# HG changeset patch
# User davidvanzessen
# Date 1424781036 18000
# Node ID 0940835d259c06c0aecdcd2e26421d5cbd2c705f
# Parent  b662fdc7eff4d21c273c957b4b84dbbc9cb2faea
Uploaded

diff -r b662fdc7eff4 -r 0940835d259c wrapper.sh
--- a/wrapper.sh	Mon Feb 23 10:37:28 2015 -0500
+++ b/wrapper.sh	Tue Feb 24 07:30:36 2015 -0500
@@ -186,6 +186,7 @@
 	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>Number of sequences_$sample2</th><th>Number of sequences_$sample3</th><th>Number of sequences_${sample1}_${sample2}</th><th>Number of sequences_${sample1}_${sample3}</th><th>Number of sequences_${sample2}_${sample3}</th></thead>" >> "$html"
 	echo "<tbody>" >> "$html"
+	scatterplot_tab="<div class='tabbertab' title='Scatter Plots Frequency'>"
 	while read locus j_segment v_segment cut_off_value all one two three one_two one_three two_three 
 	do
 		if [ "$locus" != "$oldLocus" ] ; then
@@ -219,23 +220,26 @@
 		fi
 		
 		if [ "${one_two}" != "0" ] && [ "$cut_off_value" != "0" ] ; then
-			echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${sample2}_${locus}_${cut_off_value}.txt\", \"$patient\", \"freq\")'>${one_two}</td>" >> "$html"
+			echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${sample2}_${locus}_${cut_off_value}freq.txt\", \"$patient\", \"freq\")'>${one_two}</td>" >> "$html"
 		else
 			echo "<td>${one_two}</td>" >> "$html"
 		fi
 		if [ "${one_three}" != "0" ] && [ "$cut_off_value" != "0" ] ; then
-			echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${sample3}_${locus}_${cut_off_value}.txt\", \"$patient\", \"freq\")'>${one_three}</td>" >> "$html"
+			echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${sample3}_${locus}_${cut_off_value}freq.txt\", \"$patient\", \"freq\")'>${one_three}</td>" >> "$html"
 		else
 			echo "<td>${one_three}</td>" >> "$html"
 		fi
 		if [ "${two_three}" != "0" ] && [ "$cut_off_value" != "0" ] ; then
-			echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample2}_${sample3}_${locus}_${cut_off_value}.txt\", \"$patient\", \"freq\")'>${two_three}</td>" >> "$html"
+			echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample2}_${sample3}_${locus}_${cut_off_value}freq.txt\", \"$patient\", \"freq\")'>${two_three}</td>" >> "$html"
 		else
 			echo "<td>${two_three}</td>" >> "$html"
 		fi
 		
 		echo "</tr>" >> "$html"
-		oldLocus="$locus"	
+		oldLocus="$locus"
+		if [ "${cut_off_value}" == "0" ] ; then
+			scatterplot_tab="${scatterplot_tab}<img src='${sample1}_${sample2}_${sample3}_freq_${locus}_scatter.png' /><br />"
+		fi
 	done < tmp.txt
 	echo "</tbody></table>" >> "$html"
 	echo "</td><td style='vertical-align:top;'><div id='result_div_${patient}_freq'></div></td></tr></table>" >> "$html"
@@ -243,6 +247,7 @@
 	echo "<div class='tabbertab' title='Graphs frequency'>" >> "$html"
 	echo "<a href='${patient}_freq_total_all.png'><img src='${patient}_freq_total_all.png' width='1280' height='720' /></a><br />" >> "$html"
 	echo "<a href='${patient}_freq_indiv_all.png'><img src='${patient}_freq_indiv_all.png' width='1280' height='720' /></a><br /></div>" >> "$html"
+	echo "${scatterplot_tab}</div>" >> "$html"
 	
 	tail -n+2 ${patient}_reads.txt | sed "s/>//" > tmp.txt
 	echo "<div class='tabbertab' title='Data reads'>" >> "$html"
@@ -250,6 +255,7 @@
 	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>Number of sequences_$sample2</th><th>Number of sequences_$sample3</th><th>Number of sequences_${sample1}_${sample2}</th><th>Number of sequences_${sample1}_${sample3}</th><th>Number of sequences_${sample2}_${sample3}</th></thead>" >> "$html"
 	echo "<tbody>" >> "$html"
+	scatterplot_tab="<div class='tabbertab' title='Scatter Plots Reads'>"
 	while read locus j_segment v_segment cut_off_value all one two three one_two one_three two_three 
 	do
 		if [ "$locus" != "$oldLocus" ] ; then
@@ -283,23 +289,26 @@
 		fi
 		
 		if [ "${one_two}" != "0" ] && [ "$cut_off_value" != "0" ] ; then
-			echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${sample2}_${locus}_${cut_off_value}.txt\", \"$patient\", \"reads\")'>${one_two}</td>" >> "$html"
+			echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${sample2}_${locus}_${cut_off_value}reads.txt\", \"$patient\", \"reads\")'>${one_two}</td>" >> "$html"
 		else
 			echo "<td>${one_two}</td>" >> "$html"
 		fi
 		if [ "${one_three}" != "0" ] && [ "$cut_off_value" != "0" ] ; then
-			echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${sample3}_${locus}_${cut_off_value}.txt\", \"$patient\", \"reads\")'>${one_three}</td>" >> "$html"
+			echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${sample3}_${locus}_${cut_off_value}reads.txt\", \"$patient\", \"reads\")'>${one_three}</td>" >> "$html"
 		else
 			echo "<td>${one_three}</td>" >> "$html"
 		fi
 		if [ "${two_three}" != "0" ] && [ "$cut_off_value" != "0" ] ; then
-			echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample2}_${sample3}_${locus}_${cut_off_value}.txt\", \"$patient\", \"reads\")'>${two_three}</td>" >> "$html"
+			echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample2}_${sample3}_${locus}_${cut_off_value}reads.txt\", \"$patient\", \"reads\")'>${two_three}</td>" >> "$html"
 		else
 			echo "<td>${two_three}</td>" >> "$html"
 		fi
 		
 		echo "</tr>" >> "$html"
 		oldLocus="$locus"
+		if [ "${cut_off_value}" == "0" ] ; then
+			scatterplot_tab="${scatterplot_tab}<img src='${sample1}_${sample2}_${sample3}_reads_${locus}_scatter.png' /><br />"
+		fi
 	done < tmp.txt
 	echo "</tbody></table>" >> "$html"
 	echo "</td><td style='vertical-align:top;'><div id='result_div_${patient}_reads'></div></td></tr></table>" >> "$html"
@@ -307,6 +316,7 @@
 	echo "<div class='tabbertab' title='Graphs reads'>" >> "$html"
 	echo "<a href='${patient}_reads_total_all.png'><img src='${patient}_reads_total_all.png' width='1280' height='720' /></a><br />" >> "$html"
 	echo "<a href='${patient}_reads_indiv_all.png'><img src='${patient}_reads_indiv_all.png' width='1280' height='720' /></a><br /></div>" >> "$html"
+	echo "${scatterplot_tab}</div>" >> "$html"
 	echo "</div>" >> "$html"
 	echo "</div>" >> "$html"
 	echo "</html>" >> "$html"
@@ -319,3 +329,4 @@
 echo "</table>" >> "$html"
 echo "</html>" >> "$html"
 
+