Calculate-GWAS-Enrichment.sh

#!/bin/bash

id=$1
signal=$2
regions=$3
mode=$4
pmid=$5
dataPath=$6

file=$dataPath/$signal"-List.txt"
dir=~/Lab/ENCODE/Encyclopedia/V5/GWAS/$id
scriptDir=/home/moorej3/Projects/GWAS/Updated-VIPER
sigDir=$dataPath/signal-output
i=$SLURM_ARRAY_TASK_ID
regionShort=$(echo $regions | awk -F "/" '{print $NF}' | awk -F "." '{print $1}')

mkdir -p /tmp/moorej3/$SLURM_JOBID
cd /tmp/moorej3/$SLURM_JOBID

if [[ $mode == "NoHLA" ]]
then
awk '{if ($1 != "chr6") print $0}' $dir/$pmid.bed > bed
~/bin/bedtools2/bin/bedtools intersect -wo -a bed -b $regions | \
    awk '{print $4 "\t" $5 "\t" $7 "\t" $11}' > MP.txt
else
~/bin/bedtools2/bin/bedtools intersect -wo -a $dir/$pmid.bed -b $regions | \
    awk '{print $4 "\t" $5 "\t" $7 "\t" $11}' > MP.txt
fi

total=$(awk '{print $3}' MP.txt | sort -u | wc -l | awk '{print $1}')

l=$(wc -l $file | awk '{print $1}')
for j in $(seq $l)
do
    echo $j
    columns=$(head -n 1 $file | awk '{print NF}')
    if [ "$columns" -eq 2 ]
    then
        sigFile=$(awk -F "\t" '{if (NR == '$j') print $1".txt"}' $file)
    else
        sigFile=$(awk -F "\t" '{if (NR == '$j') print $1"-"$2".txt"}' $file)
    fi
    awk 'FNR==NR {x[$4];next} ($1 in x)' MP.txt $sigDir/$sigFile > sig.txt
    python $scriptDir/count.overlap.py MP.txt sig.txt $total $signal \
        >> Overlap.$id.$signal.$regionShort.$mode.txt
done 

mv Overlap.$id.$signal.$regionShort.$mode.txt $dir/

rm -r /tmp/moorej3/$SLURM_JOBID