# HG changeset patch
# User davidvanzessen
# Date 1447075711 18000
# Node ID ee1bda8c27c8cd2193ae275974ce5dcce784e0e8
# Parent  cf1def1aaa74d2977e865a618aff0cbf9bc11f3d
Uploaded

diff -r cf1def1aaa74 -r ee1bda8c27c8 igblast/test.txt
--- a/igblast/test.txt	Fri Nov 06 05:12:17 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-test1	test2	test3
diff -r cf1def1aaa74 -r ee1bda8c27c8 report_clonality/RScript.r
--- a/report_clonality/RScript.r	Fri Nov 06 05:12:17 2015 -0500
+++ b/report_clonality/RScript.r	Mon Nov 09 08:28:31 2015 -0500
@@ -563,6 +563,7 @@
 imgtcolumns = c("X3V.REGION.trimmed.nt.nb","P3V.nt.nb", "N1.REGION.nt.nb", "P5D.nt.nb", "X5D.REGION.trimmed.nt.nb", "X3D.REGION.trimmed.nt.nb", "P3D.nt.nb", "N2.REGION.nt.nb", "P5J.nt.nb", "X5J.REGION.trimmed.nt.nb", "X3V.REGION.trimmed.nt.nb", "X5D.REGION.trimmed.nt.nb", "X3D.REGION.trimmed.nt.nb", "X5J.REGION.trimmed.nt.nb", "N1.REGION.nt.nb", "N2.REGION.nt.nb", "P3V.nt.nb", "P5D.nt.nb", "P3D.nt.nb", "P5J.nt.nb")
 if(all(imgtcolumns %in% colnames(inputdata)))
 {
+  print("found IMGT columns, running junction analysis")
   newData = data.frame(data.table(PRODF)[,list(unique=.N, 
                                                VH.DEL=mean(.SD$X3V.REGION.trimmed.nt.nb, na.rm=T),
                                                P1=mean(.SD$P3V.nt.nb, na.rm=T),
@@ -587,7 +588,6 @@
                                                            mean(.SD$P3D.nt.nb, na.rm=T) +
                                                            mean(.SD$P5J.nt.nb, na.rm=T))),
                                          by=c("Sample")])
-  print(newData)
   newData[,sapply(newData, is.numeric)] = round(newData[,sapply(newData, is.numeric)],1)
   write.table(newData, "junctionAnalysisProd.csv" , sep=",",quote=F,na="-",row.names=F,col.names=F)
   
@@ -602,18 +602,16 @@
                                                 N2=mean(.SD$N2.REGION.nt.nb, na.rm=T),
                                                 P4=mean(.SD$P5J.nt.nb, na.rm=T),
                                                 DEL.JH=mean(.SD$X5J.REGION.trimmed.nt.nb, na.rm=T),
-                                                Total.Del=(	mean(.SD$X3V.REGION.trimmed.nt.nb, na.rm=T) + 
-                                                            mean(.SD$X5D.REGION.trimmed.nt.nb, na.rm=T) + 
-                                                            mean(.SD$X3D.REGION.trimmed.nt.nb, na.rm=T) +
-                                                            mean(.SD$X5J.REGION.trimmed.nt.nb, na.rm=T)),
-                                                
-                                                Total.N=(	mean(.SD$N1.REGION.nt.nb, na.rm=T) +
-                                                          mean(.SD$N2.REGION.nt.nb, na.rm=T)),
-                                                
-																								Total.P=(	mean(.SD$P3V.nt.nb, na.rm=T) +
-																													mean(.SD$P5D.nt.nb, na.rm=T) +
-																													mean(.SD$P3D.nt.nb, na.rm=T) +
-																													mean(.SD$P5J.nt.nb, na.rm=T))),
+                                                Total.Del=(mean(.SD$X3V.REGION.trimmed.nt.nb, na.rm=T) + 
+                                                           mean(.SD$X5D.REGION.trimmed.nt.nb, na.rm=T) + 
+                                                           mean(.SD$X3D.REGION.trimmed.nt.nb, na.rm=T) +
+                                                           mean(.SD$X5J.REGION.trimmed.nt.nb, na.rm=T)),
+                                                Total.N=(  mean(.SD$N1.REGION.nt.nb, na.rm=T) +
+                                                           mean(.SD$N2.REGION.nt.nb, na.rm=T)),
+                                                Total.P=(  mean(.SD$P3V.nt.nb, na.rm=T) +
+							   mean(.SD$P5D.nt.nb, na.rm=T) +
+							   mean(.SD$P3D.nt.nb, na.rm=T) +
+						           mean(.SD$P5J.nt.nb, na.rm=T))),
                                           by=c("Sample")])
   newData[,sapply(newData, is.numeric)] = round(newData[,sapply(newData, is.numeric)],1)
   write.table(newData, "junctionAnalysisUnProd.csv" , sep=",",quote=F,na="-",row.names=F,col.names=F)
diff -r cf1def1aaa74 -r ee1bda8c27c8 report_clonality/r_wrapper.sh
--- a/report_clonality/r_wrapper.sh	Fri Nov 06 05:12:17 2015 -0500
+++ b/report_clonality/r_wrapper.sh	Mon Nov 09 08:28:31 2015 -0500
@@ -137,7 +137,7 @@
 	echo "</div></div>" >> $outputFile
 fi
 
-hasJunctionData="$(if head -n 1 $inputFile | grep -q '3V-REGION trimmed-nt nb'; then echo 'Yes'; else echo 'No'; fi)"
+hasJunctionData="$(if head -n 1 $inputFile | grep -qE '3V.REGION.trimmed.nt.nb'; then echo 'Yes'; else echo 'No'; fi)"
 
 if [[ "$hasJunctionData" == "Yes" ]] ; then
 	echo "<div class='tabbertab' title='Junction Analysis'>" >> $outputFile