Index

A

add() (bpreveal.internal.interpretUtils.FlatH5Saver method) (bpreveal.internal.interpretUtils.FlatListSaver method) (bpreveal.internal.interpretUtils.PisaH5Saver method) (bpreveal.internal.interpretUtils.Saver method) (bpreveal.tools.filterProc.Writer method) addAllMetadata() (in module bpreveal.motifAddQuantiles) addAnnotations() (in module bpreveal.internal.plotUtils) addCbar() (in module bpreveal.internal.plotUtils) addCoordsInfo() (in module bpreveal.internal.predictUtils) addEntry() (bpreveal.internal.predictUtils.H5Writer method) addFieldNameQuantileMetadata() (in module bpreveal.motifAddQuantiles) addFieldQuantileData() (in module bpreveal.motifAddQuantiles) addGenomeInfo() (in module bpreveal.internal.predictUtils) addH5Metadata() (in module bpreveal.internal.files) addHorizontalProfilePlot() (in module bpreveal.internal.plotUtils) addLegend() (in module bpreveal.internal.plotUtils)

addLine() (bpreveal.showTrainingProgress.Screen method) addLossRatios() (in module bpreveal.tools.lossWeights) addMeanCounts() (bpreveal.generators.H5BatchGenerator method) addNoise (in module bpreveal.schema) addPisaGraph() (in module bpreveal.internal.plotUtils) addPisaPlot() (in module bpreveal.internal.plotUtils) addQuery() (bpreveal.bedUtils.ParallelCounter method) addResizeCallbacks() (in module bpreveal.internal.plotUtils) addVerticalProfilePlot() (in module bpreveal.internal.plotUtils) ANNOTATION_T (class in bpreveal.internal.constants) anyCorruptorsCloserThan() (in module bpreveal.gaOptimize) ApplyAdaptiveCountsLoss (class in bpreveal.callbacks) applyAddSub() (in module bpreveal.tools.addNoiseUtils) applyCorrection() (in module bpreveal.tools.gcContents) applyShift() (in module bpreveal.tools.addNoiseUtils) arrayQuantileMap() (in module bpreveal.motifUtils) arrayToCorruptors() (in module bpreveal.gaOptimize)

B

BatchedH5Reader (class in bpreveal.shapToBigwig) batchNumber (bpreveal.callbacks.DisplayCallback attribute) BatchPredictor (class in bpreveal.utils) BedReader (class in bpreveal.internal.predictUtils) blankChromosomeArrays() (in module bpreveal.utils) bpreveal.bedUtils module bpreveal.callbacks module bpreveal.checkJson module bpreveal.colors module bpreveal.gaOptimize module bpreveal.generators module bpreveal.internal.constants module bpreveal.internal.crashQueue module bpreveal.internal.disableTensorflowLogging module bpreveal.internal.files module bpreveal.internal.interpreter module bpreveal.internal.interpretUtils module bpreveal.internal.plotUtils module bpreveal.internal.predictUtils module bpreveal.interpretFlat module bpreveal.interpretPisa module bpreveal.jaccard module bpreveal.layers module bpreveal.lengthCalc module bpreveal.logUtils module bpreveal.losses module bpreveal.makeLossPlots module bpreveal.makePisaFigure module bpreveal.makePredictions module bpreveal.metrics module bpreveal.models module bpreveal.motifAddQuantiles module bpreveal.motifScan module

bpreveal.motifSeqletCutoffs module bpreveal.motifUtils module bpreveal.plotting module bpreveal.predictToBigwig module bpreveal.prepareBed module bpreveal.prepareTrainingData module bpreveal.schema module bpreveal.shapToBigwig module bpreveal.shapToNumpy module bpreveal.showModel module bpreveal.showTrainingProgress module bpreveal.tools.addNoise module bpreveal.tools.addNoiseUtils module bpreveal.tools.bestMotifsOnly module bpreveal.tools.filterProc module bpreveal.tools.gcContents module bpreveal.tools.lossWeights module bpreveal.tools.revcompTools module bpreveal.tools.shiftBigwigs module bpreveal.tools.shiftPisa module bpreveal.tools.slurm module bpreveal.tools.tileGenome module bpreveal.trainCombinedModel module bpreveal.training module bpreveal.trainSoloModel module bpreveal.trainTransformationModel module bpreveal.ushuffle module bpreveal.utils module buildConfig() (in module bpreveal.internal.plotUtils) buildDatasets() (bpreveal.internal.predictUtils.H5Writer method) buildLosses() (in module bpreveal.training) buildRegionList() (in module bpreveal.predictToBigwig)

C

calcMatches() (bpreveal.motifUtils.Seqlet method) calculatorThread() (in module bpreveal.metrics) call() (bpreveal.layers.CountsLogSumExp method) CANDIDATE_CORRUPTOR_T (in module bpreveal.gaOptimize) checkLine() (bpreveal.tools.filterProc.Writer method) chrom (bpreveal.motifUtils.Seqlet attribute) clear() (bpreveal.utils.BatchPredictor method) (bpreveal.utils.ThreadedBatchPredictor method) close() (bpreveal.internal.crashQueue.CrashQueue method) (bpreveal.internal.predictUtils.H5Writer method) Closure (class in bpreveal.internal.interpreter) cmp() (bpreveal.gaOptimize.Organism method) COLOR_SPEC_T (in module bpreveal.internal.constants) combinedModel() (in module bpreveal.models) combineMultAndDiffref() (in module bpreveal.internal.interpretUtils) commit() (bpreveal.internal.predictUtils.H5Writer method) configSlurm() (in module bpreveal.tools.slurm) configSlurmLocal() (in module bpreveal.tools.slurm) construct() (bpreveal.internal.interpretUtils.FastaGenerator method) (bpreveal.internal.interpretUtils.FlatBedGenerator method) (bpreveal.internal.interpretUtils.FlatH5Saver method) (bpreveal.internal.interpretUtils.FlatListSaver method) (bpreveal.internal.interpretUtils.Generator method) (bpreveal.internal.interpretUtils.ListGenerator method) (bpreveal.internal.interpretUtils.PisaBedGenerator method) (bpreveal.internal.interpretUtils.PisaH5Saver method) (bpreveal.internal.interpretUtils.Saver method)

contribMagnitude (bpreveal.motifUtils.Seqlet attribute) contribMatch (bpreveal.motifUtils.Seqlet attribute) contribs (bpreveal.motifUtils.Seqlet attribute) correctLosses() (bpreveal.callbacks.FixLossCallback method) CORRUPTOR_LETTER_T (in module bpreveal.gaOptimize) CORRUPTOR_T (in module bpreveal.gaOptimize) CORRUPTOR_TO_IDX (in module bpreveal.gaOptimize) corruptorColors (in module bpreveal.gaOptimize) corruptorsToArray() (in module bpreveal.gaOptimize) CountsLogSumExp (class in bpreveal.layers) countsMetric() (in module bpreveal.interpretFlat) CrashQueue (class in bpreveal.internal.crashQueue) createTilingRegions() (in module bpreveal.bedUtils) critical() (in module bpreveal.logUtils) curEpochStartTime (bpreveal.callbacks.DisplayCallback attribute) curEpochWaitTime (bpreveal.callbacks.DisplayCallback attribute) curLabel (bpreveal.internal.predictUtils.BedReader attribute) (bpreveal.internal.predictUtils.FastaReader attribute) curSequence (bpreveal.internal.predictUtils.BedReader attribute) (bpreveal.internal.predictUtils.FastaReader attribute) cutoffContribMagnitude (bpreveal.motifUtils.Pattern attribute) cutoffContribMatch (bpreveal.motifUtils.Pattern attribute) cutoffSeqMatch (bpreveal.motifUtils.Pattern attribute) cwm (bpreveal.motifUtils.Pattern attribute) cwmTrim (bpreveal.motifUtils.Pattern attribute) cwmTrimLeftPoint (bpreveal.motifUtils.Pattern attribute) cwmTrimPoints() (in module bpreveal.motifUtils) cwmTrimRightPoint (bpreveal.motifUtils.Pattern attribute)

D

debug() (in module bpreveal.logUtils) defaultProfile (in module bpreveal.colors) deleteTick() (in module bpreveal.plotting) DisplayCallback (class in bpreveal.callbacks) DNA_COLOR_SPEC_T (class in bpreveal.internal.constants) dnaWong (in module bpreveal.colors) done() (bpreveal.bedUtils.ParallelCounter method) (bpreveal.internal.interpretUtils.FastaGenerator method) (bpreveal.internal.interpretUtils.FlatBedGenerator method) (bpreveal.internal.interpretUtils.FlatH5Saver method) (bpreveal.internal.interpretUtils.FlatListSaver method) (bpreveal.internal.interpretUtils.Generator method) (bpreveal.internal.interpretUtils.ListGenerator method) (bpreveal.internal.interpretUtils.PisaBedGenerator method) (bpreveal.internal.interpretUtils.PisaH5Saver method) (bpreveal.internal.interpretUtils.Saver method) (bpreveal.motifUtils.PatternScanner method)

doShift() (in module bpreveal.tools.shiftBigwigs) (in module bpreveal.tools.shiftPisa) dummyMse (in module bpreveal.losses)

E

easyInterpretFlat() (in module bpreveal.utils) easyPredict() (in module bpreveal.utils) empty() (bpreveal.internal.crashQueue.CrashQueue method) (bpreveal.utils.BatchPredictor method) (bpreveal.utils.ThreadedBatchPredictor method) end (bpreveal.motifUtils.Seqlet attribute)

epochNumber (bpreveal.callbacks.DisplayCallback attribute) error() (in module bpreveal.logUtils) evalAst() (in module bpreveal.internal.interpreter) evalAstRaw() (in module bpreveal.internal.interpreter) evalFile() (in module bpreveal.internal.interpreter) evalString() (in module bpreveal.internal.interpreter) exitTime (bpreveal.showTrainingProgress.Screen attribute)

F

FastaGenerator (class in bpreveal.internal.interpretUtils) FastaReader (class in bpreveal.internal.predictUtils) filterByMaxCounts() (in module bpreveal.prepareBed) filterByMinCounts() (in module bpreveal.prepareBed) findRegions() (bpreveal.motifUtils.RegionScanner method) finish() (bpreveal.metrics.MetricsCalculator method) firstBatchTime (bpreveal.callbacks.DisplayCallback attribute)

firstValBatchTime (bpreveal.callbacks.DisplayCallback attribute) FixLossCallback (class in bpreveal.callbacks) FlatBedGenerator (class in bpreveal.internal.interpretUtils) FlatH5Saver (class in bpreveal.internal.interpretUtils) FlatListSaver (class in bpreveal.internal.interpretUtils) flipAndSave() (in module bpreveal.shapToNumpy) formatStr() (bpreveal.callbacks.DisplayCallback method) full() (bpreveal.internal.crashQueue.CrashQueue method)

G

GA_ANNOTATION_T (in module bpreveal.gaOptimize) GA_RESULT_T (in module bpreveal.gaOptimize) Generator (class in bpreveal.internal.interpretUtils) GENOME_NUCLEOTIDE_FREQUENCY (in module bpreveal.internal.constants) genomicEnd (bpreveal.motifUtils.Seqlet attribute) genomicStart (bpreveal.motifUtils.Seqlet attribute) get() (bpreveal.internal.crashQueue.CrashQueue method) get_config() (bpreveal.layers.CountsLogSumExp method) getCallbacks() (in module bpreveal.callbacks) getCandidateCorruptorList() (in module bpreveal.gaOptimize) getChromInserts() (in module bpreveal.predictToBigwig) getChromVector() (in module bpreveal.predictToBigwig) getCoordinateTicks() (in module bpreveal.internal.plotUtils) (in module bpreveal.plotting) getCorrectionFactors() (in module bpreveal.tools.gcContents) getCounts() (in module bpreveal.bedUtils) getCutoffs() (bpreveal.motifUtils.Pattern method) getDistributionFromBed() (in module bpreveal.tools.gcContents) getGc() (in module bpreveal.tools.gcContents) getGraphCmap() (in module bpreveal.colors) getHead() (in module bpreveal.prepareTrainingData) getInputLength() (in module bpreveal.lengthCalc) getLengthDifference() (in module bpreveal.lengthCalc) getLogger() (in module bpreveal.logUtils) getLosses() (bpreveal.callbacks.ApplyAdaptiveCountsLoss method) getMask() (in module bpreveal.tools.shiftPisa) getMutated() (in module bpreveal.tools.addNoiseUtils) getOutput() (bpreveal.utils.BatchPredictor method) (bpreveal.utils.ThreadedBatchPredictor method) getOutputLength() (in module bpreveal.lengthCalc) getOutputProfile() (bpreveal.utils.BatchPredictor method) (bpreveal.utils.ThreadedBatchPredictor method)

getParser() (in module bpreveal.checkJson) (in module bpreveal.lengthCalc) (in module bpreveal.makeLossPlots) (in module bpreveal.metrics) (in module bpreveal.motifAddQuantiles) (in module bpreveal.predictToBigwig) (in module bpreveal.shapToBigwig) (in module bpreveal.shapToNumpy) (in module bpreveal.showModel) (in module bpreveal.showTrainingProgress) (in module bpreveal.tools.bestMotifsOnly) (in module bpreveal.tools.filterProc) (in module bpreveal.tools.gcContents) (in module bpreveal.tools.lossWeights) (in module bpreveal.tools.revcompTools) (in module bpreveal.tools.shiftBigwigs) (in module bpreveal.tools.shiftPisa) (in module bpreveal.tools.tileGenome) getPisaAxes() (in module bpreveal.internal.plotUtils) getPisaGraphAxes() (in module bpreveal.internal.plotUtils) getReader() (in module bpreveal.makePredictions) getResult() (bpreveal.bedUtils.ParallelCounter method) getScanningInfo() (bpreveal.motifUtils.Pattern method) getSequence() (bpreveal.gaOptimize.Organism method) getSequences() (in module bpreveal.prepareTrainingData) getTensorflowLoaded() (in module bpreveal.internal.constants) getValues() (bpreveal.predictToBigwig.Region method) getVerbosity() (in module bpreveal.logUtils) getWriter() (in module bpreveal.makePredictions) GLOBAL_TENSORFLOW_LOADED (in module bpreveal.internal.constants) gmstar() (in module bpreveal.tools.addNoiseUtils)

H

H5_CHUNK_SIZE (in module bpreveal.internal.constants) H5BatchGenerator (class in bpreveal.generators)

H5Writer (class in bpreveal.internal.predictUtils) Hit (class in bpreveal.motifUtils)

I

ibm (in module bpreveal.colors) IDX_TO_CORRUPTOR (in module bpreveal.gaOptimize) ignoreMetrics (bpreveal.callbacks.DisplayCallback attribute) IMPORTANCE_AR_T (in module bpreveal.internal.constants) IMPORTANCE_T (in module bpreveal.internal.constants) IN_A (in module bpreveal.gaOptimize) IN_C (in module bpreveal.gaOptimize) IN_D (in module bpreveal.gaOptimize) IN_G (in module bpreveal.gaOptimize) IN_L (in module bpreveal.gaOptimize) IN_R (in module bpreveal.gaOptimize)

IN_T (in module bpreveal.gaOptimize) index (bpreveal.motifUtils.Seqlet attribute) info() (in module bpreveal.logUtils) initialSequence (bpreveal.gaOptimize.Population attribute) interpretFlat (in module bpreveal.schema) interpretFlat() (in module bpreveal.interpretFlat) interpretPisa (in module bpreveal.schema) interpretPisa() (in module bpreveal.interpretPisa) InterpRunner (class in bpreveal.internal.interpretUtils) isNormalMessage() (in module bpreveal.showTrainingProgress) isShappable() (in module bpreveal.internal.interpretUtils)

J

jaccardRegion() (in module bpreveal.jaccard) jobsGpu() (in module bpreveal.tools.slurm)

jobsLocal() (in module bpreveal.tools.slurm) jobsNonGpu() (in module bpreveal.tools.slurm)

L

lastBatchEndTime (bpreveal.callbacks.DisplayCallback attribute) lastBatchTime (bpreveal.callbacks.DisplayCallback attribute) lastCorruptors (bpreveal.gaOptimize.Organism attribute) lastEpochEndTime (bpreveal.callbacks.DisplayCallback attribute) lastEpochStartTime (bpreveal.callbacks.DisplayCallback attribute) lastSequence (bpreveal.gaOptimize.Organism attribute) lastValBatchEndTime (bpreveal.callbacks.DisplayCallback attribute) lastValBatchTime (bpreveal.callbacks.DisplayCallback attribute) LeaveStderrAlone (class in bpreveal.internal.disableTensorflowLogging) limitMemoryUsage() (in module bpreveal.utils) linearRegression() (in module bpreveal.layers) lineToInterval() (in module bpreveal.bedUtils) ListGenerator (class in bpreveal.internal.interpretUtils) loadChromSizes() (in module bpreveal.utils) loadCoordinates() (bpreveal.motifUtils.Seqlet method) loadCwm() (bpreveal.motifUtils.Pattern method) loadData() (bpreveal.generators.H5BatchGenerator method) loadEntries() (in module bpreveal.tools.bestMotifsOnly) loadFile() (in module bpreveal.tools.addNoiseUtils)

loadFonts() (in module bpreveal.colors) loadFromBigwig() (in module bpreveal.internal.plotUtils) loadLosses() (in module bpreveal.tools.lossWeights) loadModel() (in module bpreveal.utils) loadPisa() (in module bpreveal.utils) loadPisaAnnotations() (in module bpreveal.internal.plotUtils) loadRegions() (in module bpreveal.prepareBed) loadRegionsByBed() (in module bpreveal.prepareBed) loadRegionsByChrom() (in module bpreveal.prepareBed) loadRegionsByRegex() (in module bpreveal.prepareBed) loadSeqletCoordinates() (bpreveal.motifUtils.Pattern method) loadSeqlets() (bpreveal.motifUtils.Pattern method) loadSequence() (in module bpreveal.internal.plotUtils) log() (in module bpreveal.logUtils) LOGCOUNT_T (in module bpreveal.internal.constants) logFirstN() (in module bpreveal.logUtils) logIf() (in module bpreveal.logUtils) LOGIT_AR_T (in module bpreveal.internal.constants) LOGIT_T (in module bpreveal.internal.constants) logitsToProfile() (in module bpreveal.utils)

M

main() (in module bpreveal.checkJson) (in module bpreveal.interpretFlat) (in module bpreveal.interpretPisa) (in module bpreveal.lengthCalc) (in module bpreveal.makeLossPlots) (in module bpreveal.makePisaFigure) (in module bpreveal.makePredictions) (in module bpreveal.metrics) (in module bpreveal.motifAddQuantiles) (in module bpreveal.motifScan) (in module bpreveal.motifSeqletCutoffs) (in module bpreveal.predictToBigwig) (in module bpreveal.prepareBed) (in module bpreveal.prepareTrainingData) (in module bpreveal.shapToBigwig) (in module bpreveal.shapToNumpy) (in module bpreveal.showModel) (in module bpreveal.showTrainingProgress) (in module bpreveal.tools.addNoise) (in module bpreveal.tools.bestMotifsOnly) (in module bpreveal.tools.filterProc) (in module bpreveal.tools.gcContents) (in module bpreveal.tools.lossWeights) (in module bpreveal.tools.revcompTools) (in module bpreveal.tools.shiftBigwigs) (in module bpreveal.tools.shiftPisa) (in module bpreveal.tools.tileGenome) (in module bpreveal.trainCombinedModel) (in module bpreveal.trainSoloModel) (in module bpreveal.trainTransformationModel) makePatternObjects() (in module bpreveal.motifUtils) makePisaFigure (in module bpreveal.schema) makePisaFigure() (in module bpreveal.makePisaFigure) makePredictions (in module bpreveal.schema) makePredictions() (in module bpreveal.makePredictions) makeWhitelistSegments() (in module bpreveal.bedUtils) massageTickLabels() (in module bpreveal.internal.plotUtils) maxLen (bpreveal.callbacks.DisplayCallback attribute) metaclusterName (bpreveal.motifUtils.Pattern attribute) metapeak() (in module bpreveal.bedUtils) MetricsCalculator (class in bpreveal.metrics) MiniPattern (class in bpreveal.motifUtils) mixed() (bpreveal.gaOptimize.Organism method) MODEL_ONEHOT_T (in module bpreveal.internal.constants) module bpreveal.bedUtils bpreveal.callbacks bpreveal.checkJson bpreveal.colors bpreveal.gaOptimize bpreveal.generators bpreveal.internal.constants bpreveal.internal.crashQueue bpreveal.internal.disableTensorflowLogging bpreveal.internal.files bpreveal.internal.interpreter bpreveal.internal.interpretUtils bpreveal.internal.plotUtils bpreveal.internal.predictUtils bpreveal.interpretFlat bpreveal.interpretPisa bpreveal.jaccard bpreveal.layers bpreveal.lengthCalc bpreveal.logUtils bpreveal.losses bpreveal.makeLossPlots bpreveal.makePisaFigure bpreveal.makePredictions bpreveal.metrics bpreveal.models bpreveal.motifAddQuantiles bpreveal.motifScan bpreveal.motifSeqletCutoffs bpreveal.motifUtils bpreveal.plotting bpreveal.predictToBigwig bpreveal.prepareBed bpreveal.prepareTrainingData bpreveal.schema bpreveal.shapToBigwig bpreveal.shapToNumpy bpreveal.showModel bpreveal.showTrainingProgress bpreveal.tools.addNoise bpreveal.tools.addNoiseUtils bpreveal.tools.bestMotifsOnly bpreveal.tools.filterProc bpreveal.tools.gcContents bpreveal.tools.lossWeights bpreveal.tools.revcompTools bpreveal.tools.shiftBigwigs bpreveal.tools.shiftPisa bpreveal.tools.slurm bpreveal.tools.tileGenome bpreveal.trainCombinedModel bpreveal.training bpreveal.trainSoloModel bpreveal.trainTransformationModel bpreveal.ushuffle bpreveal.utils

MOTIF_FLOAT_AR_T (in module bpreveal.internal.constants) MOTIF_FLOAT_T (in module bpreveal.internal.constants) motifScan (in module bpreveal.schema) motifScan() (in module bpreveal.motifScan) motifSeqletCutoffs (in module bpreveal.schema) motifSeqletCutoffs() (in module bpreveal.motifSeqletCutoffs) multinomialNll() (in module bpreveal.losses) multipliers (bpreveal.callbacks.DisplayCallback attribute) mutated() (bpreveal.gaOptimize.Organism method) mutateProfile() (in module bpreveal.tools.addNoiseUtils)

N

nextGeneration() (bpreveal.gaOptimize.Population method) normalizeProfileColor() (in module bpreveal.internal.plotUtils) normalizeProfileSection() (in module bpreveal.internal.plotUtils) NUM_BASES (in module bpreveal.internal.constants) numBatches (bpreveal.callbacks.DisplayCallback attribute)

numEpochs (bpreveal.callbacks.DisplayCallback attribute) numericalize() (in module bpreveal.motifAddQuantiles) numPredictions (bpreveal.internal.predictUtils.BedReader attribute) numSeqlets (bpreveal.motifUtils.Pattern attribute) numValBatches (bpreveal.callbacks.DisplayCallback attribute)

O

on_epoch_begin() (bpreveal.callbacks.DisplayCallback method) on_epoch_end() (bpreveal.callbacks.ApplyAdaptiveCountsLoss method) (bpreveal.callbacks.DisplayCallback method) (bpreveal.callbacks.FixLossCallback method) (bpreveal.generators.H5BatchGenerator method) on_test_batch_end() (bpreveal.callbacks.DisplayCallback method) (bpreveal.callbacks.FixLossCallback method) on_train_batch_end() (bpreveal.callbacks.DisplayCallback method) (bpreveal.callbacks.FixLossCallback method) on_train_begin() (bpreveal.callbacks.ApplyAdaptiveCountsLoss method) (bpreveal.callbacks.DisplayCallback method)

oneHot (bpreveal.motifUtils.Seqlet attribute) ONEHOT_AR_T (in module bpreveal.internal.constants) ONEHOT_T (in module bpreveal.internal.constants) oneHotDecode() (in module bpreveal.utils) oneHotEncode() (in module bpreveal.utils) Organism (class in bpreveal.gaOptimize) organisms (bpreveal.gaOptimize.Population attribute) outputReady() (bpreveal.utils.BatchPredictor method) (bpreveal.utils.ThreadedBatchPredictor method)

P

ParallelCounter (class in bpreveal.bedUtils) parentFinish() (bpreveal.internal.interpretUtils.FlatListSaver method) (bpreveal.internal.interpretUtils.Saver method) parseSpec() (in module bpreveal.colors) Pattern (class in bpreveal.motifUtils) patternName (bpreveal.motifUtils.Pattern attribute) PatternScanner (class in bpreveal.motifUtils) percentileStats() (in module bpreveal.metrics) PisaBedGenerator (class in bpreveal.internal.interpretUtils) pisaClip (in module bpreveal.colors) pisaGraph (in module bpreveal.schema) PisaH5Saver (class in bpreveal.internal.interpretUtils) pisaMetric() (in module bpreveal.interpretPisa) pisaNoClip (in module bpreveal.colors) pisaPlot (in module bpreveal.schema) plotHist() (in module bpreveal.tools.gcContents) plotLogo() (in module bpreveal.internal.plotUtils) (in module bpreveal.plotting) plotLosses() (in module bpreveal.makeLossPlots) plotModiscoPattern() (in module bpreveal.plotting) plotPisa() (in module bpreveal.plotting) plotPisaGraph() (in module bpreveal.plotting) plotPisaWithFiles() (in module bpreveal.plotting) plotSequenceHeatmap() (in module bpreveal.plotting)

plotTraces() (in module bpreveal.gaOptimize) pop() (bpreveal.internal.predictUtils.BedReader method) (bpreveal.internal.predictUtils.FastaReader method) Population (class in bpreveal.gaOptimize) ppm (bpreveal.motifUtils.Pattern attribute) ppmToPssm() (in module bpreveal.motifUtils) ppmToPwm() (in module bpreveal.motifUtils) PRED_AR_T (in module bpreveal.internal.constants) PRED_T (in module bpreveal.internal.constants) prepareBed (in module bpreveal.schema) prepareBed() (in module bpreveal.prepareBed) prepareTrainingData (in module bpreveal.schema) prepareTrainingData() (in module bpreveal.prepareTrainingData) preprocessMotifs() (in module bpreveal.tools.bestMotifsOnly) prevEpochLogs (bpreveal.callbacks.DisplayCallback attribute) printLine() (bpreveal.tools.filterProc.Writer method) printLocationsBatch (bpreveal.callbacks.DisplayCallback attribute) printLocationsEpoch (bpreveal.callbacks.DisplayCallback attribute) printString() (bpreveal.showTrainingProgress.Screen method) profileMetric() (in module bpreveal.interpretFlat) pssm (bpreveal.motifUtils.Pattern attribute) pssmTrim (bpreveal.motifUtils.Pattern attribute) put() (bpreveal.internal.crashQueue.CrashQueue method) pwm (bpreveal.motifUtils.Pattern attribute)

Q

quantileContribMagnitude (bpreveal.motifUtils.Pattern attribute) quantileContribMatch (bpreveal.motifUtils.Pattern attribute)

quantileSeqMatch (bpreveal.motifUtils.Pattern attribute) Query (class in bpreveal.internal.interpretUtils) QUEUE_TIMEOUT (in module bpreveal.internal.constants)

R

readScore() (bpreveal.shapToBigwig.BatchedH5Reader method) readSeq() (bpreveal.shapToBigwig.BatchedH5Reader method) readTsv() (in module bpreveal.motifAddQuantiles) receiveThread() (in module bpreveal.metrics) recordToPatternID() (in module bpreveal.motifAddQuantiles) refreshData() (bpreveal.generators.H5BatchGenerator method) Region (class in bpreveal.metrics) (class in bpreveal.predictToBigwig) regionGenThread() (in module bpreveal.metrics) RegionScanner (class in bpreveal.motifUtils) removeCorruptors() (in module bpreveal.gaOptimize) removeOverlaps() (in module bpreveal.prepareBed) (in module bpreveal.tools.bestMotifsOnly) replaceThousands() (in module bpreveal.internal.plotUtils) resetCallbacks() (bpreveal.callbacks.ApplyAdaptiveCountsLoss method) resize() (in module bpreveal.bedUtils)

Result (class in bpreveal.internal.interpretUtils) revcomp (bpreveal.motifUtils.Seqlet attribute) revcompSeq() (in module bpreveal.prepareTrainingData) reweightCountsLosses() (in module bpreveal.makeLossPlots) rewriteOldBigwigsFormat() (in module bpreveal.prepareBed) RGB_T (in module bpreveal.internal.constants) run() (bpreveal.internal.interpreter.Closure method) (bpreveal.internal.interpretUtils.InterpRunner method) (bpreveal.metrics.MetricsCalculator method) runBatch() (bpreveal.utils.BatchPredictor method) runCalculation() (bpreveal.gaOptimize.Population method) runMain() (in module bpreveal.tools.gcContents) runMetrics() (in module bpreveal.metrics) runProc() (in module bpreveal.tools.filterProc) runRegions() (bpreveal.metrics.MetricsCalculator method) runScreen() (in module bpreveal.showTrainingProgress) runShiftAlgo() (in module bpreveal.tools.addNoiseUtils)

S

Saver (class in bpreveal.internal.interpretUtils) scan() (bpreveal.motifUtils.MiniPattern method) scanBigwigs() (in module bpreveal.tools.shiftBigwigs) scanIndex() (bpreveal.motifUtils.PatternScanner method) (bpreveal.motifUtils.RegionScanner method) scannerThread() (in module bpreveal.motifUtils) scanPatterns() (in module bpreveal.motifUtils) scanWithoutCutoffs() (bpreveal.motifUtils.MiniPattern method) schemaMap (in module bpreveal.schema) Screen (class in bpreveal.showTrainingProgress) Seqlet (class in bpreveal.motifUtils) seqletContribMagnitudes (bpreveal.motifUtils.Pattern property) seqletContribMatches (bpreveal.motifUtils.Pattern property) seqletCutoffs() (in module bpreveal.motifUtils) seqletInfoIterator() (bpreveal.motifUtils.Pattern method) seqlets (bpreveal.motifUtils.Pattern attribute) seqletSeqMatches (bpreveal.motifUtils.Pattern property) seqMatch (bpreveal.motifUtils.Seqlet attribute) sequence (bpreveal.motifUtils.Seqlet attribute) sequenceChecker() (in module bpreveal.bedUtils) setBooleanVerbosity() (in module bpreveal.logUtils) setDefaultFontFamily() (in module bpreveal.internal.constants) setMemoryGrowth() (in module bpreveal.utils)

setQuantiles() (bpreveal.motifUtils.Pattern method) setScore() (bpreveal.gaOptimize.Organism method) setTensorflowLoaded() (in module bpreveal.internal.constants) setVerbosity() (in module bpreveal.logUtils) shiftPisa() (in module bpreveal.tools.shiftPisa) shiftPredictions() (in module bpreveal.tools.shiftPisa) shortName (bpreveal.motifUtils.Pattern attribute) shuffleOHE() (in module bpreveal.ushuffle) shuffleString() (in module bpreveal.ushuffle) shutdown() (bpreveal.showTrainingProgress.Screen method) slidingDotproduct() (in module bpreveal.motifUtils) slidingJaccard() (in module bpreveal.jaccard) soloModel() (in module bpreveal.models) sortBed() (in module bpreveal.bedUtils) start (bpreveal.motifUtils.Seqlet attribute) start() (bpreveal.utils.ThreadedBatchPredictor method) stop() (bpreveal.utils.ThreadedBatchPredictor method) stringToCorruptorList() (in module bpreveal.gaOptimize) submitOHE() (bpreveal.utils.BatchPredictor method) (bpreveal.utils.ThreadedBatchPredictor method) submitString() (bpreveal.utils.BatchPredictor method) (bpreveal.utils.ThreadedBatchPredictor method) SuppressStderr (class in bpreveal.internal.disableTensorflowLogging)

T

ThreadedBatchPredictor (class in bpreveal.utils) tileSegments() (in module bpreveal.bedUtils) toDict() (bpreveal.motifUtils.Hit method) tol (in module bpreveal.colors) tolLight (in module bpreveal.colors) trainBeginTime (bpreveal.callbacks.DisplayCallback attribute) trainCombinedModel (in module bpreveal.schema)

trainCombinedModel() (in module bpreveal.trainCombinedModel) trainModel() (in module bpreveal.training) trainSoloModel (in module bpreveal.schema) trainSoloModel() (in module bpreveal.trainSoloModel) trainTransformationModel (in module bpreveal.schema) trainTransformationModel() (in module bpreveal.trainTransformationModel) trainWithGenerators() (in module bpreveal.training) transformationModel() (in module bpreveal.models)

U

updateStatus() (bpreveal.showTrainingProgress.Screen method)

V

validateRegions() (in module bpreveal.prepareBed)

validCorruptorList() (in module bpreveal.gaOptimize) vectorToListOfInserts() (in module bpreveal.predictToBigwig)

W

warning() (in module bpreveal.logUtils) weightedMse() (in module bpreveal.losses) whatWouldValLossBe() (bpreveal.callbacks.ApplyAdaptiveCountsLoss method) wong (in module bpreveal.colors) wrapTqdm() (in module bpreveal.logUtils) writeBigWig() (in module bpreveal.predictToBigwig) (in module bpreveal.shapToBigwig)

writeBigwig() (in module bpreveal.utils) writeDependencyScript() (in module bpreveal.tools.slurm) writeOutput() (in module bpreveal.tools.addNoiseUtils) Writer (class in bpreveal.tools.filterProc) writerThread() (in module bpreveal.motifUtils) writeTsv() (in module bpreveal.motifAddQuantiles)