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1 #!/bin/bash
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2
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2
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3 export IGDATA=/home/david/Galaxy/galaxy-dist/toolsheddependencies/igBlastn/1.0.0/davidvanzessen/igblast_human/1c64c977624e/ncbi-igblast-1.0.0/;
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4
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5 clonalType=${@:(-3):1}
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0
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6 html=${@:(-2):1}
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7 imageDir=${@:(-1):1}
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8 dir="$(cd "$(dirname "$0")" && pwd)"
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2
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9 fileCount=`expr $# - 3`
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10 array=("$@")
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11 echo "<html><h3>Progress</h3><table><tr><td>info</td></tr>" > $html
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2
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12 for var in "$@"
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13 do
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14 echo "$var" >> $html
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15 done
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16 echo "<tr><td>-----------------------------------</td></tr>" >> $html
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17 limit=`expr $fileCount / 2`
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18
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19 function blastAndParse {
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20 echo "<tr><td>Starting blast of $2</td></tr>" >> $html
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21 fileName=$(basename $1)
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22 $IGDATA/bin/igblastn -germline_db_V $IGDATA/database/human_gl_V -germline_db_J $IGDATA/database/human_gl_J -germline_db_D $IGDATA/database/human_gl_D -domain_system imgt -query $1 -auxiliary_data $IGDATA/optional_file/human_gl.aux -show_translation -outfmt 3 > $PWD/$fileName
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23 echo "<tr><td>Finished blast of $2</td></tr>" >> $html
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24
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25 echo "<tr><td>Starting parse of $2</td></tr>" >> $html
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26 parsedFileName="${fileName%.*}"
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27 parsedFileName="$parsedFileName.parsed"
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28 perl $dir/igparse.pl $PWD/$fileName 0 | grep -v "D:" | cut -f2- > $parsedFileName
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29 echo "<tr><td>Finished parse of $2</td></tr>" >> $html
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30 }
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31
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32 for ((i=0;i<$fileCount;i=$((i+2))))
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33 do
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34 next=$((i+1))
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35 blastAndParse ${array[$i]} ${array[$next]} &
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36 done
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37 wait
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38
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39
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40
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41 echo "<tr><td>-----------------------------------</td></tr>" >> $html
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42 echo "<tr><td>merging</td></tr>" >> $html
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43
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44 count=0
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45 for ((i=0;i<$fileCount;i=$((i+2))))
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46 do
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47 id=$((i+1))
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48 place=$((count+limit))
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49 fn=$(basename ${array[$i]})
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50 fn="${fn%.*}"
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51 mergeInputs[$count]="$PWD/$fn.parsed"
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52 mergeIDs[$place]=${array[$id]}
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53 count=$((count+1))
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54 done
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55
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56 python $dir/igblastmerge.py --input ${mergeInputs[*]} --id ${mergeIDs[*]} --output $PWD/merged.txt
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57
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58 echo "<tr><td>done</td></tr>" >> $html
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59 echo "<tr><td>-----------------------------------</td></tr>" >> $html
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60 echo "<tr><td>plotting</td></tr>" >> $html
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61
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62
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63 inputFile=$PWD/merged.txt
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64 outputFile=$html
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65 outputDir=$imageDir
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66 mkdir $outputDir
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2
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67 Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputDir $clonalType 2>&1
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68 echo "<html>" > $outputFile
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69 echo "<img src='VPlot.png'/>" >> $outputFile
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70 echo "<img src='DPlot.png'/>" >> $outputFile
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71 echo "<img src='JPlot.png'/>" >> $outputFile
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72
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73 samples=`cat $outputDir/samples.txt`
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74 count=1
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75 echo "<table border='1'>" >> $outputFile
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76 for sample in $samples; do
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77 echo "<tr><td colspan='3' height='100'></td>" >> $outputFile
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78 echo "<tr><td colspan='3'><h1>$sample</h1></td></tr>" >> $outputFile
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79 echo "<tr><td><h2>V-D Heatmap:</h2></td><td><h2>V-J Heatmap:</h2></td><td><h2>D-J Heatmap:</h2></td></tr><tr>" >> $outputFile
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80 mv "$outputDir/HeatmapVD_$sample.png" "$outputDir/VD_$sample.png"
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81 echo "<td><img src='VD_$sample.png'/></td>" >> $outputFile
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82 mv "$outputDir/HeatmapVJ_$sample.png" "$outputDir/VJ_$sample.png"
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83 echo "<td><img src='VJ_$sample.png'/></td>" >> $outputFile
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84 mv "$outputDir/HeatmapDJ_$sample.png" "$outputDir/DJ_$sample.png"
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85 echo "<td><img src='DJ_$sample.png'/></td></tr>" >> $outputFile
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86 count=$((count+1))
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87 done
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88 echo "</table>" >> $outputFile
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2
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89 echo "<h1>$clonalType</h1>" >> $outputFile
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0
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90
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91 echo "</html>" >> $2
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