Mercurial > repos > davidvanzessen > report_clonality_igg
diff r_wrapper.sh @ 12:24a80d4eff0c draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Thu, 13 Nov 2014 10:36:33 -0500 |
| parents | 866d22e60e60 |
| children | c6d0ee9b3d91 |
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--- a/r_wrapper.sh Thu Nov 13 10:33:04 2014 -0500 +++ b/r_wrapper.sh Thu Nov 13 10:36:33 2014 -0500 @@ -18,10 +18,6 @@ cp $dir/style.css $outputDir cp $dir/script.js $outputDir cp $dir/jquery-1.11.0.min.js $outputDir -cp $dir/jquery.tablesorter.min.js $outputDir -cp $dir/asc.gif $outputDir -cp $dir/desc.gif $outputDir -cp $dir/bg.gif $outputDir samples=`cat $outputDir/samples.txt` 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 echo "<html><head><title>Report on:" >> $outputFile @@ -31,7 +27,6 @@ echo "</title><script type='text/javascript' src='jquery-1.11.0.min.js'></script>" >> $outputFile echo "<script type='text/javascript' src='tabber.js'></script>" >> $outputFile echo "<script type='text/javascript' src='script.js'></script>" >> $outputFile -echo "<script type='text/javascript' src='jquery.tablesorter.min.js'></script>" >> $outputFile echo "<link rel='stylesheet' type='text/css' href='style.css'></head>" >> $outputFile echo "<div class='tabber'><div class='tabbertab' title='Gene frequencies'>" >> $outputFile @@ -103,7 +98,7 @@ hasJunctionData="$(if head -n 1 $inputFile | grep -q '3V-REGION trimmed-nt nb'; then echo 'Yes'; else echo 'No'; fi)" if [[ "$hasJunctionData" == "Yes" ]] ; then - 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 + echo "<div class='tabbertab' title='Junction Analysis'><table border='1' id='junction_table'><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>" >> $outputFile while IFS=, read Sample unique VHDEL P1 N1 P2 DELDH DHDEL P3 N2 P4 DELJH TotalDel TotalN TotalP do echo "<tr><td>$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