path='/datafc/zhang/makerman/MapSplice_1.15.2'
data='/data/zhang/makerman/MapSplice'
in1=$1
in2=$2
out=$3

mkdir $in1.in
mkdir $in2.in
mkdir $out.out
mkdir $out.log
mkdir $out.sh

split -l2000000 $in1 -a5 -d in1.$in1.
split -l2000000 $in2 -a5 -d in2.$in2.

for i in in1.$in1*
do
mkdir $in1.in/$i
mv $i $in1.in/$i
done

for i in in2.$in2*
do
mkdir $in2.in/$i
mv $i $in2.in/$i
done

list1=(`ls $in1.in`)
list2=(`ls $in2.in`)
len=${#list1[*]}
i=0
while [ $i -lt $len ]; 
	do
	read1=$data"/"$in1.in"/"${list1[$i]}"/"${list1[$i]}
	read2=$data"/"$in2.in"/"${list2[$i]}"/"${list2[$i]}
	echo "python $path/bin/mapsplice_segments.py -u $read1,$read2 -c /data/zhang/wuj/database/hg18/genome/fasta -B /data/zhang/wuj/database/hg18/genome/btw/hg18 -o $data/$out.out/$out.$i -L 18 -Q fq -n 8 --pairend " > $out.sh/out.$i.sh
	qsub -V -l virtual_free=2.8G -e $data/$out.log/ -o $data/$out.log/ $out.sh/out.$i.sh
        let i++
done