--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/define_clones.r	Thu Aug 04 08:59:47 2016 -0400
@@ -0,0 +1,14 @@
+args <- commandArgs(trailingOnly = TRUE)
+
+input=args[1]
+output=args[2]
+
+change.o = read.table(input, header=T, sep="\t", quote="", stringsAsFactors=F)
+
+freq = data.frame(table(change.o$CLONE))
+freq2 = data.frame(table(freq$Freq))
+freq2$final = round(freq2$Freq / as.numeric(freq2$Var1), 2)
+
+names(freq2) = c("freq", "freq.of.freq", "divided")
+
+write.table(x=freq2, file=output, sep="\t",quote=F,row.names=F,col.names=T)