Shuffle ATAC and intersect

#!/bin/bash

#Intakes a BED file of 5kb regions around ATAC peak centers and a single position for the dREG and DSB motif centers in LZ, P and D stages, as well as a genome chromSizes file 
#and outputs the intersect counts in each of k shuffling iterations between the shuffled ATAC peaks and the dREG\DSB centers

LZ_ATAC=$1
P_ATAC=$2
D_ATAC=$3
LZ_dREG=$4
P_dREG=$5
D_dREG=$6
LZ_DMC1=$7
P_DMC1=$8
D_DMC1=$9
LZ_SPO11=$10
P_SPO11=$11
D_SPO11=$12
LZ_PRDM1=$13
P_PRDM1=$14
D_PRDM1=$15
chromSizes=$16
workDir=$17

mkdir -p ${workDir}/Random_shufled_LZ_ATAC_5kb
mkdir -p ${workDir}/Random_shufled_P_ATAC_5kb
mkdir -p ${workDir}/Random_shufled_D_ATAC_5kb

a=0

while [ $a -lt 1000 ]
do
   echo $a
   a=`expr $a + 1`
   bedtools shuffle -chrom -noOverlapping -i $LZ_ATAC -g $chromSizes > ${workDir}/LZ_ATAC.shuffled.bed
   bedtools shuffle -chrom -noOverlapping -i $LZ_ATAC -g $chromSizes > ${workDir}/P_ATAC.shuffled.bed
   bedtools shuffle -chrom -noOverlapping -i $LZ_ATAC -g $chromSizes > ${workDir}/D_ATAC.shuffled.bed
   bedtools intersect -a ${workDir}/LZ_ATAC.shuffled.bed -b $LZ_dREG $LZ_DMC1 $LZ_SPO11 $LZ_PRDM1 -C -names dREG DMC1 SPO11 PRDM9 > ${workDir}/Random_shufled_LZ_ATAC_5kb/ATAC_intersect_dREG_DMC1_SPO11_PRDM9.shuffled_${a}.bed
   bedtools intersect -a ${workDir}/P_ATAC.shuffled.bed -b $P_dREG $P_DMC1 $P_SPO11 $P_PRDM1 -C -names dREG DMC1 SPO11 PRDM9 > ${workDir}/Random_shufled_P_ATAC_5kb/ATAC_intersect_dREG_DMC1_SPO11_PRDM9.shuffled_${a}.bed
   bedtools intersect -a ${workDir}/D_ATAC.shuffled.bed -b $D_dREG $D_DMC1 $LZ_SPO11 $D_PRDM1 -C -names dREG DMC1 SPO11 PRDM9 > ${workDir}/Random_shufled_D_ATAC_5kb/ATAC_intersect_dREG_DMC1_SPO11_PRDM9.shuffled_${a}.bed

done