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1 #!/bin/bash
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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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9 clonalType=$4
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10 dir="$(cd "$(dirname "$0")" && pwd)"
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11 mkdir $3
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12 Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputDir $clonalType 2>&1
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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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17
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18 samples=`cat $outputDir/samples.txt`
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19 count=1
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20 echo "<table border='1'><caption><a href='allUnique.tsv'><h3>$clonalType</h3></a></caption>" >> $outputFile
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21 hasReplicateColumn="$(if head -n 1 $inputFile | grep -q 'Replicate'; then echo 'Yes'; else echo 'No'; fi)"
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22 for sample in $samples; do
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23 clonalityScore="$(cat $outputDir/ClonalityScore_$sample.csv)"
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24 echo "<tr><td colspan='3' height='100'></td></tr>" >> $outputFile
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25 echo "<tr><td colspan='3'><h1>$sample</h1></td></tr>" >> $outputFile
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26
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27 echo "$hasReplicateColumn"
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28 #if its a 'new' merged file with replicate info
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29 if [[ "$hasReplicateColumn" == "Yes" ]] ; then
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30 echo "<tr><td colspan='3'><a href='clonality_$sample.tsv'><h2>Clonality Score: $clonalityScore</h2></a></td></tr>" >> $outputFile
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31
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32 #replicate,reads,squared
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33 echo "<tr><td colspan='3'><table border='1'><tr><th>Replicate ID</th><th>Number of Reads</th><th>Reads Squared</th></tr>" >> $outputFile
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34 while IFS=, read replicate reads squared
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35 do
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36
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37 echo "<tr><td><a href='clonality_${sample}_$replicate.tsv'>$replicate</a></td><td>$reads</td><td>$squared</td></tr>" >> $outputFile
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38 done < $outputDir/ReplicateReads_$sample.csv
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39
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40 #sum of reads and reads squared
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41 while IFS=, read readsSum squaredSum
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42 do
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43 echo "<tr><td>Sum</td><td>$readsSum</td><td>$squaredSum</td></tr>" >> $outputFile
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44 done < $outputDir/ReplicateSumReads_$sample.csv
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45
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46 echo "</table></td></tr>" >> $outputFile
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47
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48 #overview
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49 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>" >> $outputFile
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50 while IFS=, read type count weight weightedCount
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51 do
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52 echo "<tr><td>$type</td><td>$count</td><td>$weight</td><td>$weightedCount</td></tr>" >> $outputFile
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53 done < $outputDir/ClonalityOverView_$sample.csv
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54 echo "</table></td></tr>" >> $outputFile
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55 fi
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56
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57 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>" >> $outputFile
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58 mv "$outputDir/HeatmapVD_$sample.png" "$outputDir/VD_$sample.png"
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59 echo "<td><img src='VD_$sample.png'/></td>" >> $outputFile
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60 mv "$outputDir/HeatmapVJ_$sample.png" "$outputDir/VJ_$sample.png"
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61 echo "<td><img src='VJ_$sample.png'/></td>" >> $outputFile
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62 mv "$outputDir/HeatmapDJ_$sample.png" "$outputDir/DJ_$sample.png"
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63 echo "<td><img src='DJ_$sample.png'/></td></tr>" >> $outputFile
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64 count=$((count+1))
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65 done
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66 echo "</table>" >> $outputFile
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67
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68 echo "</html>" >> $2
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69
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