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1 #!/bin/bash
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2 # Converts macs xls output to narrowPeak output
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3
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4 # Command Usage: macs2npk.sh INPUTFILE OUTPUTFILE
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5
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6 if [[ "$#" -lt 1 ]]
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7 then
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8 echo $(basename $0) 1>&2
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9 echo "Converts MACS peak caller xls output file to narrowPeak format" 1>&2
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10 echo "USAGE:" 1>&2
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11 echo "$(basename $0) <MACSXlsFile> <outputDir>" 1>&2
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12 exit 1
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13 fi
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14
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15 MACSFILE=$1
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16 if [[ ! -e ${MACSFILE} ]]
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17 then
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18 echo "MACS xls file ${MACSFILE} does not exist" 1>&2
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19 exit 1
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20 fi
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21 # ODIR=$(dirname ${MACSFILE})
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22 # [[ $# -gt 1 ]] && ODIR=$2
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23 # if [[ ! -d ${ODIR} ]]
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24 # then
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25 # echo "Output directory ${ODIR} does not exist" 1>&2
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26 # exit 1
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27 # fi
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28
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29 # OFILE="${ODIR}/$(echo $(basename ${MACSFILE} '_peaks.xls')).regionPeak.gz"
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30 OFILE="${2}"
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31
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32 # XLS format
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33 # chr start stop length summit tags -10log10(pvalue) fold_enrichment %FDR
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34
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35 # narrowPeak format
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36 # chr start stop name score strand signalValue -log10(pValue) -log10(qValue) summit
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37
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38 # Remove comments #
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39 # Remove empty lines
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40 # Remove header
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41 # Sort by p-value and then rearrange columns
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42 # adjust start coordinates
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43
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44 # Check if header has FDR column
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45 header=$(sed -r -e '/^#/d' -e '/^$/d' "${MACSFILE}" | head -1)
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46 hasFdr=0
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47 echo ${header} | grep -q 'FDR' && hasFDR=1
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48
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49 if [[ ${hasFDR} -eq 1 ]]
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50 then
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51 sed -r -e '/^#/d' -e '/^$/d' "${MACSFILE}" | \
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52 sed 1d | \
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53 sort -k7nr,7nr | \
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54 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}' > ${OFILE}
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55 else
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56 sed -r -e '/^#/d' -e '/^$/d' "${MACSFILE}" | \
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57 sed 1d | \
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58 sort -k7nr,7nr | \
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59 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}
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60 fi
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