--- a/sequence_overview.r	Wed Jun 15 04:48:41 2016 -0400
+++ b/sequence_overview.r	Thu Jun 16 05:05:47 2016 -0400
@@ -41,11 +41,14 @@
 make.link = function(id, clss, val) { paste("<a href='", clss, "_", id, ".html'>", val, "</a>", sep="") }
 tbl = function(df) { res = "<table border='1'>"; for(i in 1:nrow(df)){ res = paste(res, tr(df[i,]), sep=""); }; res = paste(res, "</table>"); }
 
+print(paste("Number of unique sequences to be written to the sequence overview page", nrow(dat)))
+
 cat("<table border='1'>", file=main.html, append=F)
 cat("<caption>CDR1+FR2+CDR2+FR3+CDR3 sequences that show up more than once</caption>", file=main.html, append=T)
 cat("<tr><th>Sequence</th><th>Functionality</th><th>ca1</th><th>ca2</th><th>cg1</th><th>cg2</th><th>cg3</th><th>cg4</th><th>cm</th></tr>", file=main.html, append=T)
 
 for(i in 1:nrow(dat)){
+	
 	ca1 = IDs[IDs$seq_conc == dat[i,c("seq_conc")] & grepl("^ca1", IDs$best_match),]
 	ca2 = IDs[IDs$seq_conc == dat[i,c("seq_conc")] & grepl("^ca2", IDs$best_match),]
 	
@@ -62,7 +65,10 @@
 	classes.sum = sum(classes)
 	
 	if(classes.sum == 1){
+		print(paste("next", i, classes.sum))
 		next
+	} else {
+		print(i)
 	}
 	
 	id = as.numeric(dat[i,"seq_conc"])
@@ -144,6 +150,10 @@
 	names(NTresult) = c(tmp, paste(clazz, c("x", "y", "z"), sep=""))
 }
 
+write.table(NToverview[,c("Sequence.ID", "best_match", "seq", "A", "C", "G", "T")], NToverview.file, quote=F, sep="\t", row.names=F, col.names=T)
+
+NToverview = NToverview[!grepl("unmatched", NToverview$best_match),]
+
 new.col.x = c(sum(NToverview$A), sum(NToverview$C), sum(NToverview$T), sum(NToverview$G))
 new.col.y = sum(new.col.x)
 new.col.z = round(new.col.x / new.col.y * 100, 2)
@@ -160,8 +170,6 @@
 
 write.table(hotspot.analysis.sum, hotspot.analysis.sum.file, quote=F, sep=",", row.names=F, col.names=F, na="0")
 
-write.table(NToverview[,c("Sequence.ID", "best_match", "seq", "A", "C", "G", "T")], NToverview.file, quote=F, sep="\t", row.names=F, col.names=T)
-