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1 #!/bin/bash
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5
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2 set -e
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1
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3 inputFiles=($1)
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4 outputDir=$3
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5 outputFile=$3/index.html #$1
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6 clonalType=$4
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7 species=$5
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8 locus=$6
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7
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9 filterproductive=$7
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1
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10
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11 html=$2
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12 dir="$(cd "$(dirname "$0")" && pwd)"
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13 array=("$@")
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14 echo "<html><h3>Progress</h3><table><tr><td>info</td></tr>" > $html
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15 echo "<tr><td>-----------------------------------</td></tr>" >> $html
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16
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17 mkdir $PWD/igblastdatabase
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18 unzip $dir/database.zip -d $PWD/igblastdatabase/
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19 export IGDATA=$PWD/igblastdatabase/
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20
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21 function blastAndParse {
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22 echo "<tr><td>Starting blast of sample $3 of patient $2</td></tr>" >> $html
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23 echo "igblastn -germline_db_V $PWD/igblastdatabase/database/human_gl_V -germline_db_J $PWD/igblastdatabase/database/human_gl_J -germline_db_D $PWD/igblastdatabase/database/human_gl_D -domain_system imgt -query $1 -auxiliary_data $PWD/igblastdatabase/optional_file/human_gl.aux -show_translation -outfmt 3 > $PWD/$4"
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24 /home/galaxy/galaxy/igblast/igblastn -germline_db_V $PWD/igblastdatabase/database/human_gl_V -germline_db_J $PWD/igblastdatabase/database/human_gl_J -germline_db_D $PWD/igblastdatabase/database/human_gl_D -domain_system imgt -query $1 -auxiliary_data $PWD/igblastdatabase/optional_file/human_gl.aux -show_translation -outfmt 3 > $PWD/$4
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25 echo "<tr><td>Finished blast of sample $3 of patient $2</td></tr>" >> $html
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26 echo "<tr><td>Starting parse of sample $3 of patient $2</td></tr>" >> $html
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27 perl $dir/igparse.pl $PWD/$4 0 | grep -v "D:" | cut -f2- > "$5"
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28 echo "<tr><td>Finished parse of sample $3 of patient $2</td></tr>" >> $html
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29 }
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30
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31 function imgtConvert {
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32 echo "<tr><td>Starting imgt convert of sample $3 of patient $2</td></tr>" >> $html
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33 bash $dir/imgt_loader.sh $1 $4 $5
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34 echo "<tr><td>Finished conversion of sample $3 of patient $2</td></tr>" >> $html
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35 }
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36
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37 id=""
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38 forwardSlash="/"
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39 mergerInput=()
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40 echo "Before loop"
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41 count=1
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42 for current in "${inputFiles[@]}"
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43 do
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44 if [[ "$current" != *"$forwardSlash"* ]]; then
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45 id="$current"
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46 mergerInput+=($id)
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47 count=1
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48 continue
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49 fi
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50 echo "working on $current"
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51 fileName=$(basename $current)
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52 parsedFileName="${fileName%.*}"
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53 parsedFileName="$PWD/$parsedFileName.parsed"
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54 f=$(file $current)
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55 zipType="Zip archive"
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56 if [[ "$f" == *"$zipType"* ]]
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57 then
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58 echo "<tr><td>Sample $count of patient $id is a zip file, using IMGT Loader</td></tr>" >> $html
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59 fileName=$(basename $current)
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60 imgtConvert $current $id $count $parsedFileName "${id}_${count}" #&
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61 else
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62 echo "<tr><td>Sample $count of patient $id is not a zip file, using igBLASTn</td></tr>" >> $html
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63 blastAndParse $current $id $count $fileName $parsedFileName &
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64 fi
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65 mergerInput+=($parsedFileName)
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66 count=$((count+1))
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67 done
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68 wait
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69
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70 echo "after loop"
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71
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72 echo "<tr><td>-----------------------------------</td></tr>" >> $html
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73 echo "<tr><td>merging</td></tr>" >> $html
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74
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75 python $dir/experimental_design.py ${mergerInput[*]} --output $PWD/merged.txt
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76
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77 echo "<tr><td>done</td></tr>" >> $html
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78 echo "<tr><td>-----------------------------------</td></tr>" >> $html
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79 echo "<tr><td>plotting</td></tr>" >> $html
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80
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81 echo "after ED"
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82
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83 $dir/r_wrapper.sh $PWD/merged.txt $2 $outputDir $clonalType $species $locus $filterproductive
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84
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