--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/naive_output.r	Thu Oct 13 10:52:24 2016 -0400
@@ -0,0 +1,45 @@
+args <- commandArgs(trailingOnly = TRUE)
+
+naive.file = args[1]
+shm.file = args[2]
+output.file.ca = args[3]
+output.file.cg = args[4]
+output.file.cm = args[5]
+
+naive = read.table(naive.file, sep="\t", header=T, quote="", fill=T)
+shm.merge = read.table(shm.file, sep="\t", header=T, quote="", fill=T)
+
+
+final = merge(naive, shm.merge[,c("Sequence.ID", "best_match")], by.x="ID", by.y="Sequence.ID")
+print(paste("nrow final:", nrow(final)))
+names(final)[names(final) == "best_match"] = "Sample"
+final.numeric = final[,sapply(final, is.numeric)]
+final.numeric[is.na(final.numeric)] = 0
+final[,sapply(final, is.numeric)] = final.numeric
+
+final.ca = final[grepl("^ca", final$Sample),]
+final.cg = final[grepl("^cg", final$Sample),]
+final.cm = final[grepl("^cm", final$Sample),]
+
+if(nrow(final.ca) > 0){
+	final.ca$Replicate = 1
+}
+
+if(nrow(final.cg) > 0){
+	final.cg$Replicate = 1
+}
+
+if(nrow(final.cm) > 0){
+	final.cm$Replicate = 1
+}
+
+#print(paste("nrow final:", nrow(final)))
+#final2 = final
+#final2$Sample = gsub("[0-9]", "", final2$Sample)
+#final = rbind(final, final2)
+#final$Replicate = 1
+
+write.table(final.ca, output.file.ca, quote=F, sep="\t", row.names=F, col.names=T)
+write.table(final.cg, output.file.cg, quote=F, sep="\t", row.names=F, col.names=T)
+write.table(final.cm, output.file.cm, quote=F, sep="\t", row.names=F, col.names=T)
+