# HG changeset patch
# User davidvanzessen
# Date 1385124677 18000
# Node ID af2834de221ce7117bd26bea94824d62d6f7c8e4
# Parent  46c5d9d396a5e0f7de632627a7c8f69d52a3c701
Uploaded

diff -r 46c5d9d396a5 -r af2834de221c RScript.r
--- a/RScript.r	Fri Nov 22 07:51:11 2013 -0500
+++ b/RScript.r	Fri Nov 22 07:51:17 2013 -0500
@@ -5,6 +5,7 @@
 inFile = args[1]
 outFile = args[2]
 outDir = args[3]
+clonalType = args[4]
 
 if (!("gridExtra" %in% rownames(installed.packages()))) {
 	install.packages("gridExtra", repos="http://cran.xl-mirror.nl/") 
@@ -33,7 +34,8 @@
 test$Top.D.Gene = gsub("[*]([0-9]+)", "", test$Top.D.Gene)
 test$Top.J.Gene = gsub("[*]([0-9]+)", "", test$Top.J.Gene)
 
-test$VDJCDR3 = do.call(paste, c(test[c("Top.V.Gene", "Top.D.Gene", "Top.J.Gene","CDR3.Seq.DNA")], sep = ":"))
+#test$VDJCDR3 = do.call(paste, c(test[c("Top.V.Gene", "Top.D.Gene", "Top.J.Gene","CDR3.Seq.DNA")], sep = ":"))
+test$VDJCDR3 = do.call(paste, c(test[unlist(strsplit(clonalType, ","))], sep = ":"))
 
 PROD = test[test$VDJ.Frame != "In-frame with stop codon" & test$VDJ.Frame != "Out-of-frame" & test$CDR3.Found.How != "NOT_FOUND" , ]