Mercurial > repos > davidvanzessen > report_clonality_igg

comparison r_wrapper.sh @ 12:24a80d4eff0c draft

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Uploaded
author davidvanzessen
date Thu, 13 Nov 2014 10:36:33 -0500
parents 866d22e60e60
children c6d0ee9b3d91
comparison
equal deleted inserted replaced
11:866d22e60e60 12:24a80d4eff0c
16 Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputDir $clonalType $species $locus $filterproductive 2>&1 16 Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputDir $clonalType $species $locus $filterproductive 2>&1
17 cp $dir/tabber.js $outputDir 17 cp $dir/tabber.js $outputDir
18 cp $dir/style.css $outputDir 18 cp $dir/style.css $outputDir
19 cp $dir/script.js $outputDir 19 cp $dir/script.js $outputDir
20 cp $dir/jquery-1.11.0.min.js $outputDir 20 cp $dir/jquery-1.11.0.min.js $outputDir
21 cp $dir/jquery.tablesorter.min.js $outputDir
22 cp $dir/asc.gif $outputDir
23 cp $dir/desc.gif $outputDir
24 cp $dir/bg.gif $outputDir
25 samples=`cat $outputDir/samples.txt` 21 samples=`cat $outputDir/samples.txt`
26 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 22 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
27 echo "<html><head><title>Report on:" >> $outputFile 23 echo "<html><head><title>Report on:" >> $outputFile
28 for sample in $samples; do 24 for sample in $samples; do
29 echo " $sample" >> $outputFile 25 echo " $sample" >> $outputFile
30 done 26 done
31 echo "</title><script type='text/javascript' src='jquery-1.11.0.min.js'></script>" >> $outputFile 27 echo "</title><script type='text/javascript' src='jquery-1.11.0.min.js'></script>" >> $outputFile
32 echo "<script type='text/javascript' src='tabber.js'></script>" >> $outputFile 28 echo "<script type='text/javascript' src='tabber.js'></script>" >> $outputFile
33 echo "<script type='text/javascript' src='script.js'></script>" >> $outputFile 29 echo "<script type='text/javascript' src='script.js'></script>" >> $outputFile
34 echo "<script type='text/javascript' src='jquery.tablesorter.min.js'></script>" >> $outputFile
35 echo "<link rel='stylesheet' type='text/css' href='style.css'></head>" >> $outputFile 30 echo "<link rel='stylesheet' type='text/css' href='style.css'></head>" >> $outputFile
36 echo "<div class='tabber'><div class='tabbertab' title='Gene frequencies'>" >> $outputFile 31 echo "<div class='tabber'><div class='tabbertab' title='Gene frequencies'>" >> $outputFile
37 32
38 echo "<img src='CDR3LengthPlot.png'/><br />" >> $outputFile 33 echo "<img src='CDR3LengthPlot.png'/><br />" >> $outputFile
39 echo "<img src='VFPlot.png'/>" >> $outputFile 34 echo "<img src='VFPlot.png'/>" >> $outputFile
101 fi 96 fi
102 97
103 hasJunctionData="$(if head -n 1 $inputFile | grep -q '3V-REGION trimmed-nt nb'; then echo 'Yes'; else echo 'No'; fi)" 98 hasJunctionData="$(if head -n 1 $inputFile | grep -q '3V-REGION trimmed-nt nb'; then echo 'Yes'; else echo 'No'; fi)"
104 99
105 if [[ "$hasJunctionData" == "Yes" ]] ; then 100 if [[ "$hasJunctionData" == "Yes" ]] ; then
106 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 101 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>" >> $outputFile
107 while IFS=, read Sample unique VHDEL P1 N1 P2 DELDH DHDEL P3 N2 P4 DELJH TotalDel TotalN TotalP 102 while IFS=, read Sample unique VHDEL P1 N1 P2 DELDH DHDEL P3 N2 P4 DELJH TotalDel TotalN TotalP
108 do 103 do
109 echo "<tr><td>$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>" >> $outputFile 104 echo "<tr><td>$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
110 done < $outputDir/junctionAnalysis.csv 105 done < $outputDir/junctionAnalysis.csv
111 echo "</tbody></table></div>" >> $outputFile 106 echo "</tbody></table></div>" >> $outputFile