Mercurial > repos > davidvanzessen > report_clonality_igg

comparison r_wrapper.sh @ 5:99834201251f draft

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Uploaded
author davidvanzessen
date Mon, 10 Mar 2014 11:06:17 -0400
parents 8803239b1770
children 18ac92a69ef1
comparison
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4:8803239b1770 5:99834201251f
1 #!/bin/bash 1 #!/bin/bash
2 echo $1
3 echo $2
4 echo $3
5 2
6 inputFile=$1 3 inputFile=$1
7 outputFile=$2
8 outputDir=$3 4 outputDir=$3
5 outputFile=$3/index.html #$2
9 clonalType=$4 6 clonalType=$4
10 dir="$(cd "$(dirname "$0")" && pwd)" 7 dir="$(cd "$(dirname "$0")" && pwd)"
11 mkdir $3 8 mkdir $3
12 Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputDir $clonalType 2>&1 9 Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputDir $clonalType 2>&1
13 echo "<html>" >> $2 10 cp $dir/tabber.js $outputDir
14 echo "<img src='VPlot.png'/>" >> $2 11 cp $dir/style.css $outputDir
15 echo "<img src='DPlot.png'/>" >> $2 12 cp $dir/script.js $outputDir
16 echo "<img src='JPlot.png'/>" >> $2 13 echo "<html><center><h1><a href='index.html'>Click here for the results</a></h1>Tip: Open it in a new tab (middle mouse button or right mouse button -> 'open in new tab' on the link above)</center></html>" > $2
17 14 echo "<html><script type='text/javascript' src='tabber.js'></script><script type='text/javascript' src='script.js'></script><link rel='stylesheet' type='text/css' href='style.css'><div class='tabber'><div class='tabbertab' title='Gene frequencies'>" >> $outputFile
18 hasReplicateColumn="$(if head -n 1 $inputFile | grep -q 'Replicate'; then echo 'Yes'; else echo 'No'; fi)" 15 echo "<img src='VPlot.png'/>" >> $outputFile
19 16 echo "<img src='DPlot.png'/>" >> $outputFile
20 if [[ "$hasReplicateColumn" == "Yes" ]] ; then 17 echo "<img src='JPlot.png'/></div>" >> $outputFile
21 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>" >> $outputFile
22 while IFS=, read Sample unique VHDEL P1 N1 P2 DELDH DHDEL P3 N2 P4 DELJH TotalDel TotalN TotalP
23 do
24 echo "<tr><td>$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
25 done < $outputDir/junctionAnalysis.csv
26 echo "</table>" >> $outputFile
27 fi
28 18
29 samples=`cat $outputDir/samples.txt` 19 samples=`cat $outputDir/samples.txt`
30 count=1 20 count=1
31 echo "<table border='1'><caption><a href='allUnique.tsv'><h3>$clonalType</h3></a></caption>" >> $outputFile 21 echo "<div class='tabbertab' title='Heatmaps'><div class='tabber'>" >> $outputFile
32 for sample in $samples; do 22 for sample in $samples; do
33 clonalityScore="$(cat $outputDir/ClonalityScore_$sample.csv)" 23 echo "<div class='tabbertab' title='$sample'><table border='1'><tr>" >> $outputFile
34 echo "<tr><td colspan='3' height='100'></td></tr>" >> $outputFile
35 echo "<tr><td colspan='3'><h1>$sample</h1></td></tr>" >> $outputFile
36 24
37 echo "$hasReplicateColumn" 25 mv "$outputDir/HeatmapVD_$sample.png" "$outputDir/VD_$sample.png"
38 #if its a 'new' merged file with replicate info 26 echo "<td><img src='VD_$sample.png'/></td>" >> $outputFile
39 if [[ "$hasReplicateColumn" == "Yes" ]] ; then 27 mv "$outputDir/HeatmapVJ_$sample.png" "$outputDir/VJ_$sample.png"
40 echo "<tr><td colspan='3'><a href='clonality_$sample.tsv'><h2>Clonality Score: $clonalityScore</h2></a></td></tr>" >> $outputFile 28 echo "<td><img src='VJ_$sample.png'/></td>" >> $outputFile
41 29 mv "$outputDir/HeatmapDJ_$sample.png" "$outputDir/DJ_$sample.png"
30 echo "<td><img src='DJ_$sample.png'/></td></tr></table></div>" >> $outputFile
31 count=$((count+1))
32 done
33 echo "</div></div>" >> $outputFile
34
35
36 hasReplicateColumn="$(if head -n 1 $inputFile | grep -q 'Replicate'; then echo 'Yes'; else echo 'No'; fi)"
37 echo "$hasReplicateColumn"
38 #if its a 'new' merged file with replicate info
39 if [[ "$hasReplicateColumn" == "Yes" ]] ; then
40 echo "<div class='tabbertab' title='Clonality'><div class='tabber'>" >> $outputFile
41 for sample in $samples; do
42 clonalityScore="$(cat $outputDir/ClonalityScore_$sample.csv)"
43 echo "<div class='tabbertab' title='$sample'><table border='1'>" >> $outputFile
44 echo "<tr><td colspan='4'>Clonality Score: $clonalityScore</td></tr>" >> $outputFile
45
42 #replicate,reads,squared 46 #replicate,reads,squared
43 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 echo "<tr><td>Replicate ID</td><td>Number of Reads</td><td>Reads Squared</td><td></td></tr>" >> $outputFile
44 while IFS=, read replicate reads squared 48 while IFS=, read replicate reads squared
45 do 49 do
46 50
47 echo "<tr><td><a href='clonality_${sample}_$replicate.tsv'>$replicate</a></td><td>$reads</td><td>$squared</td></tr>" >> $outputFile 51 echo "<tr><td>$replicate</td><td>$reads</td><td>$squared</td><td></td></tr>" >> $outputFile
48 done < $outputDir/ReplicateReads_$sample.csv 52 done < $outputDir/ReplicateReads_$sample.csv
49 53
50 #sum of reads and reads squared 54 #sum of reads and reads squared
51 while IFS=, read readsSum squaredSum 55 while IFS=, read readsSum squaredSum
52 do 56 do
53 echo "<tr><td>Sum</td><td>$readsSum</td><td>$squaredSum</td></tr>" >> $outputFile 57 echo "<tr><td>Sum</td><td>$readsSum</td><td>$squaredSum</td></tr>" >> $outputFile
54 done < $outputDir/ReplicateSumReads_$sample.csv 58 done < $outputDir/ReplicateSumReads_$sample.csv
55 59
56 echo "</table></td></tr>" >> $outputFile
57
58 #overview 60 #overview
59 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 61 echo "<tr><td>Coincidence Type</td><td>Raw Coincidence Freq</td><td>Coincidence Weight</td><td>Coincidences, Weighted</td></tr>" >> $outputFile
60 while IFS=, read type count weight weightedCount 62 while IFS=, read type count weight weightedCount
61 do 63 do
62 echo "<tr><td>$type</td><td>$count</td><td>$weight</td><td>$weightedCount</td></tr>" >> $outputFile 64 echo "<tr><td>$type</td><td>$count</td><td>$weight</td><td>$weightedCount</td></tr>" >> $outputFile
63 done < $outputDir/ClonalityOverView_$sample.csv 65 done < $outputDir/ClonalityOverView_$sample.csv
64 echo "</table></td></tr>" >> $outputFile 66 echo "</table></div>" >> $outputFile
65 fi 67 done
66 68 echo "</div></div>" >> $outputFile
67 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>" >> $outputFile 69 fi
68 mv "$outputDir/HeatmapVD_$sample.png" "$outputDir/VD_$sample.png" 70
69 echo "<td><img src='VD_$sample.png'/></td>" >> $outputFile 71 if [[ "$hasReplicateColumn" == "Yes" ]] ; then
70 mv "$outputDir/HeatmapVJ_$sample.png" "$outputDir/VJ_$sample.png" 72 echo "<div class='tabbertab' title='Junction Analysis'><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>" >> $outputFile
71 echo "<td><img src='VJ_$sample.png'/></td>" >> $outputFile 73 while IFS=, read Sample unique VHDEL P1 N1 P2 DELDH DHDEL P3 N2 P4 DELJH TotalDel TotalN TotalP
72 mv "$outputDir/HeatmapDJ_$sample.png" "$outputDir/DJ_$sample.png" 74 do
73 echo "<td><img src='DJ_$sample.png'/></td></tr>" >> $outputFile 75 echo "<tr><td>$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>" >> $outputFile
74 count=$((count+1)) 76 done < $outputDir/junctionAnalysis.csv
77 echo "</table></div>" >> $outputFile
78 fi
79
80 echo "<div class='tabbertab' title='Comparison'><table border='1'><tr><th>ID</th><th>Include</th></tr>" >> $outputFile
81 for sample in $samples; do
82 echo "<tr><td>$sample</td><td><input type='checkbox' onchange=\"javascript:compareAdd('$sample')\" id='compare_checkbox_$sample'/></td></tr>" >> $outputFile
75 done 83 done
84 echo "</table><div name='comparisonarea'>" >> $outputFile
85 echo "<table><tr id='comparison_table_vd'></tr></table>" >> $outputFile
86 echo "<table><tr id='comparison_table_vj'></tr></table>" >> $outputFile
87 echo "<table><tr id='comparison_table_dj'></tr></table>" >> $outputFile
88 echo "</div></div>" >> $outputFile
89
90 echo "<div class='tabbertab' title='Downloads'>" >> $outputFile
91 echo "<table border='1'>" >> $outputFile
92 echo "<tr><th>Description</th><th>Link</th></tr>" >> $outputFile
93 echo "<tr><td>The dataset used to generate the frequency graphs and the heatmaps (Unique based on clonaltype, $clonalType)</td><td><a href='allUnique.tsv'>Download</a></td></tr>" >> $outputFile
94 echo "<tr><td>The dataset used to calculate clonality score (Unique based on clonaltype, $clonalType)</td><td><a href='clonalityComplete.tsv'>Download</a></td></tr>" >> $outputFile
76 echo "</table>" >> $outputFile 95 echo "</table>" >> $outputFile
77 96 echo "</div>" >> $outputFile
78 echo "</html>" >> $2
79