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1 #!/bin/bash
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2
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3 # This tool has been written by Youri Hoogstrate from the Erasmus
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4 # Medical Center (Rotterdam, Netherlands) on behalf of the Translational
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5 # Research IT (TraIT) project:
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6 # http://www.ctmm.nl/en/programmas/infrastructuren/traitprojecttranslationeleresearch
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7 #
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8 # More tools by the Translational Research IT (TraIT) project can be
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9 # found in the following repository:
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10 # http://toolshed.dtls.nl/
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11
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12 exon_level="true"
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13 filename=""
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14
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15 # Parse parameters
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16 while getopts e:f: option
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17 do
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18 case "${option}"
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19 in
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20 e) exon_level=${OPTARG};;
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21 f) filename=$OPTARG;;
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22 esac
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23 done
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24
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25 # Convert the file
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26 if [ $filename == "" ]; then
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27 echo "Usage:"
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28 echo " -e [true, false] true = entry for every exon; false = line for genes first exon"
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29 echo " -f FILENAME from featureCounts"
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30 else
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31 while read line; do
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32 first=${line:0:1}
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33 if [ $first != "#" ]; then
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34 columns=($line)
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35 uid=${columns[@]:0:1}
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36 if [ $uid != "Geneid" ]; then
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37 chr=${columns[@]:1:1}
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38 start=${columns[@]:2:1}
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39 stop=${columns[@]:3:1}
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40 direction=${columns[@]:4:1}
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41 length=${columns[@]:5:1}
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42 count=${columns[@]:6:1}
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43
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44 chr_splitted=($(echo $chr | tr ";" "\n"))
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45 start_splitted=($(echo $start | tr ";" "\n"))
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46 stop_splitted=($(echo $stop | tr ";" "\n"))
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47 strand_splitted=($(echo $direction | tr ";" "\n"))
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48
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49 if [ $exon_level == "true" ]; then
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50 n=${#chr_splitted[@]}
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51 else
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52 n=1
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53 fi
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54
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55 for (( i=0; i<$n; i++ ))
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56 do
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57 echo ${chr_splitted[@]:$i:1}" "${start_splitted[@]:$i:1}" "${stop_splitted[@]:$i:1}" "$uid" ("$((${stop_splitted[@]:$i:1}-${start_splitted[@]:$i:1}))"/"$length"nt) "$count" "${strand_splitted[@]:$i:1}
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58 done
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59 fi
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60 fi
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61 done < $filename
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62 fi
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