Mercurial > repos > davidvanzessen > report_clonality_igg
comparison r_wrapper.sh @ 6:18ac92a69ef1 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Tue, 18 Mar 2014 09:03:54 -0400 |
| parents | 99834201251f |
| children | 1d0ed31089c6 |
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| 5:99834201251f | 6:18ac92a69ef1 |
|---|---|
| 8 mkdir $3 | 8 mkdir $3 |
| 9 Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputDir $clonalType 2>&1 | 9 Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputDir $clonalType 2>&1 |
| 10 cp $dir/tabber.js $outputDir | 10 cp $dir/tabber.js $outputDir |
| 11 cp $dir/style.css $outputDir | 11 cp $dir/style.css $outputDir |
| 12 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 | |
| 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 | 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 |
| 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 | 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='VFPlot.png'/>" >> $outputFile | |
| 28 echo "<img src='DFPlot.png'/>" >> $outputFile | |
| 29 echo "<img src='JFPlot.png'/>" >> $outputFile | |
| 15 echo "<img src='VPlot.png'/>" >> $outputFile | 30 echo "<img src='VPlot.png'/>" >> $outputFile |
| 16 echo "<img src='DPlot.png'/>" >> $outputFile | 31 echo "<img src='DPlot.png'/>" >> $outputFile |
| 17 echo "<img src='JPlot.png'/></div>" >> $outputFile | 32 echo "<img src='JPlot.png'/></div>" >> $outputFile |
| 18 | 33 |
| 19 samples=`cat $outputDir/samples.txt` | 34 samples=`cat $outputDir/samples.txt` |
| 20 count=1 | 35 count=1 |
| 21 echo "<div class='tabbertab' title='Heatmaps'><div class='tabber'>" >> $outputFile | 36 echo "<div class='tabbertab' title='Heatmaps'><div class='tabber'>" >> $outputFile |
| 22 for sample in $samples; do | 37 for sample in $samples; do |
| 23 echo "<div class='tabbertab' title='$sample'><table border='1'><tr>" >> $outputFile | 38 echo "<div class='tabbertab' title='$sample'><table border='1'><tr>" >> $outputFile |
| 24 | 39 echo "<td><img src='HeatmapVD_$sample.png'/></td>" >> $outputFile |
| 25 mv "$outputDir/HeatmapVD_$sample.png" "$outputDir/VD_$sample.png" | 40 echo "<td><img src='HeatmapVJ_$sample.png'/></td>" >> $outputFile |
| 26 echo "<td><img src='VD_$sample.png'/></td>" >> $outputFile | 41 echo "<td><img src='HeatmapDJ_$sample.png'/></td></tr></table></div>" >> $outputFile |
| 27 mv "$outputDir/HeatmapVJ_$sample.png" "$outputDir/VJ_$sample.png" | |
| 28 echo "<td><img src='VJ_$sample.png'/></td>" >> $outputFile | |
| 29 mv "$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)) | 42 count=$((count+1)) |
| 32 done | 43 done |
| 33 echo "</div></div>" >> $outputFile | 44 echo "</div></div>" >> $outputFile |
| 34 | 45 |
| 35 | 46 |
| 67 done | 78 done |
| 68 echo "</div></div>" >> $outputFile | 79 echo "</div></div>" >> $outputFile |
| 69 fi | 80 fi |
| 70 | 81 |
| 71 if [[ "$hasReplicateColumn" == "Yes" ]] ; then | 82 if [[ "$hasReplicateColumn" == "Yes" ]] ; then |
| 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 | 83 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>" >> $outputFile |
| 73 while IFS=, read Sample unique VHDEL P1 N1 P2 DELDH DHDEL P3 N2 P4 DELJH TotalDel TotalN TotalP | 84 while IFS=, read Sample unique VHDEL P1 N1 P2 DELDH DHDEL P3 N2 P4 DELJH TotalDel TotalN TotalP |
| 74 do | 85 do |
| 75 echo "<tr><td>$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>" >> $outputFile | 86 echo "<tr><td>$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 |
| 76 done < $outputDir/junctionAnalysis.csv | 87 done < $outputDir/junctionAnalysis.csv |
| 77 echo "</table></div>" >> $outputFile | 88 echo "</tbody></table></div>" >> $outputFile |
| 78 fi | 89 fi |
| 79 | 90 |
| 80 echo "<div class='tabbertab' title='Comparison'><table border='1'><tr><th>ID</th><th>Include</th></tr>" >> $outputFile | 91 echo "<div class='tabbertab' title='Comparison'><table border='1'><tr><th>ID</th><th>Include</th></tr>" >> $outputFile |
| 81 for sample in $samples; do | 92 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>" >> $outputFile | 93 echo "<tr><td>$sample</td><td><input type='checkbox' onchange=\"javascript:compareAdd('$sample')\" id='compare_checkbox_$sample'/></td></tr>" >> $outputFile |
| 88 echo "</div></div>" >> $outputFile | 99 echo "</div></div>" >> $outputFile |
| 89 | 100 |
| 90 echo "<div class='tabbertab' title='Downloads'>" >> $outputFile | 101 echo "<div class='tabbertab' title='Downloads'>" >> $outputFile |
| 91 echo "<table border='1'>" >> $outputFile | 102 echo "<table border='1'>" >> $outputFile |
| 92 echo "<tr><th>Description</th><th>Link</th></tr>" >> $outputFile | 103 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 | 104 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 |
| 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 | 105 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 |
| 106 | |
| 107 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 | |
| 108 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 | |
| 109 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 | |
| 110 | |
| 111 echo "<tr><td>The dataset used to generate the V gene frequency graph</td><td><a href='VFrequency.csv'>Download</a></td></tr>" >> $outputFile | |
| 112 echo "<tr><td>The dataset used to generate the D gene frequency graph</td><td><a href='DFrequency.csv'>Download</a></td></tr>" >> $outputFile | |
| 113 echo "<tr><td>The dataset used to generate the J gene frequency graph</td><td><a href='JFrequency.csv'>Download</a></td></tr>" >> $outputFile | |
| 114 | |
| 115 for sample in $samples; do | |
| 116 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 | |
| 117 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 | |
| 118 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 | |
| 119 done | |
| 120 | |
| 95 echo "</table>" >> $outputFile | 121 echo "</table>" >> $outputFile |
| 96 echo "</div>" >> $outputFile | 122 echo "</div></html>" >> $outputFile |