# HG changeset patch
# User davidvanzessen
# Date 1411045004 14400
# Node ID 68c6c7624ffc66fa63a2a8ff4bdb5234c9f27350
# Parent  8313c6cc65c50e4b0566e620c9f26c09ed00b901
Uploaded

diff -r 8313c6cc65c5 -r 68c6c7624ffc RScript.r
--- a/RScript.r	Mon Sep 15 07:40:52 2014 -0400
+++ b/RScript.r	Thu Sep 18 08:56:44 2014 -0400
@@ -34,7 +34,6 @@
 cat("<tr><td>Removing duplicates</td></tr>", file=logfile, append=T)
 dat = dat[!duplicated(dat$paste),]
 patients = split(dat, dat$Patient, drop=T)
-rm(dat)
 intervalReads = rev(c(0,10,25,50,100,1000,10000))
 intervalFreq = rev(c(0,0.01,0.05,0.1,0.5,1,5))
 V_Segments = c(".*", "IGHV", "IGHD", "IGKV", "IGKV", "IgKINTR", "TRGV", "TRDV", "TRDD" , "TRBV")
@@ -91,8 +90,6 @@
   read2Count = vector()
   locussum1 = vector()
   locussum2 = vector()
-  
-  print(patient)
   #for(iter in 1){
   for(iter in 1:length(product[,1])){
     threshhold = product[iter,threshholdIndex]
@@ -184,11 +181,6 @@
 interval = intervalFreq
 intervalOrder = data.frame("interval"=paste(">", interval, sep=""), "intervalOrder"=1:length(interval))
 product = data.frame("Titles"=rep(Titles, each=length(interval)), "interval"=rep(interval, times=10), "V_Segments"=rep(V_Segments, each=length(interval)), "J_Segments"=rep(J_Segments, each=length(interval)))
-#patientFrequencyCount(patient1)
-#lapply(patients[c(5,6,10)], FUN=patientFrequencyCount)
-#lapply(patients[c(5,6,7,8,13)], FUN=patientCountOnColumn, product = product, interval=interval, on="Frequency", appendtxt=T)
-#lapply(patients[c(6,7,8)], FUN=patientCountOnColumn, product = product, interval=interval, on="Frequency", appendtxt=T)
-#lapply(patients[c(6)], FUN=patientCountOnColumn, product = product, interval=interval, on="Frequency", appendtxt=T)
 mclapply(patients, FUN=patientCountOnColumn, product = product, interval=interval, on="Frequency", appendtxt=T)
 
 cat("<tr><td>Starting Cell Count analysis</td></tr>", file=logfile, append=T)
@@ -196,11 +188,166 @@
 interval = intervalReads
 intervalOrder = data.frame("interval"=paste(">", interval, sep=""), "intervalOrder"=1:length(interval))
 product = data.frame("Titles"=rep(Titles, each=length(interval)), "interval"=rep(interval, times=10), "V_Segments"=rep(V_Segments, each=length(interval)), "J_Segments"=rep(J_Segments, each=length(interval)))
-#patientResult = patientReadCount(patient1)
-#lapply(patients[c(5,6,10)], FUN=patientReadCount)
-#lapply(patients[c(5,6,7,8,13)], FUN=patientCountOnColumn, product = product, interval=interval, on="Clone_Molecule_Count_From_Spikes")
-#lapply(patients[c(6)], FUN=patientCountOnColumn, product = product, interval=interval, on="Clone_Molecule_Count_From_Spikes")
 mclapply(patients, FUN=patientCountOnColumn, product = product, interval=interval, on="Clone_Molecule_Count_From_Spikes")
 
 cat("</table></html>", file=logfile, append=T)
 
+
+tripletAnalysis <- function(patient1, label1, patient2, label2, patient3, label3, product, interval, on, appendTriplets= FALSE){
+  onShort = "reads"
+  if(on == "Frequency"){
+    onShort = "freq"
+  }
+  type="triplet"
+  
+  threshholdIndex = which(colnames(product) == "interval")
+  V_SegmentIndex = which(colnames(product) == "V_Segments")
+  J_SegmentIndex = which(colnames(product) == "J_Segments")
+  titleIndex = which(colnames(product) == "Titles")
+  sampleIndex = which(colnames(patient1) == "Sample")
+  patientIndex = which(colnames(patient1) == "Patient")
+  oneSample = paste(patient1[1,sampleIndex], sep="")
+  twoSample = paste(patient2[1,sampleIndex], sep="")
+  threeSample = paste(patient3[1,sampleIndex], sep="")
+  
+  patientMerge = merge(patient1, patient2, by="Clone_Sequence")
+  patientMerge = merge(patientMerge, patient3, by="Clone_Sequence")
+  colnames(patientMerge)[32:length(colnames(patientMerge))] = paste(colnames(patientMerge)[32:length(colnames(patientMerge))], ".z", sep="")
+  res1 = vector()
+  res2 = vector()
+  res3 = vector()
+  resAll = vector()
+  read1Count = vector()
+  read2Count = vector()
+  read3Count = vector()
+  
+  if(appendTriplets){
+		cat(paste(label1, label2, label3, sep="\t"), file="triplets.txt", append=T, sep="", fill=3)
+  }
+  for(iter in 1:length(product[,1])){
+    threshhold = product[iter,threshholdIndex]
+    V_Segment = paste(".*", as.character(product[iter,V_SegmentIndex]), ".*", sep="")
+    J_Segment = paste(".*", as.character(product[iter,J_SegmentIndex]), ".*", sep="")
+    all = (grepl(V_Segment, patientMerge$V_Segment_Major_Gene.x) & grepl(J_Segment, patientMerge$J_Segment_Major_Gene.x) & patientMerge[,paste(on, ".x", sep="")] > threshhold & patientMerge[,paste(on, ".y", sep="")] > threshhold & patientMerge[,paste(on, ".z", sep="")] > threshhold)
+    one = (grepl(V_Segment, patient1$V_Segment_Major_Gene) & grepl(J_Segment, patient1$J_Segment_Major_Gene) & patient1[,on] > threshhold & !(patient1$Clone_Sequence %in% patientMerge[all,]$Clone_Sequence))
+    two = (grepl(V_Segment, patient2$V_Segment_Major_Gene) & grepl(J_Segment, patient2$J_Segment_Major_Gene) & patient2[,on] > threshhold & !(patient2$Clone_Sequence %in% patientMerge[all,]$Clone_Sequence))
+    three = (grepl(V_Segment, patient3$V_Segment_Major_Gene) & grepl(J_Segment, patient3$J_Segment_Major_Gene) & patient3[,on] > threshhold & !(patient3$Clone_Sequence %in% patientMerge[all,]$Clone_Sequence))
+    
+    read1Count = append(read1Count, sum(patient1[one,]$normalized_read_count) + sum(patientMerge[all,]$normalized_read_count.x))
+    read2Count = append(read2Count, sum(patient2[two,]$normalized_read_count) + sum(patientMerge[all,]$normalized_read_count.y))
+    read3Count = append(read3Count, sum(patient3[three,]$normalized_read_count) + sum(patientMerge[all,]$normalized_read_count.z))
+    res1 = append(res1, sum(one))
+    res2 = append(res2, sum(two))
+    res3 = append(res3, sum(three))
+    resAll = append(resAll, sum(all))
+    #threshhold = 0
+    if(threshhold != 0){
+      if(sum(one) > 0){
+        dfOne = patient1[one,c("V_Segment_Major_Gene", "J_Segment_Major_Gene", "normalized_read_count", "Frequency", "Clone_Sequence", "Related_to_leukemia_clone")]
+        colnames(dfOne) = c("Proximal segment", "Distal segment", "normalized_read_count", "Frequency", "Sequence", "Related_to_leukemia_clone")
+        filenameOne = paste(label1, "_", product[iter, titleIndex], "_", threshhold, sep="")
+        write.table(dfOne, file=paste(filenameOne, ".txt", sep=""), quote=F, sep="\t", dec=",", row.names=F, col.names=T)
+      }
+      if(sum(two) > 0){
+        dfTwo = patient2[two,c("V_Segment_Major_Gene", "J_Segment_Major_Gene", "normalized_read_count", "Frequency", "Clone_Sequence", "Related_to_leukemia_clone")]
+        colnames(dfTwo) = c("Proximal segment", "Distal segment", "normalized_read_count", "Frequency", "Sequence", "Related_to_leukemia_clone")
+        filenameTwo = paste(label2, "_", product[iter, titleIndex], "_", threshhold, sep="")
+        write.table(dfTwo, file=paste(filenameTwo, ".txt", sep=""), quote=F, sep="\t", dec=",", row.names=F, col.names=T)
+      }
+      if(sum(three) > 0){
+        dfThree = patient3[three,c("V_Segment_Major_Gene", "J_Segment_Major_Gene", "normalized_read_count", "Frequency", "Clone_Sequence", "Related_to_leukemia_clone")]
+        colnames(dfThree) = c("Proximal segment", "Distal segment", "normalized_read_count", "Frequency", "Sequence", "Related_to_leukemia_clone")
+        filenameThree = paste(label3, "_", product[iter, titleIndex], "_", threshhold, sep="")
+        write.table(dfThree, file=paste(filenameThree, ".txt", sep=""), quote=F, sep="\t", dec=",", row.names=F, col.names=T)
+      }
+    }
+    if(sum(all) > 0){
+      dfAll = patientMerge[all,c("V_Segment_Major_Gene.x", "J_Segment_Major_Gene.x", "normalized_read_count.x", "Frequency.x", "Related_to_leukemia_clone.x", "Clone_Sequence", "V_Segment_Major_Gene.y", "J_Segment_Major_Gene.y", "normalized_read_count.y", "Frequency.y", "Related_to_leukemia_clone.y", "V_Segment_Major_Gene.z", "J_Segment_Major_Gene.z", "normalized_read_count.z", "Frequency.z", "Related_to_leukemia_clone.z")]
+      colnames(dfAll) = c(paste("Proximal segment", oneSample), paste("Distal segment", oneSample), paste("Normalized_Read_Count", oneSample), paste("Frequency", oneSample), paste("Related_to_leukemia_clone", oneSample),"Sequence", paste("Proximal segment", twoSample), paste("Distal segment", twoSample), paste("Normalized_Read_Count", twoSample), paste("Frequency", twoSample), paste("Related_to_leukemia_clone", twoSample), paste("Proximal segment", threeSample), paste("Distal segment", threeSample), paste("Normalized_Read_Count", threeSample), paste("Frequency", threeSample), paste("Related_to_leukemia_clone", threeSample))
+      filenameAll = paste(label1, "_", label2, "_", label3, "_", product[iter, titleIndex], "_", threshhold, sep="")
+      write.table(dfAll, file=paste(filenameAll, ".txt", sep=""), quote=F, sep="\t", dec=",", row.names=F, col.names=T)
+    }
+  }
+  patientResult = data.frame("Locus"=product$Titles, "J_Segment"=product$J_Segments, "V_Segment"=product$V_Segments, "cut_off_value"=paste(">", product$interval, sep=""), "All"=resAll, "tmp1"=res1, "read_count1" = round(read1Count), "tmp2"=res2, "read_count2"= round(read2Count), "tmp3"=res3, "read_count3"=round(read3Count))
+  colnames(patientResult)[6] = oneSample
+  colnames(patientResult)[8] = twoSample
+  colnames(patientResult)[10] = threeSample
+  
+  colnamesBak = colnames(patientResult)
+  colnames(patientResult) = c("Ig/TCR gene rearrangement type", "Distal Gene segment", "Proximal gene segment", "cut_off_value", "Number of sequences All", paste("Number of sequences", oneSample), paste("Normalized Read Count", oneSample), paste("Number of sequences", twoSample), paste("Normalized Read Count", twoSample), paste("Number of sequences", threeSample), paste("Normalized Read Count", threeSample))
+  write.table(patientResult, file=paste(label1, "_", label2, "_", label3, "_", onShort, ".txt", sep=""), quote=F, sep="\t", dec=",", row.names=F, col.names=T)
+  colnames(patientResult) = colnamesBak
+  
+  patientResult$Locus = factor(patientResult$Locus, Titles)
+  patientResult$cut_off_value = factor(patientResult$cut_off_value, paste(">", interval, sep=""))
+  
+  plt = ggplot(patientResult[,c("Locus", "cut_off_value", "All")])
+  plt = plt + geom_bar( aes( x=factor(cut_off_value), y=All), stat='identity', position="dodge", fill="#79c36a")
+  plt = plt + facet_grid(.~Locus) + theme(axis.text.x = element_text(angle = 45, hjust = 1))
+  plt = plt + geom_text(aes(ymax=max(All), x=cut_off_value,y=All,label=All), angle=90, hjust=0)
+  plt = plt + xlab("Reads per locus") + ylab("Count") + ggtitle("Number of clones in All")
+  plt = plt + theme(plot.margin = unit(c(1,8.8,0.5,1.5), "lines"))
+  png(paste(label1, "_", label2, "_", label3, "_", onShort, "_total_all.png", sep=""), width=1920, height=1080)
+  print(plt)
+  dev.off()
+  
+  fontSize = 4
+  
+  bak = patientResult
+  patientResult = melt(patientResult[,c('Locus','cut_off_value', oneSample, twoSample, threeSample)] ,id.vars=1:2)
+  patientResult$relativeValue = patientResult$value * 10
+  patientResult[patientResult$relativeValue == 0,]$relativeValue = 1
+  plt = ggplot(patientResult)
+  plt = plt + geom_bar( aes( x=factor(cut_off_value), y=relativeValue, fill=variable), stat='identity', position="dodge")
+  plt = plt + facet_grid(.~Locus) + theme(axis.text.x = element_text(angle = 45, hjust = 1))
+  plt = plt + scale_y_continuous(trans="log", breaks=10^c(0:10), labels=c(0, 10^c(0:9)))
+  plt = plt + geom_text(data=patientResult[patientResult$variable == oneSample,], aes(ymax=max(value), x=cut_off_value,y=relativeValue,label=value), angle=90, position=position_dodge(width=0.9), hjust=0, vjust=-0.7, size=fontSize)
+  plt = plt + geom_text(data=patientResult[patientResult$variable == twoSample,], aes(ymax=max(value), x=cut_off_value,y=relativeValue,label=value), angle=90, position=position_dodge(width=0.9), hjust=0, vjust=0.4, size=fontSize)
+  plt = plt + geom_text(data=patientResult[patientResult$variable == threeSample,], aes(ymax=max(value), x=cut_off_value,y=relativeValue,label=value), angle=90, position=position_dodge(width=0.9), hjust=0, vjust=1.5, size=fontSize)
+  plt = plt + xlab("Reads per locus") + ylab("Count") + ggtitle("Number of clones in only one sample")
+  png(paste(label1, "_", label2, "_", label3, "_", onShort, "_indiv_all.png", sep=""), width=1920, height=1080)
+  print(plt)
+  dev.off()
+}
+
+interval = intervalReads
+intervalOrder = data.frame("interval"=paste(">", interval, sep=""), "intervalOrder"=1:length(interval))
+product = data.frame("Titles"=rep(Titles, each=length(interval)), "interval"=rep(interval, times=10), "V_Segments"=rep(V_Segments, each=length(interval)), "J_Segments"=rep(J_Segments, each=length(interval)))
+
+one = dat[dat$Patient == "VanDongen_cALL_14696.1",]
+two = dat[dat$Patient == "VanDongen_cALL_14696.2",]
+three = dat[dat$Patient == "VanDongen_cALL_14696.3",]
+tripletAnalysis(one, "14696_1", two, "14696_2", three, "14696_3", product=product, interval=interval, on="normalized_read_count")
+
+one = dat[dat$Sample == "16278_Left",]
+two = dat[dat$Sample == "26402_Left",]
+three = dat[dat$Sample == "26759_Left",]
+tripletAnalysis(one, "16278_Left", two, "26402_Left", three, "26759_Left", product=product, interval=interval, on="normalized_read_count")
+
+one = dat[dat$Sample == "16278_Right",]
+two = dat[dat$Sample == "26402_Right",]
+three = dat[dat$Sample == "26759_Right",]
+tripletAnalysis(one, "16278_Right", two, "26402_Right", three, "26759_Right", product=product, interval=interval, on="normalized_read_count")
+
+
+interval = intervalFreq
+intervalOrder = data.frame("interval"=paste(">", interval, sep=""), "intervalOrder"=1:length(interval))
+product = data.frame("Titles"=rep(Titles, each=length(interval)), "interval"=rep(interval, times=10), "V_Segments"=rep(V_Segments, each=length(interval)), "J_Segments"=rep(J_Segments, each=length(interval)))
+
+one = dat[dat$Patient == "VanDongen_cALL_14696.1",]
+two = dat[dat$Patient == "VanDongen_cALL_14696.2",]
+three = dat[dat$Patient == "VanDongen_cALL_14696.3",]
+tripletAnalysis(one, "14696_1", two, "14696_2", three, "14696_3", product=product, interval=interval, on="Frequency", T)
+
+one = dat[dat$Sample == "16278_Left",]
+two = dat[dat$Sample == "26402_Left",]
+three = dat[dat$Sample == "26759_Left",]
+tripletAnalysis(one, "16278_Left", two, "26402_Left", three, "26759_Left", product=product, interval=interval, on="Frequency", T)
+
+one = dat[dat$Sample == "16278_Right",]
+two = dat[dat$Sample == "26402_Right",]
+three = dat[dat$Sample == "26759_Right",]
+tripletAnalysis(one, "16278_Right", two, "26402_Right", three, "26759_Right", product=product, interval=interval, on="Frequency", T)
+
+
+
diff -r 8313c6cc65c5 -r 68c6c7624ffc wrapper.sh
--- a/wrapper.sh	Mon Sep 15 07:40:52 2014 -0400
+++ b/wrapper.sh	Thu Sep 18 08:56:44 2014 -0400
@@ -9,7 +9,6 @@
 dir="$(cd "$(dirname "$0")" && pwd)"
 mkdir $outputDir
 
-echo "testtestsetset" > $outputFile
 
 Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputFile $min_freq $min_cells 2>&1
 cp $dir/jquery-1.11.0.min.js $outputDir
@@ -143,7 +142,6 @@
 	echo "</div>" >> $html
 	echo "</html>" >> $html
 done < patients.txt
-rm tmp.txt
 
 html="index.html"
 echo "<html>" > $html
@@ -170,6 +168,126 @@
 done
 echo "<tr><td><b>Triplets:</b></td></tr>" >> $html
 
+while read sample1 sample2 sample3
+do
+	sample1="$(echo ${sample1} | tr -d '\r' | tr -d '\n')"
+	sample2="$(echo ${sample2} | tr -d '\r' | tr -d '\n')"
+	sample3="$(echo ${sample3} | tr -d '\r' | tr -d '\n')"
+	patient="${sample1}_${sample2}_${sample3}"
+	echo "$patient"
+	html="${patient}.html"
+	echo "<tr><td><a href='${patient}.html'>$patient</a></td></tr>" >> "index.html"
+	echo "$header" > $html
+	oldLocus=""
+	tail -n+2 ${patient}_freq.txt | sed "s/>//" > tmp.txt
+	echo "<div class='tabber'>" >> $html
+	echo "<div class='tabbertab' title='Data frequency'>" >> $html
+	echo "<table><tr><td style='vertical-align:top;'>" >> $html
+	echo "<table border = 1 class='result_table summary_table' id='summary_table_${patient}_freq'>" >> $html
+	echo "<thead><th>Ig/TCR gene rearrangement type</th><th>Proximal gene segment</th><th>Distal gene segment</th><th>Cut off value</th><th>Number of sequences ${patient}_All</th><th>Number of sequences_$sample1</th><th>Read Count $sample1</th><th>Number of sequences_$sample2</th><th>Read Count $sample2</th><th>Number of sequences_$sample3</th><th>Read Count $sample3</th></thead>" >> $html
+	echo "<tbody>" >> $html
+	while read locus j_segment v_segment cut_off_value all one read_count1 two read_count2 three read_count3
+	do
+		if [ "$locus" != "$oldLocus" ] ; then
+			echo "<tr><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr>" >> $html
+			echo "<tr><td><b>$locus</b></td>" >> $html
+		else
+			echo "<td></td>" >> $html
+		fi
+		echo "<td>$v_segment</td>" >> $html
+		echo "<td>$j_segment</td>" >> $html
+		echo "<td>>$cut_off_value</td>" >> $html 
+		if [ "$all" != "0" ] ; then
+			echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${sample2}_${sample3}_${locus}_${cut_off_value}.txt\", \"$patient\", \"freq\")'>$all</td>" >> $html
+		else
+			echo "<td>$all</td>" >> $html
+		fi
+		if [ "$one" != "0" ] && [ "$cut_off_value" != "0" ] ; then
+			echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${locus}_${cut_off_value}.txt\", \"$patient\", \"freq\")'>$one</td>" >> $html
+		else
+			echo "<td>$one</td>" >> $html
+		fi
+		echo "<td>$read_count1</td>" >> $html
+		if [ "$two" != "0" ] && [ "$cut_off_value" != "0" ] ; then
+			echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample2}_${locus}_${cut_off_value}.txt\", \"$patient\", \"freq\")'>$two</td>" >> $html
+		else
+			echo "<td>$two</td>" >> $html
+		fi
+		echo "<td>$read_count2</td>" >> $html
+		if [ "$three" != "0" ] && [ "$cut_off_value" != "0" ] ; then
+			echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample3}_${locus}_${cut_off_value}.txt\", \"$patient\", \"freq\")'>$three</td>" >> $html
+		else
+			echo "<td>$three</td>" >> $html
+		fi
+		echo "<td>$read_count3</td>" >> $html
+		echo "</tr>" >> $html
+		oldLocus="$locus"	
+	done < tmp.txt
+	echo "</tbody></table>" >> $html
+	echo "</td><td style='vertical-align:top;'><div id='result_div_${patient}_freq'></div></td></tr></table>" >> $html
+	echo "</div>" >> $html
+	echo "<div class='tabbertab' title='Graphs frequency'>" >> $html
+	echo "<a href='${patient}_reads_total_all.png'><img src='${patient}_reads.png' width='1280' height='720' /></a><br />" >> $html
+	echo "<a href='${patient}_reads_indiv_all.png'><img src='${patient}_reads_all.png' width='1280' height='720' /></a><br />" >> $html
+	
+	tail -n+2 ${patient}_reads.txt | sed "s/>//" > tmp.txt
+	echo "<div class='tabbertab' title='Data reads'>" >> $html
+	echo "<table><tr><td style='vertical-align:top;'>" >> $html
+	echo "<table border = 1 class='result_table summary_table' id='summary_table_${patient}_reads'>" >> $html
+	echo "<thead><th>Ig/TCR gene rearrangement type</th><th>Proximal gene segment</th><th>Distal gene segment</th><th>Cut off value</th><th>Number of sequences ${patient}_All</th><th>Number of sequences_$sample1</th><th>Read Count $sample1</th><th>Number of sequences_$sample2</th><th>Read Count $sample2</th><th>Number of sequences_$sample3</th><th>Read Count $sample3</th></thead>" >> $html
+	echo "<tbody>" >> $html
+	while read locus j_segment v_segment cut_off_value all one read_count1 two read_count2 three read_count3 
+	do
+		if [ "$locus" != "$oldLocus" ] ; then
+			echo "<tr><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr>" >> $html
+			echo "<tr><td><b>$locus</b></td>" >> $html
+		else
+			echo "<td></td>" >> $html
+		fi
+		echo "<td>$v_segment</td>" >> $html
+		echo "<td>$j_segment</td>" >> $html
+		echo "<td>>$cut_off_value</td>" >> $html 
+		if [ "$all" != "0" ] ; then
+			echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${sample2}_${sample3}_${locus}_${cut_off_value}.txt\", \"$patient\", \"reads\")'>$all</td>" >> $html
+		else
+			echo "<td>$all</td>" >> $html
+		fi
+		if [ "$one" != "0" ] && [ "$cut_off_value" != "0" ] ; then
+			echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${locus}_${cut_off_value}.txt\", \"$patient\", \"reads\")'>$one</td>" >> $html
+		else
+			echo "<td>$one</td>" >> $html
+		fi
+		echo "<td>$read_count1</td>" >> $html
+		if [ "$two" != "0" ] && [ "$cut_off_value" != "0" ] ; then
+			echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample2}_${locus}_${cut_off_value}.txt\", \"$patient\", \"reads\")'>$two</td>" >> $html
+		else
+			echo "<td>$two</td>" >> $html
+		fi
+		echo "<td>$read_count2</td>" >> $html
+		if [ "$three" != "0" ] && [ "$cut_off_value" != "0" ] ; then
+			echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample3}_${locus}_${cut_off_value}.txt\", \"$patient\", \"reads\")'>$three</td>" >> $html
+		else
+			echo "<td>$three</td>" >> $html
+		fi
+		echo "<td>$read_count3</td>" >> $html
+		echo "</tr>" >> $html
+		oldLocus="$locus"
+	done < tmp.txt
+	echo "</tbody></table>" >> $html
+	echo "</td><td style='vertical-align:top;'><div id='result_div_${patient}_reads'></div></td></tr></table>" >> $html
+	echo "</div>" >> $html
+	echo "<div class='tabbertab' title='Graphs reads'>" >> $html
+	echo "<a href='${patient}_reads_total_all.png'><img src='${patient}_reads.png' width='1280' height='720' /></a><br />" >> $html
+	echo "<a href='${patient}_reads_indiv_all.png'><img src='${patient}_reads_all.png' width='1280' height='720' /></a><br />" >> $html
+	echo "</div>" >> $html
+	echo "</div>" >> $html
+	echo "</html>" >> $html
+done < triplets.txt
+rm tmp.txt
+
+
+html="index.html"
+
 echo "</table>" >> $html
 echo "</html>" >> $html