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0
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1 #!/bin/bash
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31
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2 echo $1
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3 echo $2
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4 echo $3
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5
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6 inputFile=$1
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7 outputFile=$2
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8 outputDir=$3
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41
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9 clonalType=$4
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0
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10 dir="$(cd "$(dirname "$0")" && pwd)"
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31
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11 mkdir $3
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41
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12 Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputDir $clonalType 2>&1
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31
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13 echo "<html>" >> $2
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14 echo "<img src='VPlot.png'/>" >> $2
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15 echo "<img src='DPlot.png'/>" >> $2
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16 echo "<img src='JPlot.png'/>" >> $2
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12
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17
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31
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18 samples=`cat $outputDir/samples.txt`
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19 count=1
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43
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20 echo "<table border='1'><caption><h3>$clonalType</h3><caption>" >> $outputFile
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31
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21 for sample in $samples; do
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22 echo "<tr><td colspan='3' height='100'></td>" >> $outputFile
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23 echo "<tr><td colspan='3'><h1>$sample</h1></td></tr>" >> $outputFile
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24 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>" >> $outputFile
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25 mv "$outputDir/HeatmapVD_$sample.png" "$outputDir/VD_$sample.png"
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26 echo "<td><img src='VD_$sample.png'/></td>" >> $outputFile
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27 mv "$outputDir/HeatmapVJ_$sample.png" "$outputDir/VJ_$sample.png"
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28 echo "<td><img src='VJ_$sample.png'/></td>" >> $outputFile
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29 mv "$outputDir/HeatmapDJ_$sample.png" "$outputDir/DJ_$sample.png"
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30 echo "<td><img src='DJ_$sample.png'/></td></tr>" >> $outputFile
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31 count=$((count+1))
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32 done
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33 echo "</table>" >> $outputFile
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34
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35 echo "</html>" >> $2
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36
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