runListBounds.bash

#!/bin/bash
. <(./setup.sh)
export R_LIBS_USER=/home/tholzman/R/Library
export mainDir=$1
export toBeCreatedDir=$2
export patient=$3
export lb=$4
export ub=$5
export outputDir=${mainDir}/founder-inference-bakeoff_${toBeCreatedDir}_${patient}
mkdir $outputDir
rm -rf ${outputDir}/*
export listFile=${mainDir}/processed_${patient}.list
export homeDir=`pwd`
while read fname
do
   echo $fname
   bn=`basename $fname .fasta`
   export outputFile=${outputDir}/${bn}.out
   export errFile=${outputDir}/${bn}.err
   echo $fname > $outputFile
   pushd .
   cd $outputDir
   echo "$homeDir/bin/infer.sh --verbose --toi ${lb},${ub} -p ${bn}. $fname >>$outputFile 2>>$errFile" >>$outputFile
   $homeDir/bin/infer.sh --verbose --toi ${lb},${ub} -p ${bn}. $fname >>$outputFile 2>>$errFile
   mv infer_multiple.fa ${outputFile}multiple.fa
   mv infer_single.fa   ${outputFile}single.fa
   mv infer_toi.csv     ${outputFile}toi.csv
   mv infer_beast_in.xml ${outputFile}_beast_in.xml
   popd
done < $listFile