--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/naive_output.r	Fri Mar 18 07:50:34 2016 -0400
@@ -0,0 +1,23 @@
+args <- commandArgs(trailingOnly = TRUE)
+
+naive.file = args[1]
+shm.file = args[2]
+output.file = args[3]
+
+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
+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, output.file, quote=F, sep="\t", row.names=F, col.names=T)