# THIS SCRIPT WAS RUN AFTER THE MAIN TRAIN RUN CRASHED IN ORDER TO
# DO THE REPORTTRAINBYCHAIN IN THAT SCRIPT. SO THIS SCRIPT
# JUST READS IN THE NETWORK AND TRAINING CHAINS, THEN REPORTS BY CHAIN

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

ReadAlphabet /projects/compbio/lib/alphabet/two-spot-burial.alphabet

ReadNeuralNet   networks/t04-2621-IDaaHr-5-15-7-15-9-15-13-near-backbone-11-seeded.net
NameNet                  t04-2621-IDaaHr-5-15-7-15-9-15-13-near-backbone-11-seeded.net

ReadParams /cse/faculty/karplus/dna/predict-2nd/testing/params/16-dec-01-anneal
SetOverhang
time

# THIS training uses the t04-2621 id set, not holding out
#  anything for testing.

ReadToSet train
InFilePrefix  /cse/faculty/karplus/dna/predict-2nd/testing/training-data/
Include t04-2621.t04-thin90-stride
time

ReportTrainByChain quality-reports/t04-2621-IDaaHr-5-15-7-15-9-15-13-near-backbone-11-seeded.by-chain
TestNet
ReportTrainByChain
ReportQvsPhatTo 
ReportUnitUsageTo 
time