#!/bin/bash
# ===============================
# Batch run HOMER findMotifsGenome.pl
# for all BED files in motif_finding/
# Genome: hg38
# ===============================

# Folder containing all BED files
FOLDER="motif_finding"

# Move into that folder
cd "$FOLDER" || { echo "Folder $FOLDER not found!"; exit 1; }

# Loop through all .bed files
for bedfile in *.bed; do
    # skip if no .bed files exist
    [ -e "$bedfile" ] || continue

    # Remove file extension to name output folder
    prefix=$(basename "$bedfile" .bed)
    outdir="${prefix}_MotifOutput"

    echo ">>> Running HOMER on $bedfile ..."
    findMotifsGenome.pl "$bedfile" hg38 "$outdir"

    echo ">>> Finished: results in $outdir/"
    echo
done

echo "All motif analyses completed!"