bdgToBw

#! /bin/bash

# Vivek Rai
# Parker Lab
# vivekrai@umich.edu
#
# April 20, 2019

set -eo pipefail

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

[[ $# -ne 3 ]] && echo "Usage: <PROG> [bdg-file] [chrom-sizes] [bw-file]" \
               && echo "Converts Bedgraph file to Bigwig." \
               && echo "Optionally set TMPDIR for a different scratch directory." \
               && exit 1

say() {
  echo "$@" 2> /dev/stderr
}

# Wolverine and falcon specific; default to directory of input Bedgraph file
if [[ -z $TMPDIR ]]; then
  case $(hostname) in
    wolverine | falcon)
      TMPDIR="/localscratch"
      ;;
    *)
      TMPDIR=$(dirname "$1")
      ;;
  esac
fi

# more sanity checks
[[ ! -f "$1" ]] && say "$1 not found. Exiting!" && exit 1
[[ ! -f "$2" ]] && say "$2 not found. Exiting!" && exit 1

base=$(basename "$1")

say "Converting $base, TMPDIR=$TMPDIR"

say "Clipping and sorting bedgraph.."

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

say "Converting to bigwig.."
bedGraphToBigWig "$TMPDIR/$base.sorted.bdg" "$2" "$3"

say "Cleanup.."
unlink "$TMPDIR/$base.sorted.bdg"

say "Done."