthetic) addKey() (dragonn.synthetic.util.TitledMapping method) addRow() (dragonn.synthetic.pwm.PWM method) (dragonn.synthetic.util.Titled2DMatrix method) addToParser() (dragonn.synthetic.util.ArgParseArgument method) AllEmbedders (class in dragonn.synthetic.synthetic) appendNewline() (in module dragonn.synthetic.fileProcessing)

applyMutation() (dragonn.synthetic.pwm.Mutation method) argNamePrefix() (dragonn.synthetic.util.ArgumentToAdd method) ArgParseArgument (class in dragonn.synthetic.util) args (dragonn.synthetic.util.ArgsAndKwargs attribute) ArgsAndKwargs (class in dragonn.synthetic.util) ArgumentToAdd (class in dragonn.synthetic.util) ArrArgument (class in dragonn.synthetic.util) arrayEquals() (in module dragonn.synthetic.util) ArrOfFileNamesArgument (class in dragonn.synthetic.util) arrToDict() (in module dragonn.synthetic.util) assertAllOrNone() (in module dragonn.synthetic.util) assertArrayElementsEqual() (in module dragonn.synthetic.util) assertAtLeastOneSet() (in module dragonn.synthetic.util) assertAttributesHaveTheSameLengths() (in module dragonn.synthetic.util) assertDoesNotHaveAttributes() (in module dragonn.synthetic.util) assertHasAttributes() (in module dragonn.synthetic.util) assertIsType() (in module dragonn.synthetic.util) assertLessThanOrEqual() (in module dragonn.synthetic.util) assertMutuallyExclusiveAttributes() (in module dragonn.synthetic.util) assertParameterIrrelevantForMode() (in module dragonn.synthetic.fileProcessing) assertParameterNecessaryForMode() (in module dragonn.synthetic.fileProcessing) augmentArgparseKwargsHelpWithDefault() (in module dragonn.synthetic.util) auPRC() (in module dragonn.metrics) (in module dragonn.synthetic.util) auPRG() (in module dragonn.metrics) auROC() (in module dragonn.metrics) autovivisect() (in module dragonn.synthetic.util) avgNumpyArrays() (in module dragonn.synthetic.util)

B

BackupForWriteFileHandle (class in dragonn.synthetic.fileProcessing) balanced_accuracy() (in module dragonn.metrics) BernoulliQuantityGenerator (class in dragonn.synthetic.synthetic)

BestHitPwm (class in dragonn.synthetic.synthetic) BestHitPwmFromLoadedMotifs (class in dragonn.synthetic.synthetic) BooleanArgument (class in dragonn.synthetic.util)

C

calc_auprg() (in module dragonn.prg) canEmbed() (dragonn.synthetic.synthetic.AbstractEmbeddable method) (dragonn.synthetic.synthetic.AbstractPriorEmbeddedThings method) (dragonn.synthetic.synthetic.PairEmbeddable method) (dragonn.synthetic.synthetic.PairEmbeddable_General method) (dragonn.synthetic.synthetic.PriorEmbeddedThings_numpyArrayBacked method) (dragonn.synthetic.synthetic.StringEmbeddable method) chainFunctions() (in module dragonn.synthetic.util) check_pid() (in module dragonn.synthetic.util) checkForAttributes() (in module dragonn.synthetic.util) ChooseMutationAtRandom (class in dragonn.synthetic.synthetic) ChooseValueFromASet (class in dragonn.synthetic.synthetic) ClassificationResult (class in dragonn.metrics) close() (dragonn.synthetic.fileProcessing.BackupForWriteFileHandle method) (dragonn.synthetic.util.TeeOutputStreams method) closed (dragonn.synthetic.util.TeeOutputStreams attribute) combineEnums() (in module dragonn.synthetic.util) computeBestHitGivenMatrix() (dragonn.synthetic.pwm.PWM method) computeConfusionMatrix() (in module dragonn.synthetic.util) computeCooccurence() (in module dragonn.synthetic.util) computeRunningWindowMax() (in module dragonn.synthetic.util) computeRunningWindowMaxActivation_2d() (in module dragonn.synthetic.util) computeRunningWindowOneOverMaxActivation_2d() (in module dragonn.synthetic.util)

computeRunningWindowOneOverTwoNorm_2d() (in module dragonn.synthetic.util) computeRunningWindowOp() (in module dragonn.synthetic.util) computeRunningWindowSum() (in module dragonn.synthetic.util) computeRunningWindowSum_2d() (in module dragonn.synthetic.util) computeRunningWindowTwoNorm_2d() (in module dragonn.synthetic.util) computeSingleBpMutationEffects() (dragonn.synthetic.pwm.PWM method) computeSingleBpMutationEffectsGivenMatrix() (dragonn.synthetic.pwm.PWM method) concatenateFiles() (in module dragonn.synthetic.fileProcessing) concatenateFiles_preprocess() (in module dragonn.synthetic.fileProcessing) convex_hull() (in module dragonn.prg) CoreFileNameArgument (class in dragonn.synthetic.util) create_prg_curve() (in module dragonn.prg) create_segments() (in module dragonn.prg) CROSSC_NORMFUNC (in module dragonn.synthetic.util) crossCorrelateArraysLengthwise() (in module dragonn.synthetic.util) crossCorrelation_2d() (in module dragonn.synthetic.util)

D

Data (class in dragonn.tutorial_utils) DecisionTree (class in dragonn.models) deeplift() (dragonn.models.SequenceDNN method) DefaultNameMixin (class in dragonn.synthetic.synthetic) defaultTabSeppd() (in module dragonn.synthetic.fileProcessing) defaultTransformation() (in module dragonn.synthetic.util) defaultWhitespaceSeppd() (in module dragonn.synthetic.fileProcessing) dict2str() (in module dragonn.synthetic.util) DiscreteDistribution (class in dragonn.synthetic.util) divideByPerPositionRange() (in module dragonn.synthetic.util) doesNotWorkForMultithreading_redirectStdout() (in module dragonn.synthetic.util) doPCAonFile() (in module dragonn.synthetic.util) dragonn (module)

dragonn.metrics (module) dragonn.models (module) dragonn.plot (module) dragonn.prg (module) dragonn.simulations (module) dragonn.synthetic (module) dragonn.synthetic.fileProcessing (module) dragonn.synthetic.pwm (module) dragonn.synthetic.synthetic (module) dragonn.synthetic.util (module) dragonn.tutorial_utils (module) dragonn.utils (module)

E

embed() (dragonn.synthetic.synthetic.AbstractEmbedder method) EmbeddableEmbedder (class in dragonn.synthetic.synthetic) Embedding (class in dragonn.synthetic.synthetic) EmbedInABackground (class in dragonn.synthetic.synthetic) embedInBackgroundStringArr() (dragonn.synthetic.synthetic.AbstractEmbeddable method) (dragonn.synthetic.synthetic.PairEmbeddable method) (dragonn.synthetic.synthetic.PairEmbeddable_General method) (dragonn.synthetic.synthetic.StringEmbeddable method) encode_sequence_into_fasta_file() (dragonn.models.gkmSVM static method)

Entity (class in dragonn.synthetic.util) enum() (in module dragonn.synthetic.util) enumerate_skipFirst() (in module dragonn.synthetic.util) executeAsSystemCall() (in module dragonn.synthetic.util) executeForAllFilesInDirectory() (in module dragonn.synthetic.util) exterior (dragonn.plot.Polygon attribute)

F

FastaIterator (class in dragonn.synthetic.fileProcessing) FileNameParts (class in dragonn.synthetic.fileProcessing) FileReader (class in dragonn.synthetic.fileProcessing) finalise() (dragonn.synthetic.pwm.PWM method) FixedQuantityGenerator (class in dragonn.synthetic.synthetic) FixedSubstringGenerator (class in dragonn.synthetic.synthetic)

floatRange() (in module dragonn.synthetic.util) flush() (dragonn.synthetic.util.TeeOutputStreams method) formatDictAsArgsString() (in module dragonn.synthetic.util) formattedJsonDump() (in module dragonn.synthetic.util) fracToRainbowColour() (in module dragonn.synthetic.util) fromString() (dragonn.synthetic.synthetic.Embedding class method) (dragonn.synthetic.synthetic.StringEmbeddable class method)

G

generateBackground() (dragonn.synthetic.synthetic.AbstractBackgroundGenerator method) (dragonn.synthetic.synthetic.RepeatedSubstringBackgroundGenerator method) GeneratedSequence (class in dragonn.synthetic.synthetic) generateEmbeddable() (dragonn.synthetic.synthetic.AbstractEmbeddableGenerator method) (dragonn.synthetic.synthetic.PairEmbeddableGenerator method) (dragonn.synthetic.synthetic.PairEmbeddableGenerator_General method) (dragonn.synthetic.synthetic.SubstringEmbeddableGenerator method) generateLabels() (dragonn.synthetic.synthetic.LabelGenerator method) generatePos() (dragonn.synthetic.synthetic.AbstractPositionGenerator method) generateQuantity() (dragonn.synthetic.synthetic.AbstractQuantityGenerator method) (dragonn.synthetic.synthetic.BernoulliQuantityGenerator method) (dragonn.synthetic.synthetic.ChooseValueFromASet method) (dragonn.synthetic.synthetic.FixedQuantityGenerator method) (dragonn.synthetic.synthetic.MinMaxWrapper method) (dragonn.synthetic.synthetic.PoissonQuantityGenerator method) (dragonn.synthetic.synthetic.UniformIntegerGenerator method) (dragonn.synthetic.synthetic.ZeroInflater method) generateSequence() (dragonn.synthetic.synthetic.AbstractSingleSequenceGenerator method) (dragonn.synthetic.synthetic.EmbedInABackground method) GenerateSequenceNTimes (class in dragonn.synthetic.synthetic) generateSequences() (dragonn.synthetic.synthetic.AbstractSequenceSetGenerator method) (dragonn.synthetic.synthetic.GenerateSequenceNTimes method) generateString() (in module dragonn.synthetic.synthetic) generateString_zeroOrderMarkov() (in module dragonn.synthetic.synthetic) generateSubstring() (dragonn.synthetic.synthetic.AbstractSubstringGenerator method) (dragonn.synthetic.synthetic.BestHitPwm method) (dragonn.synthetic.synthetic.FixedSubstringGenerator method) (dragonn.synthetic.synthetic.PwmSampler method) (dragonn.synthetic.synthetic.ReverseComplementWrapper method) (dragonn.synthetic.synthetic.SampleFromDiscreteDistributionSubstringGenerator method) (dragonn.synthetic.synthetic.TransformedSubstringGenerator method) geom_type (dragonn.plot.Polygon attribute) get_available_simulations() (in module dragonn.tutorial_utils) get_distribution() (in module dragonn.simulations) get_motif_scores() (in module dragonn.utils) get_point() (in module dragonn.prg) get_pssm_scores() (in module dragonn.utils) get_sequence_filters() (dragonn.models.SequenceDNN method) get_SequenceDNN() (in module dragonn.tutorial_utils) get_simulation_data() (in module dragonn.tutorial_utils) get_simulation_function() (in module dragonn.tutorial_utils) getAllPossibleSubsets() (in module dragonn.synthetic.util) getArrForKey() (dragonn.synthetic.util.TitledMapping method) getAttribute() (dragonn.synthetic.util.Entity method) GetBest (class in dragonn.synthetic.util) getBest() (dragonn.synthetic.util.GetBest method) (in module dragonn.synthetic.util) GetBest_Max (class in dragonn.synthetic.util) GetBest_Min (class in dragonn.synthetic.util) getBestHit() (dragonn.synthetic.pwm.PWM method) getBestLengthwiseCrossCorrelationOfArrays() (in module dragonn.synthetic.util) getBestObj() (dragonn.synthetic.util.GetBest method) getBestVal() (dragonn.synthetic.util.GetBest method) getClassName() (dragonn.synthetic.synthetic.AbstractApplySingleMutationFromSet method) (dragonn.synthetic.synthetic.ChooseMutationAtRandom method) getCol() (dragonn.synthetic.util.TitledArr method) getCoreFileName() (in module dragonn.synthetic.fileProcessing) getCoreFileNameAndExtension() (dragonn.synthetic.fileProcessing.FileNameParts method) getCoreFileNameWithTransformation() (dragonn.synthetic.fileProcessing.FileNameParts method) getCoreTitledMappingAction() (in module dragonn.synthetic.fileProcessing)

getDateTimeString() (in module dragonn.synthetic.util) getDefaultName() (dragonn.synthetic.synthetic.DefaultNameMixin method) getDescription() (dragonn.synthetic.synthetic.AbstractEmbeddable method) (dragonn.synthetic.synthetic.PairEmbeddable method) (dragonn.synthetic.synthetic.PairEmbeddable_General method) (dragonn.synthetic.synthetic.StringEmbeddable method) getEmbeddings() (dragonn.synthetic.synthetic.AbstractPriorEmbeddedThings method) (dragonn.synthetic.synthetic.PriorEmbeddedThings_numpyArrayBacked method) getEmbeddingsFromString() (in module dragonn.synthetic.synthetic) getErrorTraceback() (in module dragonn.synthetic.util) getExtremeN() (in module dragonn.synthetic.util) getFileHandle() (in module dragonn.synthetic.fileProcessing) getFileNameParts() (in module dragonn.synthetic.fileProcessing) getFileNamePieceFromOptions() (in module dragonn.synthetic.pwm) (in module dragonn.synthetic.synthetic) getFileNameWithTransformation() (dragonn.synthetic.fileProcessing.FileNameParts method) getFilePathWithTransformation() (dragonn.synthetic.fileProcessing.FileNameParts method) getFromEnum() (in module dragonn.synthetic.util) getFullPath() (dragonn.synthetic.fileProcessing.FileNameParts method) getGenerationOption() (in module dragonn.synthetic.synthetic) getIntervals() (in module dragonn.synthetic.util) getJsonableObject() (dragonn.synthetic.synthetic.AbstractApplySingleMutationFromSet method) (dragonn.synthetic.synthetic.AbstractBackgroundGenerator method) (dragonn.synthetic.synthetic.AbstractEmbeddableGenerator method) (dragonn.synthetic.synthetic.AbstractEmbedder method) (dragonn.synthetic.synthetic.AbstractLoadedMotifs method) (dragonn.synthetic.synthetic.AbstractPositionGenerator method) (dragonn.synthetic.synthetic.AbstractQuantityGenerator method) (dragonn.synthetic.synthetic.AbstractSequenceSetGenerator method) (dragonn.synthetic.synthetic.AbstractSetOfMutations method) (dragonn.synthetic.synthetic.AbstractSingleSequenceGenerator method) (dragonn.synthetic.synthetic.AbstractSubstringGenerator method) (dragonn.synthetic.synthetic.AbstractTransformation method) (dragonn.synthetic.synthetic.AllEmbedders method) (dragonn.synthetic.synthetic.BernoulliQuantityGenerator method) (dragonn.synthetic.synthetic.BestHitPwm method) (dragonn.synthetic.synthetic.BestHitPwmFromLoadedMotifs method) (dragonn.synthetic.synthetic.ChooseValueFromASet method) (dragonn.synthetic.synthetic.EmbedInABackground method) (dragonn.synthetic.synthetic.EmbeddableEmbedder method) (dragonn.synthetic.synthetic.FixedQuantityGenerator method) (dragonn.synthetic.synthetic.FixedSubstringGenerator method) (dragonn.synthetic.synthetic.GenerateSequenceNTimes method) (dragonn.synthetic.synthetic.InsideCentralBp method) (dragonn.synthetic.synthetic.MinMaxWrapper method) (dragonn.synthetic.synthetic.OutsideCentralBp method) (dragonn.synthetic.synthetic.PairEmbeddableGenerator method) (dragonn.synthetic.synthetic.PairEmbeddableGenerator_General method) (dragonn.synthetic.synthetic.PoissonQuantityGenerator method) (dragonn.synthetic.synthetic.PwmSampler method) (dragonn.synthetic.synthetic.PwmSamplerFromLoadedMotifs method) (dragonn.synthetic.synthetic.RandomSubsetOfEmbedders method) (dragonn.synthetic.synthetic.RepeatedEmbedder method) (dragonn.synthetic.synthetic.RepeatedSubstringBackgroundGenerator method) (dragonn.synthetic.synthetic.ReverseComplementWrapper method) (dragonn.synthetic.synthetic.RevertToReference method) (dragonn.synthetic.synthetic.SampleFromDiscreteDistributionSubstringGenerator method) (dragonn.synthetic.synthetic.SubstringEmbeddableGenerator method) (dragonn.synthetic.synthetic.TopNMutationsFromPwmRelativeToBestHit method) (dragonn.synthetic.synthetic.TopNMutationsFromPwmRelativeToBestHit_FromLoadedMotifs method) (dragonn.synthetic.synthetic.TransformedSubstringGenerator method) (dragonn.synthetic.synthetic.UniformIntegerGenerator method) (dragonn.synthetic.synthetic.UniformPositionGenerator method) (dragonn.synthetic.synthetic.XOREmbedder method) (dragonn.synthetic.synthetic.ZeroInflater method) getLoadPwmArgparse() (in module dragonn.synthetic.pwm) getLogOddsRows() (dragonn.synthetic.pwm.PWM method) getMaxIndex() (in module dragonn.synthetic.util) getMutationsArr() (dragonn.synthetic.synthetic.AbstractSetOfMutations method) getNextLine() (dragonn.synthetic.fileProcessing.FileReader method) getNthInterval() (in module dragonn.synthetic.util) getNumOccupiedPos() (dragonn.synthetic.synthetic.AbstractPriorEmbeddedThings method) (dragonn.synthetic.synthetic.PriorEmbeddedThings_numpyArrayBacked method) getParentArgparse() (in module dragonn.synthetic.synthetic) getPwm() (dragonn.synthetic.synthetic.AbstractLoadedMotifs method) getRandomString() (in module dragonn.synthetic.util) getReadPwmAction() (dragonn.synthetic.synthetic.AbstractLoadedMotifs method) (dragonn.synthetic.synthetic.LoadedEncodeMotifs method) getReadPwmAction_encodeMotifs() (in module dragonn.synthetic.pwm) getRows() (dragonn.synthetic.pwm.PWM method) getSingleton() (in module dragonn.synthetic.util) getSpecfiedPwmFromPwmFile() (in module dragonn.synthetic.pwm) getStackTrace() (in module dragonn.synthetic.util) getTempDir() (in module dragonn.synthetic.util) getTitledArrForKey() (dragonn.synthetic.util.TitledMapping method) getTitleOfFile() (in module dragonn.synthetic.fileProcessing) getTotalPos() (dragonn.synthetic.synthetic.AbstractPriorEmbeddedThings method) (dragonn.synthetic.synthetic.PriorEmbeddedThings_numpyArrayBacked method) gkmSVM (class in dragonn.models)

H

hasAttribute() (dragonn.synthetic.util.Entity method)

I

IgnoreNumpyErrors (class in dragonn.metrics) imageToSeq() (in module dragonn.synthetic.util) in_silico_mutagenesis() (dragonn.models.SequenceDNN method) insert_point() (in module dragonn.prg) InsideCentralBp (class in dragonn.synthetic.synthetic) inspect_SequenceDNN() (in module dragonn.tutorial_utils) integrityChecks() (dragonn.synthetic.fileProcessing.SubsetOfColumnsToUseOptions method) interiors (dragonn.plot.Polygon attribute) interpret_SequenceDNN_distributed() (in module dragonn.tutorial_utils) interpret_SequenceDNN_integrative() (in module dragonn.tutorial_utils)

intersects() (in module dragonn.synthetic.util) invertIndices() (in module dragonn.synthetic.util) invertPermutation() (in module dragonn.synthetic.util) isBetter() (dragonn.synthetic.util.GetBest method) (dragonn.synthetic.util.GetBest_Max method) (dragonn.synthetic.util.GetBest_Min method) (in module dragonn.synthetic.util) isBetterOrEqual() (in module dragonn.synthetic.util) isInTrace() (dragonn.synthetic.synthetic.AdditionalInfo method) IsInTraceLabelGenerator (class in dragonn.synthetic.synthetic) isNumpy() (in module dragonn.synthetic.util) iter_skipFirst() (in module dragonn.synthetic.util) IterableFromDict (class in dragonn.synthetic.util)

K

keyPresenceCheck() (dragonn.synthetic.util.TitledMapping method)

kwargs (dragonn.synthetic.util.ArgsAndKwargs attribute)

L

LabelGenerator (class in dragonn.synthetic.synthetic) lambdaMaker_dictionaryFromLine() (in module dragonn.synthetic.fileProcessing) lambdaMaker_getAtPosition() (in module dragonn.synthetic.fileProcessing) lambdaMaker_insertPrefixIntoFileName() (in module dragonn.synthetic.fileProcessing)

lambdaMaker_insertSuffixIntoFileName() (in module dragonn.synthetic.fileProcessing) linecount() (in module dragonn.synthetic.util) LoadedEncodeMotifs (class in dragonn.synthetic.synthetic)

M

makeChromStartEnd() (in module dragonn.synthetic.util) MinMaxWrapper (class in dragonn.synthetic.synthetic) Model (class in dragonn.models) model_file (dragonn.models.gkmSVM attribute) motif_density() (in module dragonn.simulations)

motif_names (dragonn.tutorial_utils.Data attribute) MotifScoreRNN (class in dragonn.models) multiprocessing_map_printProgress() (in module dragonn.synthetic.util) Mutation (class in dragonn.synthetic.pwm)

N

negative_accuracy() (in module dragonn.metrics) next() (dragonn.synthetic.fileProcessing.FastaIterator method) (dragonn.synthetic.util.IterableFromDict method) (dragonn.synthetic.util.TitledMappingIterator method) normaliseByRowsAndColumns() (in module dragonn.synthetic.util) normaliseEntriesByMeanAndSdev() (in module dragonn.synthetic.util) normaliseEntriesByMeanAndTwoNorm() (in module dragonn.synthetic.util) normaliseEntriesBySdev() (in module dragonn.synthetic.util)

normaliseEntriesByTwoNorm() (in module dragonn.synthetic.util) normaliseEntriesZeroToOne() (in module dragonn.synthetic.util) normaliseRows() (dragonn.synthetic.util.Titled2DMatrix method) normaliseRowsByMeanAndSdev() (in module dragonn.synthetic.util) normaliseRowsByMeanAndSdev_firstFourSeq() (in module dragonn.synthetic.util) npArrayIfList() (in module dragonn.synthetic.util)

O

objectFromArgsAndKwargs() (in module dragonn.synthetic.util) objectFromArgsAndKwargsFromYaml() (in module dragonn.synthetic.util) on_epoch_end() (dragonn.models.SequenceDNN.LossHistory method) (dragonn.models.SequenceDNN.PrintMetrics method) one_hot_encode() (in module dragonn.utils)

Options (class in dragonn.synthetic.util) OutsideCentralBp (class in dragonn.synthetic.synthetic) overrides() (in module dragonn.synthetic.util)

P

PairEmbeddable (class in dragonn.synthetic.synthetic) PairEmbeddable_General (class in dragonn.synthetic.synthetic) PairEmbeddableGenerator (class in dragonn.synthetic.synthetic) PairEmbeddableGenerator_General (class in dragonn.synthetic.synthetic) parentLengthAssertionCheck() (dragonn.synthetic.pwm.Mutation method) parseJsonFile() (in module dragonn.synthetic.util) parseMultipleYamlFiles() (in module dragonn.synthetic.util) parseYamlFile() (in module dragonn.synthetic.util) parseYamlFileHandle() (in module dragonn.synthetic.util) peekAtFirstLineOfFile() (in module dragonn.synthetic.fileProcessing) performActionInBatchesOnEachLineOfFile() (in module dragonn.synthetic.fileProcessing) performActionOnEachLineOfFile() (in module dragonn.synthetic.fileProcessing) PERPOS_NORMFUNC (in module dragonn.synthetic.util) plot_bases() (in module dragonn.plot) plot_motif() (in module dragonn.plot) plot_motifs() (in module dragonn.tutorial_utils) plot_pr() (in module dragonn.prg) plot_prg() (in module dragonn.prg) plot_pwm() (in module dragonn.plot) plot_sequence_filters() (in module dragonn.tutorial_utils) plot_SequenceDNN_layer_outputs() (in module dragonn.tutorial_utils) plotPRC() (in module dragonn.synthetic.util) PoissonQuantityGenerator (class in dragonn.synthetic.synthetic) Polygon (class in dragonn.plot) PolygonPatch() (in module dragonn.plot)

PolygonPath() (in module dragonn.plot) positive_accuracy() (in module dragonn.metrics) precision() (in module dragonn.prg) precision_gain() (in module dragonn.prg) predict() (dragonn.models.DecisionTree method) (dragonn.models.Model method) (dragonn.models.MotifScoreRNN method) (dragonn.models.SVC method) (dragonn.models.SequenceDNN method) (dragonn.models.gkmSVM method) presentAndNotNone() (in module dragonn.synthetic.util) presentAndNotNoneOrFalse() (in module dragonn.synthetic.util) print_available_simulations() (in module dragonn.tutorial_utils) print_simulation_info() (in module dragonn.tutorial_utils) printAttributes() (in module dragonn.synthetic.util) printCoordinatesForLabelSubsets() (in module dragonn.synthetic.util) printProgress() (in module dragonn.synthetic.fileProcessing) printRegionIds() (in module dragonn.synthetic.util) printSequences() (in module dragonn.synthetic.synthetic) printSequencesTransformationPosNeg() (in module dragonn.synthetic.synthetic) printToFile() (dragonn.synthetic.util.Titled2DMatrix method) (dragonn.synthetic.util.TitledMapping method) PriorEmbeddedThings_numpyArrayBacked (class in dragonn.synthetic.synthetic) process() (dragonn.synthetic.util.GetBest method) processLine() (in module dragonn.synthetic.fileProcessing) processOptions() (in module dragonn.synthetic.pwm) PWM (class in dragonn.synthetic.pwm) PwmSampler (class in dragonn.synthetic.synthetic) PwmSamplerFromLoadedMotifs (class in dragonn.synthetic.synthetic) PwmScore (class in dragonn.synthetic.pwm)

R

RandomForest (class in dragonn.models) randomlySampleFromArr() (in module dragonn.synthetic.util) RandomSubsetOfEmbedders (class in dragonn.synthetic.synthetic) read2DMatrix() (in module dragonn.synthetic.fileProcessing) readColIntoArr() (in module dragonn.synthetic.fileProcessing) readMultilineRawInput() (in module dragonn.synthetic.util) readPwm() (in module dragonn.synthetic.pwm) readRowsIntoArr() (in module dragonn.synthetic.fileProcessing) readTitledMapping() (in module dragonn.synthetic.fileProcessing) recall() (in module dragonn.prg) recall_at_precision_threshold() (in module dragonn.metrics) recall_gain() (in module dragonn.prg) redirectStdoutToString() (in module dragonn.synthetic.util)

RepeatedEmbedder (class in dragonn.synthetic.synthetic) RepeatedSubstringBackgroundGenerator (class in dragonn.synthetic.synthetic) restore() (dragonn.synthetic.fileProcessing.BackupForWriteFileHandle method) reverse_complement() (in module dragonn.utils) reverse_enumerate() (in module dragonn.synthetic.util) reverseComplement() (in module dragonn.synthetic.util) ReverseComplementWrapper (class in dragonn.synthetic.synthetic) revert() (dragonn.synthetic.pwm.Mutation method) RevertToReference (class in dragonn.synthetic.synthetic) roundToNearest() (in module dragonn.synthetic.util) rowNormalise() (in module dragonn.synthetic.util) runningWindowOneOver() (in module dragonn.synthetic.util)

S

sampleFromDiscreteDistribution() (in module dragonn.synthetic.util) SampleFromDiscreteDistributionSubstringGenerator (class in dragonn.synthetic.synthetic) sampleFromNumSteps() (in module dragonn.synthetic.util) sampleFromProbsArr() (in module dragonn.synthetic.util) sampleFromPwm() (dragonn.synthetic.pwm.PWM method) sampleFromRangeWithStepSize() (in module dragonn.synthetic.util) sampleIndexWithinRegionOfLength() (in module dragonn.synthetic.synthetic) sampleNinstancesFromDiscreteDistribution() (in module dragonn.synthetic.util) sampleWithoutReplacement() (in module dragonn.synthetic.util) score() (dragonn.models.Model method) scoreSeq() (dragonn.synthetic.pwm.PWM method) scoreSeqAtPos() (dragonn.synthetic.pwm.PWM method) selectMutation() (dragonn.synthetic.synthetic.AbstractApplySingleMutationFromSet method) (dragonn.synthetic.synthetic.ChooseMutationAtRandom method) sendEmail() (in module dragonn.synthetic.util) sendEmails() (in module dragonn.synthetic.util) seqTo2Dimage() (in module dragonn.synthetic.util) seqTo2DImages_fillInArray() (in module dragonn.synthetic.util) SequenceDNN (class in dragonn.models) SequenceDNN.LossHistory (class in dragonn.models) SequenceDNN.PrintMetrics (class in dragonn.models) SequenceDNN_learning_curve() (in module dragonn.tutorial_utils) setBackground() (dragonn.synthetic.pwm.PWM method) setCol() (dragonn.synthetic.util.TitledArr method) setColNames() (dragonn.synthetic.util.Titled2DMatrix method) setOfSeqsTo2Dimages() (in module dragonn.synthetic.util) shuffleArray() (in module dragonn.synthetic.util) simple_motif_embedding() (in module dragonn.simulations) simpleDictionaryFromFile() (in module dragonn.synthetic.fileProcessing)

simulate_differential_accessibility() (in module dragonn.simulations) simulate_heterodimer_grammar() (in module dragonn.simulations) simulate_motif_counting() (in module dragonn.simulations) simulate_motif_density_localization() (in module dragonn.simulations) simulate_multi_motif_embedding() (in module dragonn.simulations) simulate_single_motif_detection() (in module dragonn.simulations) sort_scores() (in module dragonn.prg) sortByLabels() (in module dragonn.synthetic.util) SparseArrFromDict (class in dragonn.synthetic.util) splitByDelimiter() (in module dragonn.synthetic.fileProcessing) splitByTabs() (in module dragonn.synthetic.fileProcessing) splitChromStartEnd() (in module dragonn.synthetic.util) splitIgnoringQuotes() (in module dragonn.synthetic.util) splitIntegerIntoProportions() (in module dragonn.synthetic.util) splitLinesIntoOtherFiles() (in module dragonn.synthetic.fileProcessing) SplitNames (in module dragonn.synthetic.util) standardize_polygons_str() (in module dragonn.plot) StringEmbeddable (class in dragonn.synthetic.synthetic) stringToFloat() (in module dragonn.synthetic.fileProcessing) stringToInt() (in module dragonn.synthetic.fileProcessing) submitProcess() (in module dragonn.synthetic.util) SubsetOfColumnsToUseOptions (class in dragonn.synthetic.fileProcessing) SubstringEmbeddableGenerator (class in dragonn.synthetic.synthetic) SubstringEmbedder (class in dragonn.synthetic.synthetic) sumAbsDifferences() (in module dragonn.synthetic.util) sumNumpyArrays() (in module dragonn.synthetic.util) SVC (class in dragonn.models) swapIndices() (in module dragonn.synthetic.util)

T

TeeOutputStreams (class in dragonn.synthetic.util) test() (dragonn.models.Model method) (in module dragonn.prg) test_SequenceDNN() (in module dragonn.tutorial_utils) throwErrorIfUnequalSets() (in module dragonn.synthetic.util) titleColumnToIndex() (in module dragonn.synthetic.fileProcessing) Titled2DMatrix (class in dragonn.synthetic.util) TitledArr (class in dragonn.synthetic.util) TitledMapping (class in dragonn.synthetic.util) TitledMappingIterator (class in dragonn.synthetic.util) TopNMutationsFromPwmRelativeToBestHit (class in dragonn.synthetic.synthetic)

TopNMutationsFromPwmRelativeToBestHit_FromLoadedMotifs (class in dragonn.synthetic.synthetic) train() (dragonn.models.DecisionTree method) (dragonn.models.Model method) (dragonn.models.MotifScoreRNN method) (dragonn.models.SVC method) (dragonn.models.SequenceDNN method) (dragonn.models.gkmSVM method) train_SequenceDNN() (in module dragonn.tutorial_utils) transform() (dragonn.synthetic.synthetic.AbstractApplySingleMutationFromSet method) (dragonn.synthetic.synthetic.AbstractTransformation method) (dragonn.synthetic.synthetic.RevertToReference method) (dragonn.synthetic.util.ArgumentToAdd method) (dragonn.synthetic.util.ArrArgument method) (dragonn.synthetic.util.BooleanArgument method) (dragonn.synthetic.util.CoreFileNameArgument method) TransformedSubstringGenerator (class in dragonn.synthetic.synthetic) transformFile() (in module dragonn.synthetic.fileProcessing) transformFileIntoArray() (in module dragonn.synthetic.fileProcessing) transformType() (in module dragonn.synthetic.util) trimNewline() (in module dragonn.synthetic.fileProcessing)

U

UniformIntegerGenerator (class in dragonn.synthetic.synthetic) UniformPositionGenerator (class in dragonn.synthetic.synthetic) unsupportedValueForMode() (in module dragonn.synthetic.fileProcessing)

updateAdditionalInfo() (dragonn.synthetic.synthetic.AdditionalInfo method) updateBestLogOddsHit() (dragonn.synthetic.pwm.PWM method) updateTrace() (dragonn.synthetic.synthetic.AdditionalInfo method)

V

valToIndexMap() (in module dragonn.synthetic.util)

VariableWrapper (class in dragonn.synthetic.util)

W

write() (dragonn.synthetic.fileProcessing.BackupForWriteFileHandle method) (dragonn.synthetic.util.TeeOutputStreams method) writeable() (dragonn.synthetic.util.TeeOutputStreams method) writelines() (dragonn.synthetic.util.TeeOutputStreams method) writeMatrixToFile() (in module dragonn.synthetic.fileProcessing)

writeRowsToFile() (in module dragonn.synthetic.fileProcessing) writeRowsToFileHandle() (in module dragonn.synthetic.fileProcessing) writeToFile() (in module dragonn.synthetic.fileProcessing) writeToFileHandle() (in module dragonn.synthetic.fileProcessing)

X

X_test (dragonn.tutorial_utils.Data attribute) X_train (dragonn.tutorial_utils.Data attribute)

X_valid (dragonn.tutorial_utils.Data attribute) XOREmbedder (class in dragonn.synthetic.synthetic)

Y

y_test (dragonn.tutorial_utils.Data attribute) y_train (dragonn.tutorial_utils.Data attribute)

y_valid (dragonn.tutorial_utils.Data attribute) yamlToArgsString() (in module dragonn.synthetic.util)

Z

ZeroInflater (class in dragonn.synthetic.synthetic)

ZeroOrderBackgroundGenerator (class in dragonn.synthetic.synthetic)