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