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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 echo $4
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6 echo $5
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7
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8 inputFile=$1
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9 outputFile=$2
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10 outputDir=$3
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11 clonalType=$4
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12 species=$5
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13 dir="$(cd "$(dirname "$0")" && pwd)"
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14 mkdir $3
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15 Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputDir $clonalType $species 2>&1
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16 echo "<html>" >> $2
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17 echo "<img src='VPlot.png'/>" >> $2
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18 echo "<img src='DPlot.png'/>" >> $2
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19 echo "<img src='JPlot.png'/>" >> $2
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20
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21 hasReplicateColumn="$(if head -n 1 $inputFile | grep -q 'Replicate'; then echo 'Yes'; else echo 'No'; fi)"
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22
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23 if [[ "$hasReplicateColumn" == "Yes" ]] ; then
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24 echo "<table border='1'><tr><th>Sample</th><th>unique</th><th>VH.DEL</th><th>P1</th><th>N1</th><th>P2</th><th>DEL.DH</th><th>DH.DEL</th><th>P3</th><th>N2</th><th>P4</th><th>DEL.JH</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th></tr>" >> $outputFile
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25 while IFS=, read Sample unique VHDEL P1 N1 P2 DELDH DHDEL P3 N2 P4 DELJH TotalDel TotalN TotalP
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26 do
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27 echo "<tr><td>$Sample</td><td>$unique</td><td>$VHDEL</td><td>$P1</td><td>$N1</td><td>$P2</td><td>$DELDH</td><td>$DHDEL</td><td>$P3</td><td>$N2</td><td>$P4</td><td>$DELJH</td><td>$TotalDel</td><td>$TotalN</td><td>$TotalP</td></tr>" >> $outputFile
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28 done < $outputDir/junctionAnalysis.csv
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29 echo "</table>" >> $outputFile
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30 fi
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31
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32 samples=`cat $outputDir/samples.txt`
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33 count=1
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34 echo "<table border='1'><caption><a href='allUnique.tsv'><h3>$clonalType</h3></a></caption>" >> $outputFile
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35 for sample in $samples; do
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36 clonalityScore="$(cat $outputDir/ClonalityScore_$sample.csv)"
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37 echo "<tr><td colspan='3' height='100'></td></tr>" >> $outputFile
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38 echo "<tr><td colspan='3'><h1>$sample</h1></td></tr>" >> $outputFile
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39
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40 echo "$hasReplicateColumn"
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41 #if its a 'new' merged file with replicate info
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42 if [[ "$hasReplicateColumn" == "Yes" ]] ; then
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43 echo "<tr><td colspan='3'><a href='clonality_$sample.tsv'><h2>Clonality Score: $clonalityScore</h2></a></td></tr>" >> $outputFile
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44
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45 #replicate,reads,squared
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46 echo "<tr><td colspan='3'><table border='1'><tr><th>Replicate ID</th><th>Number of Reads</th><th>Reads Squared</th></tr>" >> $outputFile
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47 while IFS=, read replicate reads squared
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48 do
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49
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50 echo "<tr><td><a href='clonality_${sample}_$replicate.tsv'>$replicate</a></td><td>$reads</td><td>$squared</td></tr>" >> $outputFile
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51 done < $outputDir/ReplicateReads_$sample.csv
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52
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53 #sum of reads and reads squared
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54 while IFS=, read readsSum squaredSum
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55 do
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56 echo "<tr><td>Sum</td><td>$readsSum</td><td>$squaredSum</td></tr>" >> $outputFile
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57 done < $outputDir/ReplicateSumReads_$sample.csv
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58
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59 echo "</table></td></tr>" >> $outputFile
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60
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61 #overview
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62 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>" >> $outputFile
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63 while IFS=, read type count weight weightedCount
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64 do
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65 echo "<tr><td>$type</td><td>$count</td><td>$weight</td><td>$weightedCount</td></tr>" >> $outputFile
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66 done < $outputDir/ClonalityOverView_$sample.csv
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67 echo "</table></td></tr>" >> $outputFile
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68 fi
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69
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70 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>" >> $outputFile
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71 mv "$outputDir/HeatmapVD_$sample.png" "$outputDir/VD_$sample.png"
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72 echo "<td><img src='VD_$sample.png'/></td>" >> $outputFile
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73 mv "$outputDir/HeatmapVJ_$sample.png" "$outputDir/VJ_$sample.png"
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74 echo "<td><img src='VJ_$sample.png'/></td>" >> $outputFile
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75 mv "$outputDir/HeatmapDJ_$sample.png" "$outputDir/DJ_$sample.png"
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76 echo "<td><img src='DJ_$sample.png'/></td></tr>" >> $outputFile
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77 count=$((count+1))
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78 done
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79 echo "</table>" >> $outputFile
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80
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81 echo "</html>" >> $2
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82
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