todoMISOStepThreeDetectDifferentialSpecifyingComparisons.sh

#!/bin/bash

if [ $# -ne 2 ]; then
	echo $0 MISOSettingFile "mode[normal|reduced]"
	echo "in MISOSettingFile specify COMPARISON_SAMPLEX and COMPARISON_SAMPLEY as arrays of comparison X[0] vs Y[0], .. X[n-1] vs Y[n-1]"
	exit
fi

MISOSettingFile=$1
mode=$2

source ${MISOSettingFile}

misoRunSetting=`abspath.py $misoRunSetting`

echo using miso run setting file $misoRunSetting


thisScriptDir=`pwd`

cd ..

rootDir=`pwd`

#cd $MISOPATH 

tophatOutputDir=$rootDir/$bamFileSubRoot

if [[ $mode == "normal" ]]; then
	echo differential using the normal MISO mode
	MISOOutputDir=$rootDir/${MISOOutSubRoot}/MISOOutput
	MISOSummaryDir=$rootDir/${MISOOutSubRoot}/MISOSummary
	MISOComparisonsDir=$rootDir/${MISOOutSubRoot}/MISOComparisons
elif [[ $mode == "reduced" ]]; then
	echo differential using the MISO full-transcript reduced to Splidar mode
	MISOOutputDir=$rootDir/${MISOOutSubRoot}/MISOOutput.reduced
	MISOSummaryDir=$rootDir/${MISOOutSubRoot}/MISOSummary.reduced
	MISOComparisonsDir=$rootDir/${MISOOutSubRoot}/MISOComparisons.reduced	
else
	echo unknown summary mode $mode
	bash $0
	exit
fi	

mkdir $MISOComparisonsDir


# differential, all pairwise, all directions

for ((i=0;i<${#COMPARISON_SAMPLEX[@]};i++)); do

sampleNamex=${COMPARISON_SAMPLEX[$i]}
sampleNamey=${COMPARISON_SAMPLEY[$i]}
#for sampleNamex in ${COMPARISON_SAMPLEX[@]}; do
#for sampleNamey in ${COMPARISON_SAMPLEY[@]}; do

echo "trying to compare sample $sampleNamex and $sampleNamey"


misoOutputDirPerSamplex=$MISOOutputDir/$sampleNamex
misoOutputDirPerSampley=$MISOOutputDir/$sampleNamey
misoComparisonsDirPerPairs=$MISOComparisonsDir/${sampleNamex}-${sampleNamey}

mkdir $misoComparisonsDirPerPairs

rm -f $misoComparisonsDirPerPairs/compare_samples.std*


echo "run_miso.py --compare-samples $misoOutputDirPerSamplex $misoOutputDirPerSampley $misoComparisonsDirPerPairs > $misoComparisonsDirPerPairs/compare_samples.stdout 2> $misoComparisonsDirPerPairs/compare_samples.stderr" | bsub

done


#COMMENT