Mercurial > repos > davidvanzessen > report_clonality_tcell_igg

comparison r_wrapper.sh @ 1:1ba88ffd6f4e draft

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author davidvanzessen
date Tue, 11 Mar 2014 11:13:33 -0400
parents 1d429107cd26
children fd1b76816395
comparison
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0:1d429107cd26 1:1ba88ffd6f4e
1 #!/bin/bash 1 #!/bin/bash
2 echo $1
3 echo $2
4 echo $3
5 echo $4
6 echo $5
7 2
8 inputFile=$1 3 inputFile=$1
9 outputFile=$2
10 outputDir=$3 4 outputDir=$3
5 outputFile=$3/index.html #$2
11 clonalType=$4 6 clonalType=$4
12 species=$5 7 species=$5
13 dir="$(cd "$(dirname "$0")" && pwd)" 8 dir="$(cd "$(dirname "$0")" && pwd)"
14 mkdir $3 9 mkdir $3
15 Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputDir $clonalType $species 2>&1 10 Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputDir $clonalType $species 2>&1
16 echo "<html>" >> $2 11 cp $dir/tabber.js $outputDir
17 echo "<img src='VPlot.png'/>" >> $2 12 cp $dir/style.css $outputDir
18 echo "<img src='DPlot.png'/>" >> $2 13 cp $dir/script.js $outputDir
19 echo "<img src='JPlot.png'/>" >> $2 14 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
20 15 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'>" >> $outputFile
21 hasReplicateColumn="$(if head -n 1 $inputFile | grep -q 'Replicate'; then echo 'Yes'; else echo 'No'; fi)" 16 echo "<img src='VPlot.png'/>" >> $outputFile
22 17 echo "<img src='DPlot.png'/>" >> $outputFile
23 if [[ "$hasReplicateColumn" == "Yes" ]] ; then 18 echo "<img src='JPlot.png'/></div>" >> $outputFile
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 19
32 samples=`cat $outputDir/samples.txt` 20 samples=`cat $outputDir/samples.txt`
33 count=1 21 count=1
34 echo "<table border='1'><caption><a href='allUnique.tsv'><h3>$clonalType</h3></a></caption>" >> $outputFile 22 echo "<div class='tabbertab' title='Heatmaps'><div class='tabber'>" >> $outputFile
35 for sample in $samples; do 23 for sample in $samples; do
36 clonalityScore="$(cat $outputDir/ClonalityScore_$sample.csv)" 24 echo "<div class='tabbertab' title='$sample'><table border='1'><tr>" >> $outputFile
37 echo "<tr><td colspan='3' height='100'></td></tr>" >> $outputFile
38 echo "<tr><td colspan='3'><h1>$sample</h1></td></tr>" >> $outputFile
39 25
40 echo "$hasReplicateColumn" 26 mv "$outputDir/HeatmapVD_$sample.png" "$outputDir/VD_$sample.png"
41 #if its a 'new' merged file with replicate info 27 echo "<td><img src='VD_$sample.png'/></td>" >> $outputFile
42 if [[ "$hasReplicateColumn" == "Yes" ]] ; then 28 mv "$outputDir/HeatmapVJ_$sample.png" "$outputDir/VJ_$sample.png"
43 echo "<tr><td colspan='3'><a href='clonality_$sample.tsv'><h2>Clonality Score: $clonalityScore</h2></a></td></tr>" >> $outputFile 29 echo "<td><img src='VJ_$sample.png'/></td>" >> $outputFile
44 30 mv "$outputDir/HeatmapDJ_$sample.png" "$outputDir/DJ_$sample.png"
31 echo "<td><img src='DJ_$sample.png'/></td></tr></table></div>" >> $outputFile
32 count=$((count+1))
33 done
34 echo "</div></div>" >> $outputFile
35
36
37 hasReplicateColumn="$(if head -n 1 $inputFile | grep -q 'Replicate'; then echo 'Yes'; else echo 'No'; fi)"
38 echo "$hasReplicateColumn"
39 #if its a 'new' merged file with replicate info
40 if [[ "$hasReplicateColumn" == "Yes" ]] ; then
41 echo "<div class='tabbertab' title='Clonality'><div class='tabber'>" >> $outputFile
42 for sample in $samples; do
43 clonalityScore="$(cat $outputDir/ClonalityScore_$sample.csv)"
44 echo "<div class='tabbertab' title='$sample'><table border='1'>" >> $outputFile
45 echo "<tr><td colspan='4'>Clonality Score: $clonalityScore</td></tr>" >> $outputFile
46
45 #replicate,reads,squared 47 #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 48 echo "<tr><td>Replicate ID</td><td>Number of Reads</td><td>Reads Squared</td><td></td></tr>" >> $outputFile
47 while IFS=, read replicate reads squared 49 while IFS=, read replicate reads squared
48 do 50 do
49 51
50 echo "<tr><td><a href='clonality_${sample}_$replicate.tsv'>$replicate</a></td><td>$reads</td><td>$squared</td></tr>" >> $outputFile 52 echo "<tr><td>$replicate</td><td>$reads</td><td>$squared</td><td></td></tr>" >> $outputFile
51 done < $outputDir/ReplicateReads_$sample.csv 53 done < $outputDir/ReplicateReads_$sample.csv
52 54
53 #sum of reads and reads squared 55 #sum of reads and reads squared
54 while IFS=, read readsSum squaredSum 56 while IFS=, read readsSum squaredSum
55 do 57 do
56 echo "<tr><td>Sum</td><td>$readsSum</td><td>$squaredSum</td></tr>" >> $outputFile 58 echo "<tr><td>Sum</td><td>$readsSum</td><td>$squaredSum</td></tr>" >> $outputFile
57 done < $outputDir/ReplicateSumReads_$sample.csv 59 done < $outputDir/ReplicateSumReads_$sample.csv
58 60
59 echo "</table></td></tr>" >> $outputFile
60
61 #overview 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 62 echo "<tr><td>Coincidence Type</td><td>Raw Coincidence Freq</td><td>Coincidence Weight</td><td>Coincidences, Weighted</td></tr>" >> $outputFile
63 while IFS=, read type count weight weightedCount 63 while IFS=, read type count weight weightedCount
64 do 64 do
65 echo "<tr><td>$type</td><td>$count</td><td>$weight</td><td>$weightedCount</td></tr>" >> $outputFile 65 echo "<tr><td>$type</td><td>$count</td><td>$weight</td><td>$weightedCount</td></tr>" >> $outputFile
66 done < $outputDir/ClonalityOverView_$sample.csv 66 done < $outputDir/ClonalityOverView_$sample.csv
67 echo "</table></td></tr>" >> $outputFile 67 echo "</table></div>" >> $outputFile
68 fi 68 done
69 69 echo "</div></div>" >> $outputFile
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>" >> $outputFile 70 fi
71 mv "$outputDir/HeatmapVD_$sample.png" "$outputDir/VD_$sample.png" 71
72 echo "<td><img src='VD_$sample.png'/></td>" >> $outputFile 72 if [[ "$hasReplicateColumn" == "Yes" ]] ; then
73 mv "$outputDir/HeatmapVJ_$sample.png" "$outputDir/VJ_$sample.png" 73 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>" >> $outputFile
74 echo "<td><img src='VJ_$sample.png'/></td>" >> $outputFile 74 while IFS=, read Sample unique VHDEL P1 N1 P2 DELDH DHDEL P3 N2 P4 DELJH TotalDel TotalN TotalP
75 mv "$outputDir/HeatmapDJ_$sample.png" "$outputDir/DJ_$sample.png" 75 do
76 echo "<td><img src='DJ_$sample.png'/></td></tr>" >> $outputFile 76 echo "<tr><td>$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>" >> $outputFile
77 count=$((count+1)) 77 done < $outputDir/junctionAnalysis.csv
78 echo "</table></div>" >> $outputFile
79 fi
80
81 echo "<div class='tabbertab' title='Comparison'><table border='1'><tr><th>ID</th><th>Include</th></tr>" >> $outputFile
82 for sample in $samples; do
83 echo "<tr><td>$sample</td><td><input type='checkbox' onchange=\"javascript:compareAdd('$sample')\" id='compare_checkbox_$sample'/></td></tr>" >> $outputFile
78 done 84 done
85 echo "</table><div name='comparisonarea'>" >> $outputFile
86 echo "<table><tr id='comparison_table_vd'></tr></table>" >> $outputFile
87 echo "<table><tr id='comparison_table_vj'></tr></table>" >> $outputFile
88 echo "<table><tr id='comparison_table_dj'></tr></table>" >> $outputFile
89 echo "</div></div>" >> $outputFile
90
91 echo "<div class='tabbertab' title='Downloads'>" >> $outputFile
92 echo "<table border='1'>" >> $outputFile
93 echo "<tr><th>Description</th><th>Link</th></tr>" >> $outputFile
94 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
95 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
79 echo "</table>" >> $outputFile 96 echo "</table>" >> $outputFile
80 97 echo "</div>" >> $outputFile
81 echo "</html>" >> $2
82