# DO NOT EDIT THIS FILE.
# IT WAS CREATED BY VARIABLE SUBSTITUTION FROM A TEMPLATE FILE IN
# ../../run-scripts  (i.e. from the parent directory of all the alphabets directories)
# IF YOU WANT ANOTHER VERSION, RUN 'make trAB.scripts' or 'make tAcB.scripts'
# WITH THE DESIRED Make.main MACROS

# This script must be run from the directory which has the
# subdirectories: networks,quality-reports
InFilePrefix
OutFilePrefix

SetSeed		# Start from a random starting point.
		# Set the seed to a specific value if you need
		# deterministic behavior for debugging.

ReadAlphabet /projects/compbio/lib/alphabet/p-np.alphabet
ReadBackgroundProbs /projects/compbio/lib/alphabet/dunbrack-in-scop.backgrounds

ReadNeuralNet       networks/G-3-13-7-13-9-13-11-p-np-empty.net
NameNet yeast-20pc-single-G-3-13-7-13-9-13-11-tr31-p-np-from-empty.net

ReadParams /projects/compbio/experiments/protein-predict/predict-2nd/testing/params/7-jul-05.params
SetOverhang
time

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

ReadToSet train
Include  /projects/compbio/experiments/protein-predict/predict-2nd/testing/training-data/yeast-20pc-3.single-p-np
time

ReadToSet train
Include  /projects/compbio/experiments/protein-predict/predict-2nd/testing/training-data/yeast-20pc-1.single-p-np
time

ReadToSet test
Include /projects/compbio/experiments/protein-predict/predict-2nd/testing/training-data/yeast-20pc-2.single-p-np
time


#    ReportNetQualityForTrainTo quality-reports/yeast-20pc-single-G-3-13-7-13-9-13-11-tr31-p-np-from-empty.train
ReportNetQualityForCrossTrainTo quality-reports/yeast-20pc-single-G-3-13-7-13-9-13-11-tr31-p-np-from-empty.train

TrainNet 5
ReportNeuralNet networks/yeast-20pc-single-G-3-13-7-13-9-13-11-tr31-p-np-from-empty.net
time

CenterWeights
Equilibrate
TrainNet 5
ReportNeuralNet networks/yeast-20pc-single-G-3-13-7-13-9-13-11-tr31-p-np-from-empty.net
time

CenterWeights
Equilibrate
TrainNet 5
ReportNeuralNet networks/yeast-20pc-single-G-3-13-7-13-9-13-11-tr31-p-np-from-empty.net
time

CenterWeights
Equilibrate
TrainNet 5
ReportNeuralNet networks/yeast-20pc-single-G-3-13-7-13-9-13-11-tr31-p-np-from-empty.net
time

CenterWeights
Equilibrate
TrainNet 50
ReportNeuralNet networks/yeast-20pc-single-G-3-13-7-13-9-13-11-tr31-p-np-from-empty.net
time

CenterWeights
TrainNet 50
ReportNeuralNet networks/yeast-20pc-single-G-3-13-7-13-9-13-11-tr31-p-np-from-empty.net
time

ReportNetQualityForTestTo quality-reports/yeast-20pc-single-G-3-13-7-13-9-13-11-tr31-p-np-from-empty.120.test
TestNet

CenterWeights
Equilibrate
TrainNet 50
ReportNeuralNet networks/yeast-20pc-single-G-3-13-7-13-9-13-11-tr31-p-np-from-empty.net
time

CenterWeights
TrainNet 50
ReportNeuralNet networks/yeast-20pc-single-G-3-13-7-13-9-13-11-tr31-p-np-from-empty.net
time

ReportNetQualityForTestTo quality-reports/yeast-20pc-single-G-3-13-7-13-9-13-11-tr31-p-np-from-empty.220.test
TestNet

CenterWeights
Equilibrate
TrainNet 50
ReportNeuralNet networks/yeast-20pc-single-G-3-13-7-13-9-13-11-tr31-p-np-from-empty.net
time

CenterWeights
TrainNet 50
ReportNeuralNet networks/yeast-20pc-single-G-3-13-7-13-9-13-11-tr31-p-np-from-empty.net
time

ReportNetQualityForTestTo quality-reports/yeast-20pc-single-G-3-13-7-13-9-13-11-tr31-p-np-from-empty.test
TestNet
ReportTrainByChain
ReportQvsPhatTo 
ReportUnitUsageTo 
time