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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/featurecounts_galaxy_wrapper commit 597fa3df643b54ea93a17448c722f657e3d68b60
author yhoogstrate
date Wed, 07 Oct 2015 11:38:41 -0400
parents b5c93611d2c5
children
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ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
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1 #!/bin/bash
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3 # featurecounts2bed - converts featureCounts output to BED format
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5 # Copyright 2013-2014, Youri Hoogstrate
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7 # This program is free software: you can redistribute it and/or modify
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8 # it under the terms of the GNU General Public License as published by
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9 # the Free Software Foundation, either version 3 of the License, or
ab0323782bb5 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty
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10 # (at your option) any later version.
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11
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12 # This program is distributed in the hope that it will be useful,
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13 # but WITHOUT ANY WARRANTY; without even the implied warranty of
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14 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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15 # GNU General Public License at <http://www.gnu.org/licenses/> for
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16 # more details.
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18 # This tool has been written by Youri Hoogstrate from the Erasmus
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19 # Medical Center (Rotterdam, Netherlands) on behalf of the Translational
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20 # Research IT (TraIT) project:
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21 # http://www.ctmm.nl/en/programmas/infrastructuren/traitprojecttranslationeleresearch
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24 exon_level="true"
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25 filename=""
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26
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27 # Parse parameters
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28 while getopts e:f: option
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29 do
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30 case "${option}"
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31 in
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32 e) exon_level=${OPTARG};;
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33 f) filename=$OPTARG;;
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34 esac
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35 done
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36
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37 # Convert the file
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38 if [ $filename == "" ]; then
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39 echo "Usage:"
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40 echo " -e [true, false] true = entry for every exon; false = line for genes first exon"
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41 echo " -f FILENAME from featureCounts"
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42 else
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43 while read line; do
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44 first=${line:0:1}
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45 if [ $first != "#" ]; then
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46 columns=($line)
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47 uid=${columns[@]:0:1}
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48 if [ $uid != "Geneid" ]; then
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49 chr=${columns[@]:1:1}
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50 start=${columns[@]:2:1}
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51 stop=${columns[@]:3:1}
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52 direction=${columns[@]:4:1}
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53 length=${columns[@]:5:1}
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54 count=${columns[@]:6:1}
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55
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56 chr_splitted=($(echo $chr | tr ";" "\n"))
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57 start_splitted=($(echo $start | tr ";" "\n"))
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58 stop_splitted=($(echo $stop | tr ";" "\n"))
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59 strand_splitted=($(echo $direction | tr ";" "\n"))
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60
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61 if [ $exon_level == "true" ]; then
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62 n=${#chr_splitted[@]}
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63 else
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64 n=1
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65 fi
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66
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67 for (( i=0; i<$n; i++ ))
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68 do
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69 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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70 done
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71 fi
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72 fi
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73 done < $filename
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74 fi