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run-fr-wekasmo
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#!/bin/sh
# usage: FRUtils
# -arff,--arff print out an ARFF style file from the
# data given by inputprefix
# -f,--frsprefix <arg> prefix of FRs file (e.g. HLAA-0.0-Inf)
# -g,--graphprefix <arg> prefix of graph file (e.g. HLAA)
# -m,--minsupport <arg> minimum number (not fraction) of
# supporting paths for an FR to be
# considered interesting
# -mp,--maxpvalue <arg> maximum p-value for an FR to be
# considered interesting
# -mpri,--minpriority <arg> minimum priority value for an FR to be
# considered interesting
# -p,--pathsprefix <arg> prefix of paths file (e.g. HLAA)
GRAPH=$1
FRPREFIX=$2
MINSUPPORT=0
MAXP=1
MINPRI=0
TRAINFILE=$FRPREFIX.train.arff
TESTFILE=$FRPREFIX.test.arff
## make the filtered ARFF files
java -server -cp "build/install/pangenomics/lib/*" org.ncgr.pangenomics.genotype.fr.FRUtils -arff -g $GRAPH -p $GRAPH.train -f $FRPREFIX \
--minsupport $MINSUPPORT --maxpvalue $MAXP --minpriority $MINPRI
java -server -cp "build/install/pangenomics/lib/*" org.ncgr.pangenomics.genotype.fr.FRUtils -arff -g $GRAPH -p $GRAPH.test -f $FRPREFIX \
--minsupport $MINSUPPORT --maxpvalue $MAXP --minpriority $MINPRI
## remove the extra chunk from the file names
mv $FRPREFIX.$GRAPH.train.arff $TRAINFILE
mv $FRPREFIX.$GRAPH.test.arff $TESTFILE
KFOLD=10
NGRIDSEARCH=0
CPOWERSTEP=1
GAMMAPOWERSTEP=1
GAMMAPOWERBEGIN=-30
GAMMAPOWEREND=-10
## run grid search in several batches because can't get more than about 10 threads per job
java -server -cp "build/install/pangenomics/lib/*" org.ncgr.weka.WekaSMO --gridsearch --arfffile=$TRAINFILE --kfold=$KFOLD --ngridsearch=$NGRIDSEARCH \
-cb 5 -ce 5 -cs $CPOWERSTEP -gb $GAMMAPOWERBEGIN -ge $GAMMAPOWEREND -gs $GAMMAPOWERSTEP &
java -server -cp "build/install/pangenomics/lib/*" org.ncgr.weka.WekaSMO --gridsearch --arfffile=$TRAINFILE --kfold=$KFOLD --ngridsearch=$NGRIDSEARCH \
-cb 6 -ce 6 -cs $CPOWERSTEP -gb $GAMMAPOWERBEGIN -ge $GAMMAPOWEREND -gs $GAMMAPOWERSTEP &
java -server -cp "build/install/pangenomics/lib/*" org.ncgr.weka.WekaSMO --gridsearch --arfffile=$TRAINFILE --kfold=$KFOLD --ngridsearch=$NGRIDSEARCH \
-cb 7 -ce 7 -cs $CPOWERSTEP -gb $GAMMAPOWERBEGIN -ge $GAMMAPOWEREND -gs $GAMMAPOWERSTEP &
java -server -cp "build/install/pangenomics/lib/*" org.ncgr.weka.WekaSMO --gridsearch --arfffile=$TRAINFILE --kfold=$KFOLD --ngridsearch=$NGRIDSEARCH \
-cb 8 -ce 8 -cs $CPOWERSTEP -gb $GAMMAPOWERBEGIN -ge $GAMMAPOWEREND -gs $GAMMAPOWERSTEP &
java -server -cp "build/install/pangenomics/lib/*" org.ncgr.weka.WekaSMO --gridsearch --arfffile=$TRAINFILE --kfold=$KFOLD --ngridsearch=$NGRIDSEARCH \
-cb 9 -ce 9 -cs $CPOWERSTEP -gb $GAMMAPOWERBEGIN -ge $GAMMAPOWEREND -gs $GAMMAPOWERSTEP &
java -server -cp "build/install/pangenomics/lib/*" org.ncgr.weka.WekaSMO --gridsearch --arfffile=$TRAINFILE --kfold=$KFOLD --ngridsearch=$NGRIDSEARCH \
-cb 10 -ce 10 -cs $CPOWERSTEP -gb $GAMMAPOWERBEGIN -ge $GAMMAPOWEREND -gs $GAMMAPOWERSTEP &
java -server -cp "build/install/pangenomics/lib/*" org.ncgr.weka.WekaSMO --gridsearch --arfffile=$TRAINFILE --kfold=$KFOLD --ngridsearch=$NGRIDSEARCH \
-cb 11 -ce 11 -cs $CPOWERSTEP -gb $GAMMAPOWERBEGIN -ge $GAMMAPOWEREND -gs $GAMMAPOWERSTEP &