InFilePrefix  /cse/faculty/karplus/dna/predict-2nd/testing/
OutFilePrefix /cse/faculty/karplus/dna/predict-2nd/testing/

ReadNeuralNet networks/overrep-2264-IDaa13-5-8-7-10-5-9-11-ehl-seeded-trained.net
NameNet overrep-2259-IDaa13-5-8-7-10-5-9-11-ehl-seeded-trained.net

ReadParams params/11-jan-00

# Note: the following includes read the training set(s),
# and, in doing so, reset the InFilePrefix

ReadToSet train
InFilePrefix  /cse/faculty/karplus/dna/predict-2nd/testing/training-data/
Include overrep-2259.t99-read

SetOverhang

ReportNetQualityForTrainTo quality-reports/overrep-2259-IDaa13-5-8-7-10-5-9-11-ehl-seeded-t.quality
ReportNetQualityForCrossTrainTo quality-reports/overrep-2259-IDaa13-5-8-7-10-5-9-11-ehl-seeded.quality



unfreeze 0
unfreeze 1
unfreeze 2
unfreeze 3

TrainNet 50
ReportNeuralNet networks/overrep-2259-IDaa13-5-8-7-10-5-9-11-ehl-seeded-trained.net


TrainNet 50
ReportNeuralNet networks/overrep-2259-IDaa13-5-8-7-10-5-9-11-ehl-seeded-trained.net

TrainNet 50
ReportNeuralNet networks/overrep-2259-IDaa13-5-8-7-10-5-9-11-ehl-seeded-trained.net

TrainNet 50
ReportNeuralNet networks/overrep-2259-IDaa13-5-8-7-10-5-9-11-ehl-seeded-trained.net

TrainNet 50
ReportNeuralNet networks/overrep-2259-IDaa13-5-8-7-10-5-9-11-ehl-seeded-trained.net

TrainNet 50
ReportNeuralNet networks/overrep-2259-IDaa13-5-8-7-10-5-9-11-ehl-seeded-trained.net

TrainNet 50
ReportNeuralNet networks/overrep-2259-IDaa13-5-8-7-10-5-9-11-ehl-seeded-trained.net


ReportTrainByChain quality-reports/overrep-2259-IDaa13-5-8-7-10-5-9-11-ehl-seeded-trained.by-chain

ReportQvsPhatTo quality-reports/overrep-2259-IDaa13-5-8-7-10-5-9-11-ehl-seeded-trained.q-vs-phat

ReportUnitUsageTo quality-reports/overrep-2259-IDaa13-5-8-7-10-5-9-11-ehl-seeded-trained.unit-usage

TestNet