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53
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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 name=$3
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5 dir="$(cd "$(dirname "$0")" && pwd)"
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6 mkdir -p $PWD/$name/files
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7 f=$(file $input)
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8 zip7Type="7-zip archive"
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9 tarType="tar archive"
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10 bzip2Type="bzip2 compressed"
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11 gzipType="gzip compressed"
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12 zipType="Zip archive"
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13 rarType="RAR archive"
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14 zxType="XZ compressed data"
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15
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16 if [[ "$f" == *"$zip7Type"* ]]; then
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17 echo "7-zip"
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18 echo "Trying: 7za e $input -o$PWD/files/"
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19 7za e $input -o$PWD/$name/files
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20 fi
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21
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22 if [[ "$f" == *"$tarType"* ]]
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23 then
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24 echo "tar archive"
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25 echo "Trying: tar xvf $input -C $PWD/files/"
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26 tar -xvf $input -C $PWD/$name/files
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27 fi
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28
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29 if [[ "$f" == *"$bzip2Type"* ]]
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30 then
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31 echo "bzip2 compressed data"
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32 echo "Trying: tar jxf $input -C $PWD/files/"
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33 tar -jxf $input -C $PWD/$name/files
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34 fi
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35
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36 if [[ "$f" == *"$gzipType"* ]]
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37 then
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38 echo "gzip compressed data"
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39 echo "Trying: tar xvzf $input -C $PWD/files/"
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40 tar -xvzf $input -C $PWD/$name/files
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41 fi
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42
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43 if [[ "$f" == *"$zipType"* ]]
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44 then
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45 echo "Zip archive"
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46 echo "Trying: unzip $input -d $PWD/files/"
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47 unzip $input -d $PWD/$name/files > $PWD/unziplog.log
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48 fi
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49
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50 if [[ "$f" == *"$rarType"* ]]
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51 then
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52 echo "RAR archive"
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53 echo "Trying: unrar e $input $PWD/files/"
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54 unrar e $input $PWD/$name/files
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55 fi
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56
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57 if [[ "$f" == *"$zxType"* ]]
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58 then
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59 echo "xz compressed data"
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60 echo "Trying: tar -xJf $input -C $PWD/files/"
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61 tar xJf $input -C $PWD/$name/files
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62 fi
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63 find $PWD/$name/files -iname "1_*" -exec cat {} + > $PWD/$name/summ.txt
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64 find $PWD/$name/files -iname "3_*" -exec cat {} + > $PWD/$name/sequences.txt
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65 find $PWD/$name/files -iname "4_*" -exec cat {} + > $PWD/$name/gapped_aa.txt
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66 find $PWD/$name/files -iname "5_*" -exec cat {} + > $PWD/$name/aa.txt
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67 find $PWD/$name/files -iname "6_*" -exec cat {} + > $PWD/$name/junction.txt
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68
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69 echo "summ.txt `cat $PWD/$name/summ.txt | wc -l`"
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70 echo "aa.txt `cat $PWD/$name/aa.txt | wc -l`"
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71
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72 #python $dir/imgt_loader.py --summ $PWD/$name/summ.txt --aa $PWD/$name/aa.txt --junction $PWD/$name/junction.txt --output $output
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73
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74 Rscript --verbose $dir/imgt_loader.r $PWD/$name/summ.txt $PWD/$name/sequences.txt $PWD/$name/aa.txt $PWD/$name/junction.txt $PWD/$name/gapped_aa.txt $output 2>&1
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