--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macs2npk.sh	Fri Jan 18 11:18:11 2013 -0500
@@ -0,0 +1,60 @@
+#!/bin/bash
+# Converts macs xls output to narrowPeak output
+
+# Command Usage: macs2npk.sh INPUTFILE OUTPUTFILE
+
+if [[ "$#" -lt 1 ]]
+    then
+    echo $(basename $0) 1>&2
+    echo "Converts MACS peak caller xls output file to narrowPeak format" 1>&2
+    echo "USAGE:" 1>&2
+    echo "$(basename $0) <MACSXlsFile> <outputDir>" 1>&2
+    exit 1 
+fi
+
+MACSFILE=$1
+if [[ ! -e ${MACSFILE} ]]
+    then
+    echo "MACS xls file ${MACSFILE} does not exist" 1>&2
+    exit 1
+fi
+# ODIR=$(dirname ${MACSFILE})
+# [[ $# -gt 1 ]] && ODIR=$2
+# if [[ ! -d ${ODIR} ]]
+#    then
+#    echo "Output directory ${ODIR} does not exist" 1>&2
+#    exit 1
+# fi
+
+# OFILE="${ODIR}/$(echo $(basename ${MACSFILE} '_peaks.xls')).regionPeak.gz"
+OFILE="${2}"
+
+# XLS format
+# chr start stop length summit tags -10log10(pvalue) fold_enrichment %FDR
+
+# narrowPeak format
+# chr start stop name score strand signalValue -log10(pValue) -log10(qValue) summit
+
+# Remove comments #
+# Remove empty lines
+# Remove header
+# Sort by p-value and then rearrange columns
+# adjust start coordinates
+
+# Check if header has FDR column
+header=$(sed -r -e '/^#/d' -e '/^$/d' "${MACSFILE}" | head -1)
+hasFdr=0
+echo ${header} | grep -q 'FDR' && hasFDR=1
+
+if [[ ${hasFDR} -eq 1 ]]
+    then
+    sed -r -e '/^#/d' -e '/^$/d' "${MACSFILE}" | \
+	sed 1d | \
+	sort -k7nr,7nr | \
+	awk '$2 < 1 {$2=1} {printf "%s\t%d\t%d\t%d\t%s\t.\t%s\t%s\t%f\t%d\n",$1,$2-1,$3,NR,$6,$8,$7/10,-log(($9+1e-30)/100)/log(10),$5}' > ${OFILE}
+else
+    sed -r -e '/^#/d' -e '/^$/d' "${MACSFILE}" | \
+	sed 1d | \
+	sort -k7nr,7nr | \
+	awk '$2 < 1 {$2=1} {printf "%s\t%d\t%d\t%d\t%s\t.\t%s\t%s\t-1\t%d\n",$1,$2-1,$3,NR,$6,$8,$7/10,$5}' > ${OFILE}
+fi