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1 #!/bin/bash
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2
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9
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3 export IGDATA=/home/david/tmp/ncbi-igblast-1.0.0;
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2
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4
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5 clonalType=${@:(-3):1}
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6 html=${@:(-2):1}
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7 imageDir=${@:(-1):1}
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9
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8 dataCount=`expr $# - 3`
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9 inputData=${@:(1):dataCount}
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10 dir="$(cd "$(dirname "$0")" && pwd)"
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11 array=("$@")
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12 echo "<html><h3>Progress</h3><table><tr><td>info</td></tr>" > $html
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13 echo "<tr><td>-----------------------------------</td></tr>" >> $html
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14
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9
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15 id=${inputData[0]}
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16 forwardSlash="/"
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17 mergerInput=()
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18 count=0
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19 for current in $inputData; do
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20 if [[ "$current" != *"$forwardSlash"* ]]; then
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21 id=$current
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22 count=0
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23 mergerInput+=($id)
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24 continue
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25 fi
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26 fileName=$(basename $current)
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27 convertedFileName="${fileName%.*}"
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28 convertedFileName="$PWD/$convertedFileName.converted"
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29 bash $dir/imgtconvert.sh $current $id $count $convertedFileName
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30 mergerInput+=($convertedFileName)
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31 count=$((count+1))
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0
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32 done
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33
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34
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35
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36 echo "<tr><td>-----------------------------------</td></tr>" >> $html
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37 echo "<tr><td>merging</td></tr>" >> $html
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38
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9
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39 python $dir/igblastmerge.py ${mergerInput[*]} --output $PWD/merged.txt
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40
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41 echo "<tr><td>done</td></tr>" >> $html
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42 echo "<tr><td>-----------------------------------</td></tr>" >> $html
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43 echo "<tr><td>plotting</td></tr>" >> $html
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44
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45
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46 inputFile=$PWD/merged.txt
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47 outputFile=$html
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48 outputDir=$imageDir
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49 mkdir $outputDir
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2
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50 Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputDir $clonalType 2>&1
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51 echo "<html>" > $outputFile
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52 echo "<img src='VPlot.png'/>" >> $outputFile
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53 echo "<img src='DPlot.png'/>" >> $outputFile
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54 echo "<img src='JPlot.png'/>" >> $outputFile
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55
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56 samples=`cat $outputDir/samples.txt`
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57 count=1
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58 echo "<table border='1'><caption><a href='allUnique.tsv'><h3>$clonalType</h3></a></caption>" >> $outputFile
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59 hasReplicateColumn="$(if head -n 1 $inputFile | grep -q 'Replicate'; then echo 'Yes'; else echo 'No'; fi)"
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60 for sample in $samples; do
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61 clonalityScore="$(cat $outputDir/ClonalityScore_$sample.csv)"
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62 echo "<tr><td colspan='3' height='100'></td></tr>" >> $outputFile
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63 echo "<tr><td colspan='3'><h1>$sample</h1></td></tr>" >> $outputFile
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64
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65 echo "$hasReplicateColumn"
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66 #if its a 'new' merged file with replicate info
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67 if [[ "$hasReplicateColumn" == "Yes" ]] ; then
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68 echo "<tr><td colspan='3'><a href='clonality_$sample.tsv'><h2>Clonality Score: $clonalityScore</h2></a></td></tr>" >> $outputFile
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69
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70 #replicate,reads,squared
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71 echo "<tr><td colspan='3'><table border='1'><tr><th>Replicate ID</th><th>Number of Reads</th><th>Reads Squared</th></tr>" >> $outputFile
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72 while IFS=, read replicate reads squared
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73 do
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74
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75 echo "<tr><td><a href='clonality_${sample}_$replicate.tsv'>$replicate</a></td><td>$reads</td><td>$squared</td></tr>" >> $outputFile
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76 done < $outputDir/ReplicateReads_$sample.csv
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77
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78 #sum of reads and reads squared
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79 while IFS=, read readsSum squaredSum
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80 do
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81 echo "<tr><td>Sum</td><td>$readsSum</td><td>$squaredSum</td></tr>" >> $outputFile
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82 done < $outputDir/ReplicateSumReads_$sample.csv
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83
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84 echo "</table></td></tr>" >> $outputFile
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85
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86 #overview
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87 echo "<tr><td colspan='3'><table border='1'><tr><th>Coincidence Type</th><th>Raw Coincidence Freq</th><th>Coincidence Weight</th><th>Coincidences, Weighted</th></tr>" >> $outputFile
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88 while IFS=, read type count weight weightedCount
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89 do
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90 echo "<tr><td>$type</td><td>$count</td><td>$weight</td><td>$weightedCount</td></tr>" >> $outputFile
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91 done < $outputDir/ClonalityOverView_$sample.csv
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92 echo "</table></td></tr>" >> $outputFile
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93 fi
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94
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95 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>" >> $outputFile
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96 mv "$outputDir/HeatmapVD_$sample.png" "$outputDir/VD_$sample.png"
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97 echo "<td><img src='VD_$sample.png'/></td>" >> $outputFile
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98 mv "$outputDir/HeatmapVJ_$sample.png" "$outputDir/VJ_$sample.png"
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99 echo "<td><img src='VJ_$sample.png'/></td>" >> $outputFile
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100 mv "$outputDir/HeatmapDJ_$sample.png" "$outputDir/DJ_$sample.png"
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101 echo "<td><img src='DJ_$sample.png'/></td></tr>" >> $outputFile
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102 count=$((count+1))
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103 done
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104 echo "</table>" >> $outputFile
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105
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9
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106 echo "</html>" >> $outputFile
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