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1 #!/bin/bash
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2
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3 #set -euo pipefail # this is something like string in perl
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4 IFS=$'\n\t'
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5
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6 # run filtering
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7 WD="`dirname $0`"
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8 ORIDIR=$PWD
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9 cd $WD
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10 WD=$PWD # absolute path to this script
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11 cd $ORIDIR
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12 SAMPLING=""
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13 TRIM_END=""
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14 TRIM_START=""
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15 PERCENT_ABOVE="95"
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16 CUTADAPT=""
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17 FILTER_SEQ=""
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18 while getopts "a:o:n:c:p:e:s:N:C:G:F:" OPTION
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19 do
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20 case $OPTION in
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21 a)
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22 FASTAA=$OPTARG;;
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23 o)
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24 OUTPUT=$OPTARG;;
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25 n)
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26 SAMPLING=( -n ${OPTARG} );;
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27 c)
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28 CUT_OFF=$OPTARG;;
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29 p)
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30 PERCENT_ABOVE=$OPTARG;;
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31 e)
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32 TRIM_END=( -e ${OPTARG} );;
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33 s)
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34 TRIM_START=( -s ${OPTARG} );;
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35 N)
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36 MAX_N=${OPTARG};;
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37 C)
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38 CUTADAPT=(-C " "${OPTARG}" " );;
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39 G)
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40 PNG_OUTPUT=${OPTARG};;
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41 F)
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42 FILTER_SEQ=( -F ${OPTARG} );;
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43 esac
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44 done
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45
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46
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47
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48 if [ -z "$CUTADAPT" ] # test if $CUTADAPT is empty
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49 then
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50 ${WD}/single_fastq_filtering.R -a $FASTAA -x $OUTPUT ${SAMPLING[@]} -c $CUT_OFF\
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51 -p $PERCENT_ABOVE ${TRIM_START[@]} ${TRIM_END[@]} -N $MAX_N -G $PNG_OUTPUT ${FILTER_SEQ[@]}
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52 else
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53 ${WD}/single_fastq_filtering.R -a $FASTAA -x $OUTPUT ${SAMPLING[@]} -c $CUT_OFF -G $PNG_OUTPUT\
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54 -p $PERCENT_ABOVE ${TRIM_START[@]} ${TRIM_END[@]} -N $MAX_N "${CUTADAPT[@]}" ${FILTER_SEQ[@]}
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55 fi
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56
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57
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58
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59
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