#!/bin/bash

TSS=gencode_mm10_gene_TSS_pc_lncRNA.sorted.bed
PEAKDIR=sorted_peaks
OUTDIR=nearest_TSS_1Mb_pc_lncRNA_mm10

mkdir -p "$OUTDIR"

for PEAK in "$PEAKDIR"/*.bed; do
  BASENAME=$(basename "$PEAK" .bed)

  bedtools closest \
    -a "$PEAK" \
    -b "$TSS" \
    -D a \
    -k 1 \
    -sorted \
  | awk 'BEGIN{OFS="\t"} $NF != "." && ($NF <= 1000000 && $NF >= -1000000)' \
  > "$OUTDIR/${BASENAME}_peak_gene_1Mb.txt"
done