#!/bin/bash
#$ -S /bin/bash
#$ -N getGenes
#$ -o /dev/null -j y
#$ -q HPblg7,HP8g7,galaxy
cd /san/personal/dan/ag1kg/shicScanPhaseI

python /san/personal/dan/ag1kg/shicScanPhaseI/getExonsOverlappingEachBedElement.py /nfs/kernlab_ISI/data/ag1kg/phaseIShicScan/permutedSets5State//AOM/permutation_101/soft.bed /san/data/ag1kg/geneset/Anopheles-gambiae-PEST_BASEFEATURES_AgamP4.7.gff3.gz 5000 > /nfs/kernlab_ISI/data/ag1kg/phaseIShicScan/permutedSets5StateGenes//AOM/permutation_101/soft.bed