#PBS -q xl230g9q
#PBS -l select=1:ncpus=5:mem=10g
#PBS -l walltime=01:00:00
#PBS -l cput=01:00:00

source activate nn_Polina_tf2;
WORK_DIR=/mnt/scratch/ws/psbelokopytova/202312241147Polina/loxP_project/2023-05-18
cd $WORK_DIR;
[ -d stat ] || mkdir stat
# Declare a string array with type
declare -a files=('sum_rear1')
for file in "${files[@]}"
do
cd $WORK_DIR/align/${file}/;
[ -d stat ] || mkdir ${file}_scores_pictures
echo ${file}
python ~/scratch/202312241147Polina/loxP_project/find_insertions.py $WORK_DIR/align/${file}/${file}_aboveMapq30_nodup2_prim.sorted.bam $WORK_DIR/align/${file}/${file}_aboveMapq30_nodup2_prim.modified.bedgraph $WORK_DIR/stat/${file}_ins_sites.txt $WORK_DIR/align/${file}/${file}_scores_pictures
done
