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predictMPRASequences.sh
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python /home/ikaplow/RegulatoryElementEvolutionProject/src/OCROrthologPrediction/src/predictNewSequencesNoEvaluation.py --architectureFileName /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/cortexEnhancerVsOtherSpeciesEnhMouseMacaqueRatBatPeakLessThan1kb_data_train.KerasModels/cortexEnhancerShort_multiSpecies_enhLooseNeg_500bp_conv5TotalTotalFiltNoInterPoolVeryHighMomL2SmallBatchPretrainBal_architecture.json --weightsFileName /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/cortexEnhancerVsOtherSpeciesEnhMouseMacaqueRatBatPeakLessThan1kb_data_train.KerasModels/cortexEnhancerShort_multiSpecies_enhLooseNeg_500bp_conv5TotalTotalFiltNoInterPoolVeryHighMomL2SmallBatchPretrainBal.hdf5 --fastaFileName /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MPRAOneDesign/MPRAOneEnhancers.fa --padUpstream 190 --padDownstream 190 --sequenceLength 500 --predictedProbaFileName /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MPRAOneDesign/MPRAOneEnhancers_motorCortex_multiSpecies_conv5TotalTotalFiltNoInterPoolVeryHighMomL2SmallBatchPretrainBal_predictedProba.txt --classification
python /home/ikaplow/RegulatoryElementEvolutionProject/src/OCROrthologPrediction/src/predictNewSequencesNoEvaluation.py --architectureFileName /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/liverEnhancerVsOtherSpeciesEnhMouseMacaqueRatCowPigPeakLessThan1kb_data_train.KerasModels/liver_mouseMacaqueRatCowPig_otherSpeciesEnhLooseNeg_500bp_conv5AllFiltNoInterPoolVeryHighMomL2SmallBatchPretrainBal_architecture.json --weightsFileName /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/liverEnhancerVsOtherSpeciesEnhMouseMacaqueRatCowPigPeakLessThan1kb_data_train.KerasModels/liver_mouseMacaqueRatCowPig_otherSpeciesEnhLooseNeg_500bp_conv5AllFiltNoInterPoolVeryHighMomL2SmallBatchPretrainBal.hdf5 --fastaFileName /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MPRAOneDesign/MPRAOneEnhancers.fa --padUpstream 190 --padDownstream 190 --sequenceLength 500 --predictedProbaFileName /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MPRAOneDesign/MPRAOneEnhancers_liver_5Species_conv5AllFiltNoInterPoolVeryHighMomL2SmallBatchPretrainBal_predictedProba.txt --classification
python /home/ikaplow/RegulatoryElementEvolutionProject/src/OCROrthologPrediction/src/predictNewSequencesNoEvaluation.py --architectureFileName /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/brainEnhancerVsOtherEuarchontaglireEnhMouseHumanMacaqueRatPeakLessThan1kb_data_train.KerasModels/hybrid_brainEnhancerShort_humanMouseMacaqueRat_euarchontaglireEnhLooseNeg_500bp_conv5MostFiltNoInterPoolVeryHighMomHighLRL2SmallBatchPretrainBal_architecture.json --weightsFileName /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/brainEnhancerVsOtherEuarchontaglireEnhMouseHumanMacaqueRatPeakLessThan1kb_data_train.KerasModels/hybrid_brainEnhancerShort_humanMouseMacaqueRat_euarchontaglireEnhLooseNeg_500bp_conv5MostFiltNoInterPoolVeryHighMomHighLRL2SmallBatchPretrainBal.hdf5 --fastaFileName /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MPRAOneDesign/MPRAOneEnhancers.fa --padUpstream 190 --padDownstream 190 --sequenceLength 500 --predictedProbaFileName /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MPRAOneDesign/MPRAOneEnhancers_brain_multiSpecies_conv5MostFiltNoInterPoolVeryHighMomHighLRL2SmallBatchPretrainBal_predictedProba.txt --classification
python /home/ikaplow/RegulatoryElementEvolutionProject/src/OCROrthologPrediction/src/predictNewSequencesNoEvaluation.py --architectureFileName /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/striatumEnhancerVsOtherSpeciesEnhLoosePeakLessThan1kb500bp_data_train.KerasModels/striatumEnhancerShort_enhLooseNeg_500bp_conv5MuchMuchMoreFiltNoInterPoolLargeDenseVeryHighMomL2SmallBatchPretrainBal_architecture.json --weightsFileName /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/striatumEnhancerVsOtherSpeciesEnhLoosePeakLessThan1kb500bp_data_train.KerasModels/striatumEnhancerShort_enhLooseNeg_500bp_conv5MuchMuchMoreFiltNoInterPoolLargeDenseVeryHighMomL2SmallBatchPretrainBal.hdf5 --fastaFileName /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MPRAOneDesign/MPRAOneEnhancers.fa --padUpstream 190 --padDownstream 190 --sequenceLength 500 --predictedProbaFileName /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MPRAOneDesign/MPRAOneEnhancers_striatum_mouse_conv5MuchMuchMoreFiltNoInterPoolLargeDenseVeryHighMomL2SmallBatchPretrainBal_predictedProba.txt --classification
python /home/ikaplow/RegulatoryElementEvolutionProject/src/OCROrthologPrediction/src/predictNewSequencesNoEvaluation.py --architectureFileName /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/tissueSpecificEnhancerPeakLessThan1kbSummitsPlusMinus1kb_data_train.KerasModels/hybrid_brainLiverEnhancerShort_1000bp_conv5SmallFiltLessFiltNoInterPoolLowDropVeryHighMom_architecture.json --weightsFileName /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/tissueSpecificEnhancerPeakLessThan1kbSummitsPlusMinus1kb_data_train.KerasModels/hybrid_brainLiverEnhancerShort_1000bp_conv5SmallFiltLessFiltNoInterPoolLowDropVeryHighMom.hdf5 --fastaFileName /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MPRAOneDesign/MPRAOneEnhancers.fa --padUpstream 440 --padDownstream 440 --sequenceLength 1000 --predictedProbaFileName /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MPRAOneDesign/MPRAOneEnhancers_brainVsLiver_mouse_1000bp_summitCtr_conv5SmallFiltLessFiltNoInterPoolLowDropVeryHighMom_predictedProba.txt --classification
python /home/ikaplow/RegulatoryElementEvolutionProject/src/OCROrthologPrediction/src/predictNewSequencesNoEvaluation.py --architectureFileName /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/tissueSpecificEnhancerPeakLessThan1kbSummitsPlusMinus500bpBinned_data_train.KerasModels/hybrid_brainLiverEnhancerShort_500bp_binned_conv5VeryVerySmallFiltLessFiltNoInterPoolVeryHighMomL1PretrainBal_architecture.json --weightsFileName /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/tissueSpecificEnhancerPeakLessThan1kbSummitsPlusMinus500bpBinned_data_train.KerasModels/hybrid_brainLiverEnhancerShort_500bp_binned_conv5VeryVerySmallFiltLessFiltNoInterPoolVeryHighMomL1PretrainBal.hdf5 --fastaFileName /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MPRAOneDesign/MPRAOneEnhancers.fa --padUpstream 190 --padDownstream 190 --sequenceLength 500 --predictedProbaFileName /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MPRAOneDesign/MPRAOneEnhancers_brainVsLiver_mouse_500bp_binned_conv5VeryVerySmallFiltLessFiltNoInterPoolVeryHighMomL1PretrainBal_predictedProba.txt --classification
python /home/ikaplow/RegulatoryElementEvolutionProject/src/OCROrthologPrediction/src/predictNewSequencesNoEvaluation.py --architectureFileName /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/tissueSpecificEnhancerPeakLessThan1kbSummitsPlusMinus120bpBinned_data_train.KerasModels/hybrid_brainLiverEnhancerShort_120bp_binned_conv5VeryVerySmallFiltLessFiltNoInterPoolSmallPoolVeryHighMomL1_architecture.json --weightsFileName /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/tissueSpecificEnhancerPeakLessThan1kbSummitsPlusMinus120bpBinned_data_train.KerasModels/hybrid_brainLiverEnhancerShort_120bp_binned_conv5VeryVerySmallFiltLessFiltNoInterPoolSmallPoolVeryHighMomL1.hdf5 --fastaFileName /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MPRAOneDesign/MPRAOneEnhancers.fa --sequenceLength 120 --predictedProbaFileName /projects/pfenninggroup/machineLearningForComputationalBiology/regElEvoGrant/MPRAOneDesign/MPRAOneEnhancers_brainVsLiver_mouse_120bp_binned_conv5VeryVerySmallFiltLessFiltNoInterPoolSmallPoolVeryHighMomL1_predictedProba.txt --classification