Mercurial > repos > davidvanzessen > report_clonality_tcell_igg

comparison r_wrapper.sh @ 0:1d429107cd26 draft

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author davidvanzessen
date Fri, 07 Mar 2014 05:42:31 -0500
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children 1ba88ffd6f4e
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-1:000000000000 0:1d429107cd26
1 #!/bin/bash
2 echo $1
3 echo $2
4 echo $3
5 echo $4
6 echo $5
7
8 inputFile=$1
9 outputFile=$2
10 outputDir=$3
11 clonalType=$4
12 species=$5
13 dir="$(cd "$(dirname "$0")" && pwd)"
14 mkdir $3
15 Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputDir $clonalType $species 2>&1
16 echo "<html>" >> $2
17 echo "<img src='VPlot.png'/>" >> $2
18 echo "<img src='DPlot.png'/>" >> $2
19 echo "<img src='JPlot.png'/>" >> $2
20
21 hasReplicateColumn="$(if head -n 1 $inputFile | grep -q 'Replicate'; then echo 'Yes'; else echo 'No'; fi)"
22
23 if [[ "$hasReplicateColumn" == "Yes" ]] ; then
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>" >> $outputFile
25 while IFS=, read Sample unique VHDEL P1 N1 P2 DELDH DHDEL P3 N2 P4 DELJH TotalDel TotalN TotalP
26 do
27 echo "<tr><td>$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
28 done < $outputDir/junctionAnalysis.csv
29 echo "</table>" >> $outputFile
30 fi
31
32 samples=`cat $outputDir/samples.txt`
33 count=1
34 echo "<table border='1'><caption><a href='allUnique.tsv'><h3>$clonalType</h3></a></caption>" >> $outputFile
35 for sample in $samples; do
36 clonalityScore="$(cat $outputDir/ClonalityScore_$sample.csv)"
37 echo "<tr><td colspan='3' height='100'></td></tr>" >> $outputFile
38 echo "<tr><td colspan='3'><h1>$sample</h1></td></tr>" >> $outputFile
39
40 echo "$hasReplicateColumn"
41 #if its a 'new' merged file with replicate info
42 if [[ "$hasReplicateColumn" == "Yes" ]] ; then
43 echo "<tr><td colspan='3'><a href='clonality_$sample.tsv'><h2>Clonality Score: $clonalityScore</h2></a></td></tr>" >> $outputFile
44
45 #replicate,reads,squared
46 echo "<tr><td colspan='3'><table border='1'><tr><th>Replicate ID</th><th>Number of Reads</th><th>Reads Squared</th></tr>" >> $outputFile
47 while IFS=, read replicate reads squared
48 do
49
50 echo "<tr><td><a href='clonality_${sample}_$replicate.tsv'>$replicate</a></td><td>$reads</td><td>$squared</td></tr>" >> $outputFile
51 done < $outputDir/ReplicateReads_$sample.csv
52
53 #sum of reads and reads squared
54 while IFS=, read readsSum squaredSum
55 do
56 echo "<tr><td>Sum</td><td>$readsSum</td><td>$squaredSum</td></tr>" >> $outputFile
57 done < $outputDir/ReplicateSumReads_$sample.csv
58
59 echo "</table></td></tr>" >> $outputFile
60
61 #overview
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>" >> $outputFile
63 while IFS=, read type count weight weightedCount
64 do
65 echo "<tr><td>$type</td><td>$count</td><td>$weight</td><td>$weightedCount</td></tr>" >> $outputFile
66 done < $outputDir/ClonalityOverView_$sample.csv
67 echo "</table></td></tr>" >> $outputFile
68 fi
69
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>" >> $outputFile
71 mv "$outputDir/HeatmapVD_$sample.png" "$outputDir/VD_$sample.png"
72 echo "<td><img src='VD_$sample.png'/></td>" >> $outputFile
73 mv "$outputDir/HeatmapVJ_$sample.png" "$outputDir/VJ_$sample.png"
74 echo "<td><img src='VJ_$sample.png'/></td>" >> $outputFile
75 mv "$outputDir/HeatmapDJ_$sample.png" "$outputDir/DJ_$sample.png"
76 echo "<td><img src='DJ_$sample.png'/></td></tr>" >> $outputFile
77 count=$((count+1))
78 done
79 echo "</table>" >> $outputFile
80
81 echo "</html>" >> $2
82