## Note: fssp-12345 means that training is done on the FSSP core plus
## parts 1-5, leaving nothing for cross-training or testing.

InFilePrefix  /projects/compbio/usr/sugato/nnet/testing/
OutFilePrefix /projects/compbio/usr/sugato/nnet/testing/

ReadNeuralNet networks/fssp-guide-12345-IDaa13-9-6-11-9-3-8-7-ehl-seeded-trained.net
NameNet fssp-12345-IDaa13-9-6-11-9-3-8-7-ehl-seeded-trained.net
SetOverhang	// turn ON overhangs (max width)

ReadParams params/sov-29-may-98

InFilePrefix /projects/compbio/lib/
WeightingRegularizer recode2.20comp
SequenceWeight HenikoffWeight 1.3 0.6

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

ReadToSet train
InFilePrefix  /projects/compbio/usr/sugato/nnet/testing/training-data/
Include fssp-3-5-98-core.read

InFilePrefix  /projects/compbio/usr/sugato/nnet/testing/training-data/
Include fssp-3-5-98-1.read

InFilePrefix  /projects/compbio/usr/sugato/nnet/testing/training-data/
Include fssp-3-5-98-2.read

InFilePrefix  /projects/compbio/usr/sugato/nnet/testing/training-data/
Include fssp-3-5-98-3.read

InFilePrefix  /projects/compbio/usr/sugato/nnet/testing/training-data/
Include fssp-3-5-98-4.read


InFilePrefix  /projects/compbio/usr/sugato/nnet/testing/training-data/
Include fssp-3-5-98-5.read


ReportNetQualityForTrainTo quality-reports/fssp-12345-IDaa13-9-6-11-9-3-8-7-ehl-seeded-t.quality
ReportNetQualityForCrossTrainTo quality-reports/fssp-12345-IDaa13-9-6-11-9-3-8-7-ehl-seeded.quality

# Doing just a couple of iterations is a hack to see if the bad
# behavior of the training is just on the first iteration.
unfreeze 0
freeze 1
freeze 2
freeze 3
TrainNet 2

unfreeze 0
freeze 1 
freeze 2
freeze 3
TrainNet 10

unfreeze 0
freeze 1
freeze 2
freeze 3
TrainNet 100

ReportNeuralNet networks/fssp-12345-IDaa13-9-6-11-9-3-8-7-ehl-seeded-trained.net