Mercurial > repos > davidvanzessen > report_clonality_tcell_igg

comparison r_wrapper.sh @ 2:fd1b76816395 draft

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Uploaded
author davidvanzessen
date Thu, 27 Mar 2014 10:54:03 -0400
parents 1ba88ffd6f4e
children b850200d4335
comparison
equal deleted inserted replaced
1:1ba88ffd6f4e 2:fd1b76816395
2 2
3 inputFile=$1 3 inputFile=$1
4 outputDir=$3 4 outputDir=$3
5 outputFile=$3/index.html #$2 5 outputFile=$3/index.html #$2
6 clonalType=$4 6 clonalType=$4
7 species=$5
8 dir="$(cd "$(dirname "$0")" && pwd)" 7 dir="$(cd "$(dirname "$0")" && pwd)"
9 mkdir $3 8 mkdir $3
10 Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputDir $clonalType $species 2>&1 9 Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputDir $clonalType 2>&1
11 cp $dir/tabber.js $outputDir 10 cp $dir/tabber.js $outputDir
12 cp $dir/style.css $outputDir 11 cp $dir/style.css $outputDir
13 cp $dir/script.js $outputDir 12 cp $dir/script.js $outputDir
13 cp $dir/jquery-1.11.0.min.js $outputDir
14 cp $dir/jquery.tablesorter.min.js $outputDir
15 cp $dir/asc.gif $outputDir
16 cp $dir/desc.gif $outputDir
17 cp $dir/bg.gif $outputDir
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 18 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
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 19 echo "<html<head>" >> $outputFile
20 echo "<script type='text/javascript' src='jquery-1.11.0.min.js'></script>" >> $outputFile
21 echo "<script type='text/javascript' src='tabber.js'></script>" >> $outputFile
22 echo "<script type='text/javascript' src='script.js'></script>" >> $outputFile
23 echo "<script type='text/javascript' src='jquery.tablesorter.min.js'></script>" >> $outputFile
24 echo "<link rel='stylesheet' type='text/css' href='style.css'></head>" >> $outputFile
25 echo "<div class='tabber'><div class='tabbertab' title='Gene frequencies'>" >> $outputFile
26
27 echo "<img src='CDR3LengthPlot.png'/><br />" >> $outputFile
28 echo "<img src='VFPlot.png'/>" >> $outputFile
29 echo "<img src='DFPlot.png'/>" >> $outputFile
30 echo "<img src='JFPlot.png'/>" >> $outputFile
16 echo "<img src='VPlot.png'/>" >> $outputFile 31 echo "<img src='VPlot.png'/>" >> $outputFile
17 echo "<img src='DPlot.png'/>" >> $outputFile 32 echo "<img src='DPlot.png'/>" >> $outputFile
18 echo "<img src='JPlot.png'/></div>" >> $outputFile 33 echo "<img src='JPlot.png'/></div>" >> $outputFile
19 34
20 samples=`cat $outputDir/samples.txt` 35 samples=`cat $outputDir/samples.txt`
21 count=1 36 count=1
22 echo "<div class='tabbertab' title='Heatmaps'><div class='tabber'>" >> $outputFile 37 echo "<div class='tabbertab' title='Heatmaps'><div class='tabber'>" >> $outputFile
23 for sample in $samples; do 38 for sample in $samples; do
24 echo "<div class='tabbertab' title='$sample'><table border='1'><tr>" >> $outputFile 39 echo "<div class='tabbertab' title='$sample'><table border='1'><tr>" >> $outputFile
25 40 echo "<td><img src='HeatmapVD_$sample.png'/></td>" >> $outputFile
26 mv "$outputDir/HeatmapVD_$sample.png" "$outputDir/VD_$sample.png" 41 echo "<td><img src='HeatmapVJ_$sample.png'/></td>" >> $outputFile
27 echo "<td><img src='VD_$sample.png'/></td>" >> $outputFile 42 echo "<td><img src='HeatmapDJ_$sample.png'/></td></tr></table></div>" >> $outputFile
28 mv "$outputDir/HeatmapVJ_$sample.png" "$outputDir/VJ_$sample.png"
29 echo "<td><img src='VJ_$sample.png'/></td>" >> $outputFile
30 mv "$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)) 43 count=$((count+1))
33 done 44 done
34 echo "</div></div>" >> $outputFile 45 echo "</div></div>" >> $outputFile
35 46
36 47
67 echo "</table></div>" >> $outputFile 78 echo "</table></div>" >> $outputFile
68 done 79 done
69 echo "</div></div>" >> $outputFile 80 echo "</div></div>" >> $outputFile
70 fi 81 fi
71 82
72 if [[ "$hasReplicateColumn" == "Yes" ]] ; then 83 hasJunctionData="$(if head -n 1 $inputFile | grep -q '3V-REGION trimmed-nt nb'; then echo 'Yes'; else echo 'No'; fi)"
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>" >> $outputFile 84
85 if [[ "$hasJunctionData" == "Yes" ]] ; then
86 echo "<div class='tabbertab' title='Junction Analysis'><table border='1' id='junction_table' class='tablesorter'><thead><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><thead></tr><tbody>" >> $outputFile
74 while IFS=, read Sample unique VHDEL P1 N1 P2 DELDH DHDEL P3 N2 P4 DELJH TotalDel TotalN TotalP 87 while IFS=, read Sample unique VHDEL P1 N1 P2 DELDH DHDEL P3 N2 P4 DELJH TotalDel TotalN TotalP
75 do 88 do
76 echo "<tr><td>$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>" >> $outputFile 89 echo "<tr><td>$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 done < $outputDir/junctionAnalysis.csv 90 done < $outputDir/junctionAnalysis.csv
78 echo "</table></div>" >> $outputFile 91 echo "</tbody></table></div>" >> $outputFile
79 fi 92 fi
80 93
81 echo "<div class='tabbertab' title='Comparison'><table border='1'><tr><th>ID</th><th>Include</th></tr>" >> $outputFile 94 echo "<div class='tabbertab' title='Comparison'><table border='1'><tr><th>ID</th><th>Include</th></tr>" >> $outputFile
82 for sample in $samples; do 95 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>" >> $outputFile 96 echo "<tr><td>$sample</td><td><input type='checkbox' onchange=\"javascript:compareAdd('$sample')\" id='compare_checkbox_$sample'/></td></tr>" >> $outputFile
89 echo "</div></div>" >> $outputFile 102 echo "</div></div>" >> $outputFile
90 103
91 echo "<div class='tabbertab' title='Downloads'>" >> $outputFile 104 echo "<div class='tabbertab' title='Downloads'>" >> $outputFile
92 echo "<table border='1'>" >> $outputFile 105 echo "<table border='1'>" >> $outputFile
93 echo "<tr><th>Description</th><th>Link</th></tr>" >> $outputFile 106 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 107 echo "<tr><td>The dataset used to generate the frequency graphs and the heatmaps (Unique based on clonaltype, $clonalType)</td><td><a href='allUnique.csv'>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 108 echo "<tr><td>The dataset used to calculate clonality score (Unique based on clonaltype, $clonalType)</td><td><a href='clonalityComplete.csv'>Download</a></td></tr>" >> $outputFile
109
110 echo "<tr><td>The dataset used to generate the CDR3 length frequency graph</td><td><a href='CDR3LengthPlot.csv'>Download</a></td></tr>" >> $outputFile
111
112 echo "<tr><td>The dataset used to generate the V gene family frequency graph</td><td><a href='VFFrequency.csv'>Download</a></td></tr>" >> $outputFile
113 echo "<tr><td>The dataset used to generate the D gene family frequency graph</td><td><a href='DFFrequency.csv'>Download</a></td></tr>" >> $outputFile
114 echo "<tr><td>The dataset used to generate the J gene family frequency graph</td><td><a href='JFFrequency.csv'>Download</a></td></tr>" >> $outputFile
115
116 echo "<tr><td>The dataset used to generate the V gene frequency graph</td><td><a href='VFrequency.csv'>Download</a></td></tr>" >> $outputFile
117 echo "<tr><td>The dataset used to generate the D gene frequency graph</td><td><a href='DFrequency.csv'>Download</a></td></tr>" >> $outputFile
118 echo "<tr><td>The dataset used to generate the J gene frequency graph</td><td><a href='JFrequency.csv'>Download</a></td></tr>" >> $outputFile
119
120 for sample in $samples; do
121 echo "<tr><td>The data used to generate the VD heatmap for $sample.</td><td><a href='HeatmapVD_$sample.csv'>Download</a></td></tr>" >> $outputFile
122 echo "<tr><td>The data used to generate the VJ heatmap for $sample.</td><td><a href='HeatmapVJ_$sample.csv'>Download</a></td></tr>" >> $outputFile
123 echo "<tr><td>The data used to generate the DJ heatmap for $sample.</td><td><a href='HeatmapDJ_$sample.csv'>Download</a></td></tr>" >> $outputFile
124 done
125
96 echo "</table>" >> $outputFile 126 echo "</table>" >> $outputFile
97 echo "</div>" >> $outputFile 127 echo "</div></html>" >> $outputFile