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1 #!/bin/bash
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2 set -euo pipefail
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3 IFS=$'\n\t'
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4
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5 # run filtering
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6 WD="`dirname $0`"
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7 ORIDIR=$PWD
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8 cd $WD
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9 WD=$PWD # absolute path to this script
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10 cd $ORIDIR
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11 SAMPLING=""
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12 TRIM_END=""
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13 TRIM_START=""
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14 PERCENT_ABOVE="95"
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15 CUTADAPT=""
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16 RENAME=""
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17 FILTER_SEQ=""
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18 while getopts "a:b:o:n:c:p:e:s:N:C:G:F:R" 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 b)
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24 FASTAB=$OPTARG;;
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25 o)
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26 PAIRED_OUTPUT=$OPTARG;;
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27 n)
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28 SAMPLING=( -n ${OPTARG} );;
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29 c)
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30 CUT_OFF=$OPTARG;;
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31 p)
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32 PERCENT_ABOVE=$OPTARG;;
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33 e)
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34 TRIM_END=( -e ${OPTARG} );;
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35 s)
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36 TRIM_START=( -s ${OPTARG} );;
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37 N)
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38 MAX_N=${OPTARG};;
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39 C)
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40 CUTADAPT=(-C " "${OPTARG}" " );;
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41 G)
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42 PNG_OUTPUT=${OPTARG};;
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43 R)
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44 RENAME="-R";;
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45 F)
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46 FILTER_SEQ=( -F ${OPTARG} );;
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47
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48 esac
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49 done
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50 fasta_tmp_fileX=$(mktemp)
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51 fasta_tmp_fileY=$(mktemp)
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52
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53 if [ -z "$CUTADAPT" ] # test if$CUTADAPT is empty
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54 then
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55 ${WD}/paired_fastq_filtering.R -a $FASTAA -b $FASTAB -x $fasta_tmp_fileX -y $fasta_tmp_fileY ${SAMPLING[@]} -c $CUT_OFF -G $PNG_OUTPUT\
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56 -p $PERCENT_ABOVE ${TRIM_START[@]} ${TRIM_END[@]} -N $MAX_N $RENAME ${FILTER_SEQ[@]}
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57 else
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58 ${WD}/paired_fastq_filtering.R -a $FASTAA -b $FASTAB -x $fasta_tmp_fileX -y $fasta_tmp_fileY ${SAMPLING[@]} -c $CUT_OFF -G $PNG_OUTPUT\
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59 -p $PERCENT_ABOVE ${TRIM_START[@]} ${TRIM_END[@]} -N $MAX_N "${CUTADAPT[@]}" $RENAME ${FILTER_SEQ[@]}
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60 fi
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61
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62 ${WD}/fasta_interlacer.py -a $fasta_tmp_fileX -b $fasta_tmp_fileY -p $PAIRED_OUTPUT -x fasta_tmp_single
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63
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64
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65 rm $fasta_tmp_fileX
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66 rm $fasta_tmp_fileY
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