# HG changeset patch
# User davidvanzessen
# Date 1464964552 14400
# Node ID 5e237c2430881ffce6914a85c18de86b92d4ae18
# Parent  f0e8dac22c6e8a16178bc5cca37c3752451027ba
Uploaded

diff -r f0e8dac22c6e -r 5e237c243088 merge_and_filter.r
--- a/merge_and_filter.r	Wed Jun 01 05:03:24 2016 -0400
+++ b/merge_and_filter.r	Fri Jun 03 10:35:52 2016 -0400
@@ -116,15 +116,7 @@
 
 print(paste("Number of sequences in result after merging with sequences:", nrow(result)))
 
-print(paste("Number of N in CDR1:", sum(grepl("n|N", result$CDR1.IMGT.seq))))
-print(paste("Number of N in FR2:", sum(grepl("n|N", result$FR2.IMGT.seq))))
-print(paste("Number of N in CDR2:", sum(grepl("n|N", result$CDR2.IMGT.seq))))
-print(paste("Number of N in FR3:", sum(grepl("n|N", result$FR3.IMGT.seq))))
-
-print(paste("Number of sequences with N in CDR1 or FR2 or CDR2 or FR3:", sum(grepl("n|N", result$FR2.IMGT.seq) | grepl("n|N", result$FR3.IMGT.seq) | grepl("n|N", result$CDR1.IMGT.seq) | grepl("n|N", result$CDR2.IMGT.seq))))
-
-
-result = result[!(grepl("n|N", result$FR2.IMGT.seq) | grepl("n|N", result$FR3.IMGT.seq) | grepl("n|N", result$CDR1.IMGT.seq) | grepl("n|N", result$CDR2.IMGT.seq)),]
+result = result[!(grepl("n|N", result$FR2.IMGT.seq) | grepl("n|N", result$FR3.IMGT.seq) | grepl("n|N", result$CDR1.IMGT.seq) | grepl("n|N", result$CDR2.IMGT.seq) | grepl("n|N", result$CDR3.IMGT.seq)),]
 
 print(paste("Number of sequences in result after n filtering:", nrow(result)))
 
diff -r f0e8dac22c6e -r 5e237c243088 sequence_overview.r
--- a/sequence_overview.r	Wed Jun 01 05:03:24 2016 -0400
+++ b/sequence_overview.r	Fri Jun 03 10:35:52 2016 -0400
@@ -22,11 +22,13 @@
 
 #dat = data.frame(data.table(dat)[, list(freq=.N), by=c("best_match", "seq_conc")])
 
-dat = data.frame(table(merged$seq_conc, merged$Functionality))
+dat = data.frame(table(merged$seq_conc))
+#dat = data.frame(table(merged$seq_conc, merged$Functionality))
 
 #dat = dat[dat$Freq > 1,]
 
-names(dat) = c("seq_conc", "Functionality", "Freq")
+#names(dat) = c("seq_conc", "Functionality", "Freq")
+names(dat) = c("seq_conc", "Freq")
 
 dat$seq_conc = factor(dat$seq_conc)
 
@@ -43,15 +45,16 @@
 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$seq_conc == dat[i,c("seq_conc")] & IDs$best_match == "ca1",]
-	ca2 = IDs[IDs$seq_conc == dat[i,c("seq_conc")] & IDs$best_match == "ca2",]
+	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),]
 	
-	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",]
+	cg1 = IDs[IDs$seq_conc == dat[i,c("seq_conc")] & grepl("^cg1", IDs$best_match),]
+	cg2 = IDs[IDs$seq_conc == dat[i,c("seq_conc")] & grepl("^cg2", IDs$best_match),]
+	cg3 = IDs[IDs$seq_conc == dat[i,c("seq_conc")] & grepl("^cg3", IDs$best_match),]
+	cg4 = IDs[IDs$seq_conc == dat[i,c("seq_conc")] & grepl("^cg4", IDs$best_match),]
 	
-	cm = IDs[IDs$seq_conc == dat[i,c("seq_conc")] & IDs$best_match == "cm",]
+	cm = IDs[IDs$seq_conc == dat[i,c("seq_conc")] & grepl("^cm", IDs$best_match),]
+	allc = rbind(ca1, ca2, cg1, cg2, cg3, cg4, cm)
 	
 	classes = c(nrow(ca1), nrow(ca2), nrow(cg1), nrow(cg2), nrow(cg3), nrow(cg4), nrow(cm))
 	
@@ -63,7 +66,7 @@
 	
 	id = as.numeric(dat[i,"seq_conc"])
 	
-	functionality = dat[i,"Functionality"]
+	functionality = paste(unique(allc[,"Functionality"], sep=","))
 
 	if(nrow(ca1) > 0){
 		cat(tbl(ca1), file=paste("ca1_", id, ".html", sep=""))
@@ -104,6 +107,7 @@
 	cm.html = make.link(id, "cm", nrow(cm))
 	
 	rw = c(as.character(dat[i,"seq_conc"]), as.character(functionality), ca1.html, ca2.html, cg1.html, cg2.html, cg3.html, cg4.html, cm.html)
+	#print(rw)
 
 	cat(tr(rw), file=main.html, append=T)
 }
@@ -132,7 +136,7 @@
 NTresult = data.frame(nt=c("A", "C", "T", "G"))
 
 for(clazz in gene.classes){
-	NToverview.sub = NToverview[grepl(clazz, paste("^", NToverview$best_match, sep="")),]
+	NToverview.sub = NToverview[grepl(paste("^", clazz, sep=""), NToverview$best_match),]
 	new.col.x = c(sum(NToverview.sub$A), sum(NToverview.sub$C), sum(NToverview.sub$T), sum(NToverview.sub$G))
 	new.col.y = sum(new.col.x)
 	new.col.z = round(new.col.x / new.col.y * 100, 2)
@@ -158,8 +162,7 @@
 
 write.table(hotspot.analysis.sum, hotspot.analysis.sum.file, quote=F, sep=",", row.names=F, col.names=F, na="0")
 
-
-write.table(NToverview, NToverview.file, quote=F, sep="\t", row.names=F, col.names=T)
+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)