--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/check_unique_id.r	Mon Jul 17 10:44:40 2017 -0400
@@ -0,0 +1,25 @@
+args <- commandArgs(trailingOnly = TRUE) #first argument must be the summary file so it can grab the 
+
+current_file = args[1]
+
+current = read.table(current_file, header=T, sep="\t", fill=T, stringsAsFactors=F, quote="", check.names=F)
+
+if(!("Sequence number" %in% names(current))){
+	stop("First argument doesn't contain the 'Sequence number' column")
+}
+
+tbl = table(current$Sequence.ID)
+l_tbl = length(tbl)
+check = any(tbl > 1)
+
+#if(l_tbl != nrow(current)){ # non unique IDs?
+if(check){
+	print("Sequence.ID is not unique for every sequence, adding sequence number to IDs")
+	for(i in 1:length(args)){
+		current_file = args[i]
+		print(paste("Appending 'Sequence number' column to 'Sequence ID' column in", current_file))
+		current = read.table(current_file, header=T, sep="\t", fill=T, stringsAsFactors=F, quote="", check.names=F)
+		current[,"Sequence ID"] = paste(current[,"Sequence ID"], current[,"Sequence number"], sep="_")
+		write.table(x = current, file = current_file, quote = F, sep = "\t", na = "", row.names = F, col.names = T)
+	}
+}