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comparison r_wrapper.sh @ 0:5391c639d6da draft default tip

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author davidvanzessen
date Thu, 23 Jan 2014 08:19:04 -0500
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-1:000000000000 0:5391c639d6da
1 #!/bin/bash
2 echo $1
3 echo $2
4 echo $3
5
6 inputFile=$1
7 outputFile=$2
8 outputDir=$3
9 clonalType=$4
10 dir="$(cd "$(dirname "$0")" && pwd)"
11 mkdir $3
12 Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputDir $clonalType 2>&1
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
17
18 samples=`cat $outputDir/samples.txt`
19 count=1
20 echo "<table border='1'><caption><a href='allUnique.tsv'><h3>$clonalType</h3></a></caption>" >> $outputFile
21 hasReplicateColumn="$(if head -n 1 $inputFile | grep -q 'Replicate'; then echo 'Yes'; else echo 'No'; fi)"
22 for sample in $samples; do
23 clonalityScore="$(cat $outputDir/ClonalityScore_$sample.csv)"
24 echo "<tr><td colspan='3' height='100'></td></tr>" >> $outputFile
25 echo "<tr><td colspan='3'><h1>$sample</h1></td></tr>" >> $outputFile
26
27 echo "$hasReplicateColumn"
28 #if its a 'new' merged file with replicate info
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
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>" >> $outputFile
34 while IFS=, read replicate reads squared
35 do
36
37 echo "<tr><td><a href='clonality_${sample}_$replicate.tsv'>$replicate</a></td><td>$reads</td><td>$squared</td></tr>" >> $outputFile
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
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