--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/define_clones.r	Mon Jul 17 07:44:27 2017 -0400
@@ -0,0 +1,15 @@
+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$final = as.numeric(freq2$Freq) * as.numeric(as.character(freq2$Var1))
+
+names(freq2) = c("Clone size", "Nr of clones", "Nr of sequences")
+
+write.table(x=freq2, file=output, sep="\t",quote=F,row.names=F,col.names=T)