rjBitSeq

#!/bin/bash

if [ $# -eq 0 ]
  then
	echo "No arguments supplied"
	echo "Display usage info: rjBitSeq --help"
	exit 0
fi

if [ $1 == C ]
then
	echo "ERROR: Two sets of files should be provided, separated by C"
	echo "Display usage info: rjBitSeq --help"
	echo "exiting."
	exit 0
fi

if [ $1 == --help ]
then
	echo ""
	echo ".............................................................................................."
	echo ". Usage: rjBitSeq <outputDir> <.prob files condition A> C <.prob files condition B>          ."
	echo ".                                                                                            ."
	echo ". Reversible Jump algorithm for Differential Expression analysis                             ."	
	echo ".                                                                                            ."
	echo ". Arguments:                                                                                 ."
	echo ".    <outputDir>: Name of the output directory.                                              ."
	echo ".                                                                                            ."
	echo ".    <.prob files condition A>: Space-separated list of '.prob' files for the first sample.  ."
	echo ".                                                                                            ."
	echo ".    <.prob files condition B>: Space-separated list of '.prob' files for the second sample. ."
	echo ".                                                                                            ."
	echo ". Note: '.prob' files contain alignment probabilities for each read                          ."
	echo ".       and they are computed using the 'parseAlignment' command of Bitseq.                  ."
	echo ".                                                                                            ."
	echo ". Detailed documentation and examples: https://github.com/mqbssppe/rjBitSeq-1.0/wiki         ."
	echo ".............................................................................................."
	echo ""
	exit 0
fi

if test -d $1; then echo "Directory exists! Please provide different name."; exit 0; fi

mkdir $1
CWD=$(pwd)
echo "output written to $CWD/$1"
a=`expr 1`
b=`expr 0`
c=`expr 2`


echo "First condition files:"
for i in $*
do
	if [ $i == $1 ]
	then
		a=`expr 2`
	fi
	if [ $a -eq 1 ]
	then
		if [ $i == C ]
		then
			a=`expr 2`
			c=`expr 1`
		else
			b=$((b+1))
			echo "	: $i, $b"
			if [ ! -f $i ]; then
				echo "ERROR: File not found!"
				echo "exiting."
				echo "Display usage info: rjBitSeq --help"
				exit 0
			fi
			cd $1
			ln -s ../$i conditionA_$b.prob
			sed '3d' conditionA_$b.prob > tmpfile
			mv tmpfile conditionA_$b.prob
			cd ..
		fi
	fi
	if [ $i == $1 ]
	then
		a=`expr 1`
	fi
done
a=`expr 1`
b=`expr 0`
echo "Second condition files:"
for i in $*
do
	if [ $i == C ]
	then
		a=`expr 2`
		c=`expr 1`
	fi
	if [ $a -eq 2 ]
	then
		if [ $i != C ]
		then
			b=$((b+1))
			echo "	: $i, $b"
			if [ ! -f $i ]; then
				echo "ERROR: File not found!"
				echo "Display usage info: rjBitSeq --help"
				echo "exiting."
				exit 0
			fi
			cd $1
			ln -s ../$i conditionB_$b.prob
			sed '3d' conditionB_$b.prob > tmpfile
			mv tmpfile conditionB_$b.prob
			cd ..
		fi
	fi
done

if [ $c -eq 2 ]
then
	echo "ERROR: Two sets of files should be provided, separated by C"
	echo "Display usage info: rjBitSeq --help"
	echo "exiting."
	exit 0
fi

cd $1
cpThis.bash
echo "computing clusters (output written to $CWD/$1/partitionMerge2.Rout)"
time R CMD BATCH partitionMerge2.R
echo "done!"
echo "Running Reversible Jump using parallel GNU"
time ./parallelGNU.bash
echo "Done!"
echo "Estimates written to $CWD/$1/estimates.txt"

exit 0