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

ReadNeuralNet networks/overrep-2260-IDaa13-5-8-7-10-5-9-11-ehl-blanked3.net
NameNet fssp-1929-1-IDaa13-5-8-7-10-5-9-11-ehl-blanked-retrained.net

ReadParams params/2-feb-00-fast

# 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 fssp-1929-1.t99-read

SetOverhang

ReportNetQualityForTrainTo quality-reports/fssp-1929-1-IDaa13-5-8-7-10-5-9-11-ehl-blanked-t.quality
ReportNetQualityForCrossTrainTo quality-reports/fssp-1929-1-IDaa13-5-8-7-10-5-9-11-ehl-blanked.quality



unfreeze 0
freeze 1
freeze 2
freeze 3

TrainNet 100
ReportNeuralNet networks/fssp-1929-1-IDaa13-5-8-7-10-5-9-11-ehl-blanked-retrained3.net

TrainNet 100
ReportNeuralNet networks/fssp-1929-1-IDaa13-5-8-7-10-5-9-11-ehl-blanked-retrained3.net

TrainNet 100
ReportNeuralNet networks/fssp-1929-1-IDaa13-5-8-7-10-5-9-11-ehl-blanked-retrained3.net

TrainNet 100
ReportNeuralNet networks/fssp-1929-1-IDaa13-5-8-7-10-5-9-11-ehl-blanked-retrained3.net


ReadToSet test
InFilePrefix  /cse/faculty/karplus/dna/predict-2nd/testing/training-data/
Include fssp-1929-2.t99-read


ReportNetQualityForTestTo quality-reports/fssp-1929-1-IDaa13-5-8-7-10-5-9-11-ehl-blanked-test.quality

ReportTestByChain quality-reports/fssp-1929-1-IDaa13-5-8-7-10-5-9-11-ehl-blanked-test.by-chain

ReportQvsPhatTo quality-reports/fssp-1929-1-IDaa13-5-8-7-10-5-9-11-ehl-blanked-test.q-vs-phat

ReportUnitUsageTo quality-reports/fssp-1929-1-IDaa13-5-8-7-10-5-9-11-ehl-blanked-test.unit-usage

TestNet