Mercurial > repos > davidvanzessen > report_clonality_igg
comparison r_wrapper.sh @ 10:06777331fbd8 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Thu, 15 May 2014 09:27:22 -0400 |
| parents | 712f3e9924d5 |
| children | 866d22e60e60 |
comparison
equal
deleted
inserted
replaced
| 9:712f3e9924d5 | 10:06777331fbd8 |
|---|---|
| 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 locus=$6 | |
| 9 selection=$7 | |
| 10 useD="false" | |
| 11 if [[ "$species" == "human" && "$locus" = "igh" ]] ; then | |
| 12 useD="true" | |
| 13 fi | |
| 7 dir="$(cd "$(dirname "$0")" && pwd)" | 14 dir="$(cd "$(dirname "$0")" && pwd)" |
| 8 mkdir $3 | 15 mkdir $3 |
| 9 Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputDir $clonalType 2>&1 | 16 Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputDir $clonalType $species $locus $selection 2>&1 |
| 10 cp $dir/tabber.js $outputDir | 17 cp $dir/tabber.js $outputDir |
| 11 cp $dir/style.css $outputDir | 18 cp $dir/style.css $outputDir |
| 12 cp $dir/script.js $outputDir | 19 cp $dir/script.js $outputDir |
| 13 cp $dir/jquery-1.11.0.min.js $outputDir | 20 cp $dir/jquery-1.11.0.min.js $outputDir |
| 14 cp $dir/jquery.tablesorter.min.js $outputDir | 21 cp $dir/jquery.tablesorter.min.js $outputDir |
| 15 cp $dir/asc.gif $outputDir | 22 cp $dir/asc.gif $outputDir |
| 16 cp $dir/desc.gif $outputDir | 23 cp $dir/desc.gif $outputDir |
| 17 cp $dir/bg.gif $outputDir | 24 cp $dir/bg.gif $outputDir |
| 25 samples=`cat $outputDir/samples.txt` | |
| 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 | 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 |
| 19 echo "<html<head>" >> $outputFile | 27 echo "<html><head><title>Report on:" >> $outputFile |
| 20 echo "<script type='text/javascript' src='jquery-1.11.0.min.js'></script>" >> $outputFile | 28 for sample in $samples; do |
| 29 echo " $sample" >> $outputFile | |
| 30 done | |
| 31 echo "</title><script type='text/javascript' src='jquery-1.11.0.min.js'></script>" >> $outputFile | |
| 21 echo "<script type='text/javascript' src='tabber.js'></script>" >> $outputFile | 32 echo "<script type='text/javascript' src='tabber.js'></script>" >> $outputFile |
| 22 echo "<script type='text/javascript' src='script.js'></script>" >> $outputFile | 33 echo "<script type='text/javascript' src='script.js'></script>" >> $outputFile |
| 23 echo "<script type='text/javascript' src='jquery.tablesorter.min.js'></script>" >> $outputFile | 34 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 | 35 echo "<link rel='stylesheet' type='text/css' href='style.css'></head>" >> $outputFile |
| 25 echo "<div class='tabber'><div class='tabbertab' title='Gene frequencies'>" >> $outputFile | 36 echo "<div class='tabber'><div class='tabbertab' title='Gene frequencies'>" >> $outputFile |
| 26 | 37 |
| 27 echo "<img src='CDR3LengthPlot.png'/><br />" >> $outputFile | 38 echo "<img src='CDR3LengthPlot.png'/><br />" >> $outputFile |
| 28 echo "<img src='VFPlot.png'/>" >> $outputFile | 39 echo "<img src='VFPlot.png'/>" >> $outputFile |
| 29 echo "<img src='DFPlot.png'/>" >> $outputFile | 40 if [[ "$useD" == "true" ]] ; then |
| 41 echo "<img src='DFPlot.png'/>" >> $outputFile | |
| 42 fi | |
| 30 echo "<img src='JFPlot.png'/>" >> $outputFile | 43 echo "<img src='JFPlot.png'/>" >> $outputFile |
| 31 echo "<img src='VPlot.png'/>" >> $outputFile | 44 echo "<img src='VPlot.png'/>" >> $outputFile |
| 32 echo "<img src='DPlot.png'/>" >> $outputFile | 45 if [[ "$useD" == "true" ]] ; then |
| 46 echo "<img src='DPlot.png'/>" >> $outputFile | |
| 47 fi | |
| 33 echo "<img src='JPlot.png'/></div>" >> $outputFile | 48 echo "<img src='JPlot.png'/></div>" >> $outputFile |
| 34 | 49 |
| 35 samples=`cat $outputDir/samples.txt` | |
| 36 count=1 | 50 count=1 |
| 37 echo "<div class='tabbertab' title='Heatmaps'><div class='tabber'>" >> $outputFile | 51 echo "<div class='tabbertab' title='Heatmaps'><div class='tabber'>" >> $outputFile |
| 38 for sample in $samples; do | 52 for sample in $samples; do |
| 39 echo "<div class='tabbertab' title='$sample'><table border='1'><tr>" >> $outputFile | 53 echo "<div class='tabbertab' title='$sample'><table border='1'><tr>" >> $outputFile |
| 40 echo "<td><img src='HeatmapVD_$sample.png'/></td>" >> $outputFile | 54 if [[ "$useD" == "true" ]] ; then |
| 55 echo "<td><img src='HeatmapVD_$sample.png'/></td>" >> $outputFile | |
| 56 fi | |
| 41 echo "<td><img src='HeatmapVJ_$sample.png'/></td>" >> $outputFile | 57 echo "<td><img src='HeatmapVJ_$sample.png'/></td>" >> $outputFile |
| 42 echo "<td><img src='HeatmapDJ_$sample.png'/></td></tr></table></div>" >> $outputFile | 58 if [[ "$useD" == "true" ]] ; then |
| 59 echo "<td><img src='HeatmapDJ_$sample.png'/></td>" >> $outputFile | |
| 60 fi | |
| 61 echo "</tr></table></div>" >> $outputFile | |
| 43 count=$((count+1)) | 62 count=$((count+1)) |
| 44 done | 63 done |
| 45 echo "</div></div>" >> $outputFile | 64 echo "</div></div>" >> $outputFile |
| 46 | 65 |
| 66 #echo "<div class='tabbertab' title='Interactive'><svg class='chart'></svg><script src='http://d3js.org/d3.v3.min.js'></script></div>" >> $outputFile | |
| 47 | 67 |
| 48 hasReplicateColumn="$(if head -n 1 $inputFile | grep -q 'Replicate'; then echo 'Yes'; else echo 'No'; fi)" | 68 hasReplicateColumn="$(if head -n 1 $inputFile | grep -q 'Replicate'; then echo 'Yes'; else echo 'No'; fi)" |
| 49 echo "$hasReplicateColumn" | 69 echo "$hasReplicateColumn" |
| 50 #if its a 'new' merged file with replicate info | 70 #if its a 'new' merged file with replicate info |
| 51 if [[ "$hasReplicateColumn" == "Yes" ]] ; then | 71 if [[ "$hasReplicateColumn" == "Yes" ]] ; then |
| 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 | 128 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 | 129 |
| 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 | 130 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 | 131 |
| 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 | 132 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>" >> $outputFile | 133 if [[ "$useD" == "true" ]] ; then |
| 134 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 | |
| 135 fi | |
| 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 | 136 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 | 137 |
| 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 | 138 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>" >> $outputFile | 139 if [[ "$useD" == "true" ]] ; then |
| 140 echo "<tr><td>The dataset used to generate the D gene frequency graph</td><td><a href='DFrequency.csv'>Download</a></td></tr>" >> $outputFile | |
| 141 fi | |
| 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 | 142 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 | 143 |
| 120 for sample in $samples; do | 144 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>" >> $outputFile | 145 if [[ "$useD" == "true" ]] ; then |
| 146 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 | |
| 147 fi | |
| 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 | 148 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>" >> $outputFile | 149 if [[ "$useD" == "true" ]] ; then |
| 150 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 | |
| 151 fi | |
| 124 done | 152 done |
| 125 | 153 |
| 126 echo "</table>" >> $outputFile | 154 echo "</table>" >> $outputFile |
| 127 echo "</div></html>" >> $outputFile | 155 echo "</div></html>" >> $outputFile |