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

#
# First read the alphabet
#
ReadAlphabet /projects/compbio/lib/alphabet/str.alphabet

#
# Then read the neural net which should already be 
#  trained (in this case with the 1st and 2nd thirds of the data)
#
ReadNeuralNet   networks/dunbrack-30pc-1763-t2k-thin90-IDGaaH13-3-13-7-13-9-13-11-t3c1-str2-from-empty.net

#
# Do I have to re-name the net? It's not like I'm 
#  training a new one at all.
#
#NameNet                 dunbrack-30pc-1763-t2k-thin90-IDGaaH13-3-13-7-13-9-13-11-t1c2-str2-from-empty.net

#
# I don't think I need any of this.
#
#ReadParams /cse/faculty/karplus/dna/predict-2nd/testing/params/16-dec-01-anneal
#SetOverhang
#time

#
# Read in all  of the data to be tested
#
ReadToSet test
InFilePrefix  /cse/faculty/karplus/dna/predict-2nd/testing/training-data/
Include dunbrack-30pc-1763-1.t2k-thin90-str2
time

ReadToSet test
InFilePrefix  /cse/faculty/karplus/dna/predict-2nd/testing/training-data/
Include dunbrack-30pc-1763-2.t2k-thin90-str2
time

ReadToSet test
InFilePrefix  /cse/faculty/karplus/dna/predict-2nd/testing/training-data/
Include dunbrack-30pc-1763-3.t2k-thin90-str2
time

#
# Report the testing to quality reports by chain
#
ReportNetQualityForTestTo quality-reports/dunbrack-30pc-1763-t2k-thin90-IDGaaH13-3-13-7-13-9-13-11-t3c1-str2-testall.test
#TestNet
#ReportTrainByChain 
#ReportQvsPhatTo
#ReportUnitUsageTo
#time
#
#ReportTrainByChain quality-reports/t2k-2621-IDGaaH13-3-13-7-13-9-13-11-str2-seeded.by-chain
#
ReportTestByChain quality-reports/dunbrack-30pc-1763-t2k-thin90-IDGaaH13-3-13-7-13-9-13-11-t3c1-str2-testall.by-chain
TestNet
ReportTestByChain
ReportQvsPhatTo
ReportUnitUsageTo
time