#!/usr/bin/env bash
set -euo pipefail

HOMER="/home/zhangbo/Tools/homer/bin/findMotifsGenome.pl"
GENOME="mm10"
PREPARSED="preparsed"

for file in OCR_adt_br_DAR_*_BPA*_*.sorted.bed
do
    [ -e "$file" ] || continue

    outdir="${file%.sorted.bed}"

    echo "Running motif analysis for: $file"
    echo "Output directory: $outdir"

    "$HOMER" "$file" "$GENOME" "$outdir" \
        -size given \
        -preparsedDir "$PREPARSED"
done