track_merge_convert

#!/bin/bash

source code/custom-bashrc

usage()
{
cat << EOF

#########################################
-----------------------------------------
USAGE:
 $0 [PATH to chromInfo.txt] OUT-DIR [TRACK Name] <FILES(bw,bigwig,wig,wig.gz,bedgraph,bdg)>
-----------------------------------------

EOF
}

if [ "$#" -lt 3 ]; then
       usage
       exit
fi

CHROM_INFO=$1
shift
OUTDIR=$1
shift
TITLE=$1
shift
FILES=($@)

mkdir $OUTDIR
FILE_LIST=""

echo >&2
echo "Converting WIG/BEDGRAPH Files (if any)..." >&2

for FILE in ${FILES[@]}
do
       if echo $FILE | grep -iq "\.wig$"
       then
                echo "** Converting..." >&2
                echo "** `basename $FILE`" >&2
                wigToBigWig $FILE $CHROM_INFO ${FILE%.*}.bw >&2
                FILE_LIST=$FILE_LIST" "${FILE%.*}".bw"
       elif echo $FILE | grep -iq "\.wig.gz$"
       then
                echo "** Converting..." >&2
                echo "** `basename $FILE`" >&2
                zcat $FILE | wigToBigWig stdin $CHROMINFO ${FILE%.*}.bw >&2
                FILE_LIST=$FILE_LIST" "${FILE%.*}".bw"
       elif echo $FILE | grep -iq "\.bedgraph$\|\.bdg$"
       then
                echo "** Converting..." >&2
                echo "** `basename $FILE`" >&2
                bedGraphToBigWig $FILE $CHROMINFO ${FILE%.*}.bw  >&2
                FILE_LIST=$FILE_LIST" "${FILE%.*}".bw"
       elif echo $FILE | grep -iq "\.bigwig$\|\.bw"
       then                echo "** Skipping..." >&2
                echo "** `basename $FILE`" >&2
                FILE_LIST=$FILE_LIST" "${FILE}
       else
               usage
               exit 1
       fi
done

n=$#
if (( $n>1))
then
        f=$(echo "1 / $n" | bc -l)
#	f=1
        echo >&2
        echo "Merging $n Files..." >&2
        echo "** Norm Factor: $f" >&2

# merge bigwig files; this creates a bedgraph file which
# is saved as a temporary file
        tmp=$(mktemp)
        bigWigMerge $FILE_LIST stdout | awk -v f=$f 'BEGIN{OFS="\t"}{$4=f*$4; print}' > ${tmp}

        echo >&2
        echo "Converting to BigWig..." >&2
        # create new bigwig file from temporary bedgraph file
        bedGraphToBigWig ${tmp} ${CHROM_INFO} $OUTDIR/${TITLE}.bw >&2

        echo >&2
        echo "Cleaning Up..." >&2
        rm ${tmp}
else
        echo "Skiping Merge..." >&2
        cp ${FILE%.*}.bw $OUTDIR/$TITLE.bw
fi

echo "Done!" >&2