Mercurial > repos > davidvanzessen > report_clonality_tcell_igg
diff r_wrapper.sh @ 0:1d429107cd26 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Fri, 07 Mar 2014 05:42:31 -0500 |
| parents | |
| children | 1ba88ffd6f4e |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/r_wrapper.sh Fri Mar 07 05:42:31 2014 -0500 @@ -0,0 +1,82 @@ +#!/bin/bash +echo $1 +echo $2 +echo $3 +echo $4 +echo $5 + +inputFile=$1 +outputFile=$2 +outputDir=$3 +clonalType=$4 +species=$5 +dir="$(cd "$(dirname "$0")" && pwd)" +mkdir $3 +Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputDir $clonalType $species 2>&1 +echo "<html>" >> $2 +echo "<img src='VPlot.png'/>" >> $2 +echo "<img src='DPlot.png'/>" >> $2 +echo "<img src='JPlot.png'/>" >> $2 + +hasReplicateColumn="$(if head -n 1 $inputFile | grep -q 'Replicate'; then echo 'Yes'; else echo 'No'; fi)" + +if [[ "$hasReplicateColumn" == "Yes" ]] ; then + echo "<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>" >> $outputFile + while IFS=, read Sample unique VHDEL P1 N1 P2 DELDH DHDEL P3 N2 P4 DELJH TotalDel TotalN TotalP + do + echo "<tr><td>$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 + done < $outputDir/junctionAnalysis.csv + echo "</table>" >> $outputFile +fi + +samples=`cat $outputDir/samples.txt` +count=1 +echo "<table border='1'><caption><a href='allUnique.tsv'><h3>$clonalType</h3></a></caption>" >> $outputFile +for sample in $samples; do + clonalityScore="$(cat $outputDir/ClonalityScore_$sample.csv)" + echo "<tr><td colspan='3' height='100'></td></tr>" >> $outputFile + echo "<tr><td colspan='3'><h1>$sample</h1></td></tr>" >> $outputFile + + echo "$hasReplicateColumn" + #if its a 'new' merged file with replicate info + if [[ "$hasReplicateColumn" == "Yes" ]] ; then + echo "<tr><td colspan='3'><a href='clonality_$sample.tsv'><h2>Clonality Score: $clonalityScore</h2></a></td></tr>" >> $outputFile + + #replicate,reads,squared + echo "<tr><td colspan='3'><table border='1'><tr><th>Replicate ID</th><th>Number of Reads</th><th>Reads Squared</th></tr>" >> $outputFile + while IFS=, read replicate reads squared + do + + echo "<tr><td><a href='clonality_${sample}_$replicate.tsv'>$replicate</a></td><td>$reads</td><td>$squared</td></tr>" >> $outputFile + done < $outputDir/ReplicateReads_$sample.csv + + #sum of reads and reads squared + while IFS=, read readsSum squaredSum + do + echo "<tr><td>Sum</td><td>$readsSum</td><td>$squaredSum</td></tr>" >> $outputFile + done < $outputDir/ReplicateSumReads_$sample.csv + + echo "</table></td></tr>" >> $outputFile + + #overview + echo "<tr><td colspan='3'><table border='1'><tr><th>Coincidence Type</th><th>Raw Coincidence Freq</th><th>Coincidence Weight</th><th>Coincidences, Weighted</th></tr>" >> $outputFile + while IFS=, read type count weight weightedCount + do + echo "<tr><td>$type</td><td>$count</td><td>$weight</td><td>$weightedCount</td></tr>" >> $outputFile + done < $outputDir/ClonalityOverView_$sample.csv + echo "</table></td></tr>" >> $outputFile + fi + + echo "<tr><td><h2>V-D Heatmap:</h2></td><td><h2>V-J Heatmap:</h2></td><td><h2>D-J Heatmap:</h2></td></tr><tr>" >> $outputFile + mv "$outputDir/HeatmapVD_$sample.png" "$outputDir/VD_$sample.png" + echo "<td><img src='VD_$sample.png'/></td>" >> $outputFile + mv "$outputDir/HeatmapVJ_$sample.png" "$outputDir/VJ_$sample.png" + echo "<td><img src='VJ_$sample.png'/></td>" >> $outputFile + mv "$outputDir/HeatmapDJ_$sample.png" "$outputDir/DJ_$sample.png" + echo "<td><img src='DJ_$sample.png'/></td></tr>" >> $outputFile + count=$((count+1)) +done +echo "</table>" >> $outputFile + +echo "</html>" >> $2 +