#!/bin/bash
#
#SBATCH --output=/home/jvierstra/proj/footprinting.2019/index/0p01/variation/logs/%A.%a.out
#SBATCH --mem=12G
#SBATCH --cpus-per-task=4

set -o pipefail

TMPDIR=`mktemp -d`

ARGS=(`cat /home/jvierstra/proj/footprinting.2019/index/0p01/variation/slurm.params | head -n ${SLURM_ARRAY_TASK_ID} | tail -n 1`)

motif=${ARGS[0]}

mkdir -p /home/jvierstra/proj/footprinting.2019/index/0p01/variation/${motif}

grep -w "${motif}" index/masterlist_DHSs_733samples_WM20180608_all_indexIDs_243subset.5kb.motifs-coords.bed |  awk -F"\t" '!seen[$1, $2, $3]++' >  /home/jvierstra/proj/footprinting.2019/index/0p01/variation/${motif}/intervals.bed

python2 /home/jvierstra/proj/footprinting.2019/motif_con_var.py 	 /home/jvierstra/proj/footprinting.2019/index/0p01/variation/${motif}/intervals.bed /home/jvierstra/data/genomes/hg38/phyloP100way/hg38.phyloP100way.bed.gz /home/jvierstra/data/topmed_variants/ALL.TOPMed_freeze5_hg38_dbSNP.ancestral.vcf.gz /home/jvierstra/data/genomes/hg38/hg.all.fa /home/jvierstra/data/genomes/hg38/ancestral/homo_sapiens_ancestor_GRCh38/homo_sapiens_ancestor.fixed.fa /home/jvierstra/proj/footprinting.2019/index/0p01/variation/${motif}

rm -rf ${TMPDIR}