Mercurial > repos > davidvanzessen > clonal_sequences_in_paired_samples

diff wrapper.sh @ 7:68c6c7624ffc draft

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Uploaded
author davidvanzessen
date Thu, 18 Sep 2014 08:56:44 -0400
parents f11df36f43bb
children fa240d1c57a9
line wrap: on
line diff
--- 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