taoliu · November 3, 2024 17:01 · brentp · Apr 23, 2012 · taoliu · Apr 23, 2012
diff --git a/bdg2bw b/bdg2bw
 #!/bin/bash

 # check commands: slopBed, bedGraphToBigWig and bedClip

 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; }

 # end of checking

 if [ $# -lt 2 ];then
    echo "Need 2 parameters! <bedgraph> <chrom info>"
    exit
 fi

 F=$1
 G=$2

 bedtools slop -i ${F} -g ${G} -b 0 | bedClip stdin ${G} ${F}.clip

 LC_COLLATE=C sort -k1,1 -k2,2n ${F}.clip > ${F}.sort.clip

 bedGraphToBigWig ${F}.sort.clip ${G} ${F/bdg/bw}

 rm -f ${F}.clip ${F}.sort.clip
	#!/bin/bash

	# check commands: slopBed, bedGraphToBigWig and bedClip

	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; }

	# end of checking

	if [ $# -lt 2 ];then
	echo "Need 2 parameters! <bedgraph> <chrom info>"
	exit
	fi

	F=$1
	G=$2

	bedtools slop -i ${F} -g ${G} -b 0 \| bedClip stdin ${G} ${F}.clip

	LC_COLLATE=C sort -k1,1 -k2,2n ${F}.clip > ${F}.sort.clip

	bedGraphToBigWig ${F}.sort.clip ${G} ${F/bdg/bw}

	rm -f ${F}.clip ${F}.sort.clip