#!/bin/bash
# ===============================
# Run FIMO motif scans sequentially
# ===============================

# Path to FIMO binary
FIMO_BIN="/home/litd/meme/bin/fimo"

# Input FASTA file
FASTA="MergedChipseq_peaks.fa"

# Check that FIMO exists
if [ ! -x "$FIMO_BIN" ]; then
  echo "Error: FIMO not found at $FIMO_BIN"
  exit 1
fi

# Check that FASTA exists
if [ ! -f "$FASTA" ]; then
  echo "Error: Input FASTA file not found: $FASTA"
  exit 1
fi

# Run FIMO for AR_full
echo "Running FIMO: AR_full.meme ..."
$FIMO_BIN --oc AR_full_out AR_full.meme "$FASTA"

# Run FIMO for AR_half
echo "Running FIMO: AR_half.meme ..."
$FIMO_BIN --oc AR_half_out AR_half.meme "$FASTA"

# Run FIMO for FOXA1
echo "Running FIMO: FOXA1.meme ..."
$FIMO_BIN --oc FOXA1_out FOXA1.meme "$FASTA"

echo "✅ All FIMO analyses completed."