# HG changeset patch
# User davidvanzessen
# Date 1390910258 18000
# Node ID 81b9673b29be2509ae3d663ba271135395830a5f
# Parent  08aa67564858c4c25daf96f366466b6ef6191239
Uploaded

diff -r 08aa67564858 -r 81b9673b29be RScript.r
--- a/RScript.r	Tue Jan 28 03:44:44 2014 -0500
+++ b/RScript.r	Tue Jan 28 06:57:38 2014 -0500
@@ -315,3 +315,32 @@
 	clonalityOverviewSplit = split(clonalityOverview, f=clonalityOverview$Sample)
 	lapply(clonalityOverviewSplit, FUN=ClonalityOverviewPrint)
 }
+
+if("Functionality" %in% colnames(test))
+{
+	newData = data.frame(data.table(PROD)[,list(unique=.N, 
+											VH.DEL=mean(X3V.REGION.trimmed.nt.nb),
+											P1=mean(P3V.nt.nb),
+											N1=mean(N1.REGION.nt.nb),
+											P2=mean(P5D.nt.nb),
+											DEL.DH=mean(X5D.REGION.trimmed.nt.nb),
+											DH.DEL=mean(X3D.REGION.trimmed.nt.nb),
+											P3=mean(P3D.nt.nb),
+											N2=mean(N2.REGION.nt.nb),
+											P4=mean(P5J.nt.nb),
+											DEL.JH=mean(X5J.REGION.trimmed.nt.nb),
+											Total.Del=(	mean(X3V.REGION.trimmed.nt.nb) + 
+														mean(X5D.REGION.trimmed.nt.nb) + 
+														mean(X3D.REGION.trimmed.nt.nb) +
+														mean(X5J.REGION.trimmed.nt.nb)),
+														
+											Total.N=(	mean(N1.REGION.nt.nb) +
+														mean(N2.REGION.nt.nb)),
+														
+											Total.P=(	mean(P3V.nt.nb) +
+														mean(P5D.nt.nb) +
+														mean(P3D.nt.nb) +
+														mean(P5J.nt.nb))),
+											by=c("Sample")])
+	write.table(newData, "junctionAnalysis.csv" , sep=",",quote=F,na="-",row.names=F,col.names=F)
+}
\ No newline at end of file
diff -r 08aa67564858 -r 81b9673b29be r_wrapper.sh
--- a/r_wrapper.sh	Tue Jan 28 03:44:44 2014 -0500
+++ b/r_wrapper.sh	Tue Jan 28 06:57:38 2014 -0500
@@ -15,10 +15,20 @@
 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'><th><td>Sample</td><td>unique</td><td>VH.DEL</td><td>P1</td><td>N1</td><td>P2</td><td>DEL.DH</td><td>DH.DEL</td><td>P3</td><td>N2</td><td>P4</td><td>DEL.JH</td><td>Total.Del</td><td>Total.N</td><td>Total.P</td></th>" >> $outputFile
+	while IFS=, Sample unique VH.DEL P1 N1 P2 DEL.DH DH.DEL P3 N2 P4 DEL.JH Total.Del Total.N Total.P
+	do
+		echo "<tr><td>$Sample</td><td>$unique</td><td>$VH.DEL</td><td>$P1</td><td>$N1</td><td>$P2</td><td>$DEL.DH</td><td>$DH.DEL</td><td>$P3</td><td>$N2</td><td>$P4</td><td>$DEL.JH</td><td>$Total.Del</td><td>$Total.N</td><td>$Total.P</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>" >> $outputFile
-hasReplicateColumn="$(if head -n 1 $inputFile | grep -q 'Replicate'; then echo 'Yes'; else echo 'No'; fi)"
 for sample in $samples; do
 	clonalityScore="$(cat $outputDir/ClonalityScore_$sample.csv)"
 	echo "<tr><td colspan='3' height='100'></td></tr>" >> $outputFile