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1 #!/bin/bash
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2 input="$1"
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3 output="$2"
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4 outDir="$3"
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5 mkdir "$outDir"
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6 EOL="$4"
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7 mismatches="$5"
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8 partial="$6"
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9 name=$(basename "$7")
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10 ext="${name##*.}"
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11 name="${name%.*}"
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12 name="${name// /_}"
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13 prefix="${name}_"
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14 dir="$(cd "$(dirname "$0")" && pwd)"
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15
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16 unzip $dir/fastqc_v0.11.2.zip -d $PWD/ > $PWD/unziplog.log
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17 chmod 755 $PWD/FastQC/fastqc
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18
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19 declare -A trim_start
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20 declare -A trim_end
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21 for ((i=8;i<=$#;i=i+4))
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22 do
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23 j=$((i+1))
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24 start_int=$((i+2))
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25 end_int=$((i+3))
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26 id="${!i}"
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27 echo "$id, ${start_int}, ${end_int}"
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28 trim_start[$id]=${!start_int}
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29 trim_end[$id]=${!end_int}
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30 echo -e "$id\t${!j}" >> $outDir/barcodes.txt
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31
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32 done
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33 trim_start["unmatched"]=0
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34 trim_end["unmatched"]=0
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35
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36 echo "trim_start = ${trim_start[@]}"
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37 echo "trim_end = ${trim_end[@]}"
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38
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39 workdir=$PWD
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40 cd $outDir
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41 echo "$3"
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42 filetype=`file $input`
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43 result=""
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44 if [[ $filetype == *ASCII* ]]
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45 then
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46 result=`cat $input | $dir/fastx_barcode_splitter.pl --bcfile $outDir/barcodes.txt --prefix "$prefix" --suffix ".fastq" --$EOL --mismatches $mismatches --partial $partial`
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47 else
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48 result=`$dir/sff2fastq $input | $dir/fastx_barcode_splitter.pl --bcfile $outDir/barcodes.txt --prefix "$prefix" --suffix ".fastq" --$EOL --mismatches $mismatches --partial $partial`
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49 fi
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50
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51 echo "$result" | tail -n +2 | sed 's/\t/,/g' > output.txt
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52 echo "<html><head><title>$name demultiplex</title></head><body><table border='1'><thead><tr><th>ID</th><th>Count</th><th>FASTQ</th><th>FASTA</th><th>Trimmed FASTA</th><th>FASTQC</th></tr></thead><tbody>" >> $output
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53 while IFS=, read barcode count location
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54 do
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55 if [ "total" == "$barcode" ]
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56 then
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57 echo "<tr><td>$barcode</td><td>$count</td><td></td><td></td><td></td><td></td><td></td><td></td></tr>" >> $output
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58 break
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59 fi
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60 file="${name}_${barcode}"
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61 mkdir "$outDir/fastqc_$barcode"
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62 $workdir/FastQC/fastqc "$file.fastq" -o "$outDir" 2> /dev/null
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63 cat "$file.fastq" | awk 'NR%4==1{printf ">%s\n", substr($0,2)}NR%4==2{print}' > "$file.fasta"
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64 python $dir/trim.py --input "$file.fasta" --output "${file}_trimmed.fasta" --start "${trim_start[$barcode]}" --end "${trim_end[$barcode]}"
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65 echo "<tr><td>$barcode</td><td>$count</td><td><a href='$file.fastq'>$file.fastq</a></td><td><a href='$file.fasta'>$file.fasta</a></td><td><a href='${file}_trimmed.fasta'>${file}_trimmed.fasta</a></td><td><a href='${name}_${barcode}_fastqc.html'>Report</a></td></tr>" >> $output
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66 done < output.txt
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67 echo "</tbody></body></html>" >> $output
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