# HG changeset patch
# User davidvanzessen
# Date 1421059067 18000
# Node ID b79ad381ced0673298e4cb44ad2a86a5c1ccb8a1
# Parent  c5256a227d2d846bbee1f53d4e3286679fd7908d
Uploaded

diff -r c5256a227d2d -r b79ad381ced0 RScript.r
--- a/RScript.r	Mon Jan 12 04:30:30 2015 -0500
+++ b/RScript.r	Mon Jan 12 05:37:47 2015 -0500
@@ -50,11 +50,14 @@
 inputdata$Top.J.Gene = gsub("[*]([0-9]+)", "", inputdata$Top.J.Gene)
 inputdata$clonaltype = 1:nrow(inputdata)
 PRODF = inputdata
+UNPROD = inputdata
 if(filterproductive){
   if("Functionality" %in% colnames(inputdata)) { # "Functionality" is an IMGT column
     PRODF = inputdata[inputdata$Functionality == "productive" | inputdata$Functionality == "productive (see comment)", ]
+    UNPROD = inputdata[!(inputdata$Functionality == "productive" | inputdata$Functionality == "productive (see comment)"), ]
   } else {
     PRODF = inputdata[inputdata$VDJ.Frame != "In-frame with stop codon" & inputdata$VDJ.Frame != "Out-of-frame" & inputdata$CDR3.Found.How != "NOT_FOUND" , ]
+    UNPROD = inputdata[!(inputdata$VDJ.Frame != "In-frame with stop codon" & inputdata$VDJ.Frame != "Out-of-frame" & inputdata$CDR3.Found.How != "NOT_FOUND" ), ]
   }
 }
 
@@ -62,6 +65,8 @@
 if(clonaltype != "none"){
   PRODF$clonaltype = do.call(paste, c(PRODF[unlist(strsplit(clonaltype, ","))], sep = ":"))
   PRODF = PRODF[!duplicated(PRODF$clonaltype), ]
+  UNPROD$clonaltype = do.call(paste, c(UNPROD[unlist(strsplit(clonaltype, ","))], sep = ":"))
+  UNPROD = UNPROD[!duplicated(UNPROD$clonaltype), ]
 }
 
 PRODF$freq = 1
@@ -576,5 +581,31 @@
                                                           mean(P3D.nt.nb, na.rm=T) +
                                                           mean(P5J.nt.nb, na.rm=T))),
                                         by=c("Sample")])
-  write.table(newData, "junctionAnalysis.csv" , sep=",",quote=F,na="-",row.names=F,col.names=F)
+  write.table(newData, "junctionAnalysisProd.csv" , sep=",",quote=F,na="-",row.names=F,col.names=F)
+  
+	newData = data.frame(data.table(UNPROD)[,list(unique=.N, 
+                                              VH.DEL=mean(X3V.REGION.trimmed.nt.nb, na.rm=T),
+                                              P1=mean(P3V.nt.nb, na.rm=T),
+                                              N1=mean(N1.REGION.nt.nb, na.rm=T),
+                                              P2=mean(P5D.nt.nb, na.rm=T),
+                                              DEL.DH=mean(X5D.REGION.trimmed.nt.nb, na.rm=T),
+                                              DH.DEL=mean(X3D.REGION.trimmed.nt.nb, na.rm=T),
+                                              P3=mean(P3D.nt.nb, na.rm=T),
+                                              N2=mean(N2.REGION.nt.nb, na.rm=T),
+                                              P4=mean(P5J.nt.nb, na.rm=T),
+                                              DEL.JH=mean(X5J.REGION.trimmed.nt.nb, na.rm=T),
+                                              Total.Del=(	mean(X3V.REGION.trimmed.nt.nb, na.rm=T) + 
+                                                            mean(X5D.REGION.trimmed.nt.nb, na.rm=T) + 
+                                                            mean(X3D.REGION.trimmed.nt.nb, na.rm=T) +
+                                                            mean(X5J.REGION.trimmed.nt.nb, na.rm=T)),
+                                              
+                                              Total.N=(	mean(N1.REGION.nt.nb, na.rm=T) +
+                                                          mean(N2.REGION.nt.nb, na.rm=T)),
+                                              
+                                              Total.P=(	mean(P3V.nt.nb, na.rm=T) +
+                                                          mean(P5D.nt.nb, na.rm=T) +
+                                                          mean(P3D.nt.nb, na.rm=T) +
+                                                          mean(P5J.nt.nb, na.rm=T))),
+                                        by=c("Sample")])
+  write.table(newData, "junctionAnalysisUnProd.csv" , sep=",",quote=F,na="-",row.names=F,col.names=F)
 }
diff -r c5256a227d2d -r b79ad381ced0 r_wrapper.sh
--- a/r_wrapper.sh	Mon Jan 12 04:30:30 2015 -0500
+++ b/r_wrapper.sh	Mon Jan 12 05:37:47 2015 -0500
@@ -112,12 +112,22 @@
 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'><thead><tr><th>Sample</th><th>count</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'>" >> $outputFile
+	echo "<table border='1' id='junction_table'> <caption>Productive</caption><thead><tr><th>Sample</th><th>count</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
-	done < $outputDir/junctionAnalysis.csv
-	echo "</tbody></table></div>" >> $outputFile
+	done < $outputDir/junctionAnalysisProd.csv
+	echo "</tbody></table>" >> $outputFile
+	
+	echo "<table border='1' id='junction_table'> <caption>Unproductive</caption><thead><tr><th>Sample</th><th>count</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
+	done < $outputDir/junctionAnalysisUnProd.csv
+	echo "</tbody></table>" >> $outputFile
+	
+	echo "</div>" >> $outputFile
 fi
 
 echo "<div class='tabbertab' title='Comparison'><table border='1'><tr><th>ID</th><th>Include</th></tr>" >> $outputFile