--- a/mutation_analysis.py	Wed May 04 08:44:16 2016 -0400
+++ b/mutation_analysis.py	Mon May 09 03:45:39 2016 -0400
@@ -57,7 +57,6 @@
 		linesplt = line.split("\t")
 		ID = linesplt[IDIndex]
 		genedic[ID] = linesplt[best_matchIndex]
-		print line
 		try:
 			mutationdic[ID + "_FR1"] = [mutationMatcher.match(x).groups() for x in linesplt[fr1Index].split("|") if x] if include_fr1 else []
 			mutationdic[ID + "_CDR1"] = [mutationMatcher.match(x).groups() for x in linesplt[cdr1Index].split("|") if x]

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sequence_overview.r	Mon May 09 03:45:39 2016 -0400
@@ -0,0 +1,99 @@
+library(reshape2)
+
+args <- commandArgs(trailingOnly = TRUE)
+
+gene.matches = args[1]
+sequence.file = args[2]
+outputdir = args[3]
+main.html = "index.html"
+
+setwd(outputdir)
+
+genes = read.table(gene.matches, header=T, sep="\t", fill=T)
+sequences = read.table(sequence.file, header=T, sep="\t", fill=T, stringsAsFactors=F, quote="")
+
+dat = merge(sequences, genes, by="Sequence.ID")
+
+dat$seq_conc = paste(dat$CDR1.IMGT, dat$CDR2.IMGT, dat$CDR3.IMGT, dat$FR2.IMGT, dat$FR3.IMGT)
+
+IDs = dat[,c("Sequence.ID", "seq_conc", "best_match")]
+IDs$best_match = as.character(IDs$best_match)
+
+#dat = data.frame(data.table(dat)[, list(freq=.N), by=c("best_match", "seq_conc")])
+
+dat = data.frame(table(dat$best_match, dat$seq_conc))
+
+dat = dat[dat$Freq > 1,]
+
+names(dat) = c("best_match", "seq_conc", "Freq")
+
+dat$seq_conc = factor(dat$seq_conc)
+
+dat = dat[order(nchar(as.character(dat$seq_conc))),]
+
+#writing html from R...
+td = function(val) { paste("<td>", val, "</td>", sep="") }
+tr = function(val) { capture.output(cat("<tr>", td(val), "</tr>", sep="")) }
+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>"); }
+
+cat("<table border='1'>", file=main.html, append=F)
+cat("<tr><th>Sequence</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$seq_conc == dat[i,c("seq_conc")] & IDs$best_match == "ca1",]
+	ca2 = IDs[IDs$seq_conc == dat[i,c("seq_conc")] & IDs$best_match == "ca2",]
+	
+	cg1 = IDs[IDs$seq_conc == dat[i,c("seq_conc")] & IDs$best_match == "cg1",]
+	cg2 = IDs[IDs$seq_conc == dat[i,c("seq_conc")] & IDs$best_match == "cg2",]
+	cg3 = IDs[IDs$seq_conc == dat[i,c("seq_conc")] & IDs$best_match == "cg3",]
+	cg4 = IDs[IDs$seq_conc == dat[i,c("seq_conc")] & IDs$best_match == "cg4",]
+	
+	cm = IDs[IDs$seq_conc == dat[i,c("seq_conc")] & IDs$best_match == "cm",]
+	
+	id = as.numeric(dat[i,"seq_conc"])
+
+	if(nrow(ca1) > 0){
+		cat(tbl(ca1), file=paste("ca1_", id, ".html", sep=""))
+	}
+
+	if(nrow(ca2) > 0){
+		cat(tbl(ca2), file=paste("ca2_", id, ".html", sep=""))
+	}
+
+	if(nrow(cg1) > 0){
+		cat(tbl(cg1), file=paste("cg1_", id, ".html", sep=""))
+	}
+
+	if(nrow(cg2) > 0){
+		cat(tbl(cg2), file=paste("cg2_", id, ".html", sep=""))
+	}
+
+	if(nrow(cg3) > 0){
+		cat(tbl(cg3), file=paste("cg3_", id, ".html", sep=""))
+	}
+
+	if(nrow(cg4) > 0){
+		cat(tbl(cg4), file=paste("cg4_", id, ".html", sep=""))
+	}
+
+	if(nrow(cm) > 0){
+		cat(tbl(cm), file=paste("cm_", id, ".html", sep=""))
+	}
+	
+	ca1.html = make.link(id, "ca1", nrow(ca1))
+	ca2.html = make.link(id, "ca2", nrow(ca2))
+	
+	cg1.html = make.link(id, "cg1", nrow(cg1))
+	cg2.html = make.link(id, "cg2", nrow(cg2))
+	cg3.html = make.link(id, "cg3", nrow(cg3))
+	cg4.html = make.link(id, "cg4", nrow(cg4))
+	
+	cm.html = make.link(id, "cm", nrow(cm))
+	
+	rw = c(as.character(dat[i,"seq_conc"]), ca1.html, ca2.html, cg1.html, cg2.html, cg3.html, cg4.html, cm.html)
+
+	cat(tr(rw), file=main.html, append=T)
+}
+
+cat("</table>", file=main.html, append=T)

--- a/wrapper.sh	Wed May 04 08:44:16 2016 -0400
+++ b/wrapper.sh	Mon May 09 03:45:39 2016 -0400
@@ -229,7 +229,11 @@
 	Rscript $dir/naive_output.r $naive_output_ca $outdir/merged.txt $naive_output_ca $naive_output_cg $naive_output_cm 2>&1
 fi
 
+echo "---------------- sequence_overview.r ----------------"
 
+mkdir $outdir/sequence_overview
+
+Rscript $dir/sequence_overview.r $outdir/identified_genes.txt $PWD/sequences.txt $outdir/sequence_overview 2>&1