bdgTobw

#! /bin/bash

command -v bedtools &>/dev/null || { echo "bedtools not found! Download bedTools: <http://code.google.com/p/bedtools/>"; exit 1; }
command -v bedGraphToBigWig &>/dev/null || { echo "bedGraphToBigWig not found! Download: <http://hgdownload.cse.ucsc.edu/admin/exe/>"; exit 1; }
command -v bedClip &>/dev/null || { echo "bedClip not found! Download: <http://hgdownload.cse.ucsc.edu/admin/exe/>"; exit 1; }

[[ $# -lt 3 ]] && echo "USAGE: <PROG> [bdg-file] [chrom-sizes] [bw-file] [tmp-dir]" \
               && echo "Converts Bedgraph file to Bigwig." \
               && echo "  [tmp-dir]: Set to /dev/shm if not specified" \
               && exit 1

base=$(basename "$1")

tmpdir="$4"
[[ -z "$tmpdir" ]] && tmpdir="/dev/shm"

echo "Using $base."
echo "TMPDIR set to $tmpdir."

echo "Clipping and sorting bedgraph.."

bedtools slop -i "$1" -g "$2" -b 0 \
  | bedClip stdin "$2" stdout \
  | LC_COLLATE=C sort -k1,1 -k2,2n > "$tmpdir/$base.sorted.bdg"

echo "Converting to bigwig.."
bedGraphToBigWig "$tmpdir/$base.sorted.bdg" "$2" "$3"
echo "Wrote to $3."

echo "Cleanup.."
rm "$tmpdir/$base.sorted.bdg"

echo "Done."