--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/experimental_design/experimental_design.r	Mon Aug 29 05:41:20 2016 -0400
@@ -0,0 +1,38 @@
+args <- commandArgs(trailingOnly = TRUE)
+
+print(args)
+
+inputs = args[1:(length(args) - 1)]
+output = args[length(args)]
+
+current.id = ""
+counter = 1
+
+result = NULL
+
+for(current in inputs){
+	if(grepl("/", current)){ #its a path to a file
+		print(paste("Adding file", counter, "to", current.id))
+		dat = read.table(current, sep="\t", header=T, quote="", fill=T)
+		
+		#IMGT check
+		
+		dat$Sample = current.id
+		dat$Replicate = counter
+		
+		if(is.null(result)){
+			result = dat[NULL,]
+		}
+		
+		result = rbind(result, dat)
+		
+		counter = counter + 1
+		
+	} else { #its an ID of a patient
+		print(paste("New patient", current))
+		current.id = current
+		counter = 1
+	}
+}
+
+write.table(result, output, sep="\t", quote=F, row.names=F, col.names=T)