mergeBigWigs.bsh

#!/usr/bin/bash
#
#CHINFO=/fs/cbsudanko/storage/data/hg19/hg19.chromInfo

function show_help {
  echo "bash mergeBigWigs.bsh --chrom-info=PATH out.bigWig input_bigWig1 input_bigWig2 [ input_bigWig3 ...]"
  echo " "
  echo "-c, "
  echo "--chrom-info=PATH    Location of the chromInfo table."
  echo ""
  echo "options:"
  echo " "
  echo "To get help:"
  echo "-h,"
  echo "--help    show this brief help menu."
  echo " "
  echo " "
  exit 0
}


bwFiles=()
while test $# -gt 0; do
    case "$1" in
        -h|--help)
                show_help
                exit 0
                ;;
        --chrom-info*)
                export CHINFO=`echo $1 | sed -e 's/^[^=]*=//g'`
                shift
                ;;                
        -c)
               shift
               if test $# -gt 0; then
                  export CHINFO=$1
               else
                  echo "No chromInfo table is specified."
                 exit 1
               fi
               shift
               ;;
                
        *)
               bwFiles+=($1)
               shift
               ;;
        esac
done

if [ ${#bwFiles[@]} -eq 0 ]
then
    show_help
    exit 0
fi

if [ ${#bwFiles[@]} -lt 3 ] 
then
    echo "Error: Input files less than 2"
    exit 1
fi

if [ "$CHINFO" = "" ] 
then
   echo "Error: No chromInfo table is specified."
   exit 1
fi

#get the final file name
mergeBw=${bwFiles[0]}
echo "Output bigWig: $mergeBw"
#remove the first element
unset bwFiles[0]
echo "Input bigWigs: ${bwFiles[*]}"

for tool in bedtools bedGraphToBigWig bigWigToBedGraph
    do command -v ${tool} >/dev/null 2>&1 || { echo >&2 ${tool}" is required. Please make sure you can call the bioinformatics tools from your current working directoryb.  Aborting."; exit 1; }
done

WORKDIR=`mktemp -d`

for i in ${bwFiles[*]}
do
   bigWigToBedGraph $i $WORKDIR/$(basename $i).bedGraph
done

bedtools unionbedg -i `ls ${WORKDIR}/*.bedGraph` | awk 'BEGIN{OFS="\t"} {sum=0; for (i=4; i<=NF; i++) { sum+= $i } print $1,$2,$3, sum}' > ${WORKDIR}/all.bed

bedGraphToBigWig ${WORKDIR}/all.bed $CHINFO $mergeBw

#echo $WORKDIR

rm -rf $WORKDIR