diff report_clonality/r_wrapper.sh @ 35:d7580295e13b draft

Uploaded

--- a/report_clonality/r_wrapper.sh	Mon Jan 18 07:55:31 2016 -0500
+++ b/report_clonality/r_wrapper.sh	Fri Jan 22 08:45:29 2016 -0500
@@ -51,15 +51,31 @@
 
 mkdir $outputDir/circos
 cp $dir/circos/* $outputDir/circos/
-for sample in $samples; do
+sed -i "s%DATA_DIR%$outputDir/circos%" $outputDir/circos/circos.conf
+for sample in $samples; do #output the samples to a file and create the circos plots with the R script output
 	echo " $sample" >> $outputFile
 	
+	circos_file="$outputDir/${sample}_VJ_circos.txt"
+	echo -e -n "labels$(cat ${circos_file})" > ${circos_file}
+	cat "${circos_file}" | $CIRCOSTOOLS/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/tableviewer/bin/make-conf -dir $outputDir/circos/
+	/home/galaxy/Downloads/circos-master/bin/circos -conf $outputDir/circos/circos.conf 2>&1
+	mv $outputDir/circos/circos.png $outputDir/circosVJ_${sample}.png
+	
+	
+	if [[ "$useD" == "true" ]] ; then
 		circos_file="$outputDir/${sample}_VD_circos.txt"
 		echo -e -n "labels$(cat ${circos_file})" > ${circos_file}
-		#echo -n "labels" > $outputDir/tmp.txt
-		#cat ${circos_file} >> $outputDir/tmp.txt
-		#mv $outputDir/tmp.txt ${circos_file}
-		#cat "${circos_file}" | $CIRCOSTOOLS/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/tableviewer/bin/make-conf -dir $outputDir/circos/; /home/galaxy/Downloads/circos-master/bin/circos -param karyotype=$outputDir/circos/karyotype.txt -conf $dir/circos/circos.conf 2>&1
+		cat "${circos_file}" | $CIRCOSTOOLS/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/tableviewer/bin/make-conf -dir $outputDir/circos/
+		/home/galaxy/Downloads/circos-master/bin/circos -conf $outputDir/circos/circos.conf 2>&1
+		mv $outputDir/circos/circos.png $outputDir/circosVD_${sample}.png
+		
+		circos_file="$outputDir/${sample}_DJ_circos.txt"
+		echo -e -n "labels$(cat ${circos_file})" > ${circos_file}
+		cat "${circos_file}" | $CIRCOSTOOLS/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/tableviewer/bin/make-conf -dir $outputDir/circos/
+		/home/galaxy/Downloads/circos-master/bin/circos -conf $outputDir/circos/circos.conf 2>&1
+		mv $outputDir/circos/circos.png $outputDir/circosDJ_${sample}.png
+		
+	fi
 done
 echo "</title><script type='text/javascript' src='jquery-1.11.0.min.js'></script>" >> $outputFile
 echo "<script type='text/javascript' src='tabber.js'></script>" >> $outputFile
@@ -80,6 +96,8 @@
 echo "<img src='JPlot.png'/>" >> $outputFile
 echo "<img src='AAComposition.png'/></div>" >> $outputFile
 
+#Heatmaps
+
 count=1
 echo "<div class='tabbertab' title='Heatmaps'><div class='tabber'>" >> $outputFile
 for sample in $samples; do
@@ -96,6 +114,23 @@
 done
 echo "</div></div>" >> $outputFile
 
+#circos
+
+echo "<div class='tabbertab' title='Circos'><div class='tabber'>" >> $outputFile
+for sample in $samples; do
+	echo "<div class='tabbertab' title='$sample'><table border='1'><center>" >> $outputFile
+	if [[ "$useD" == "true" ]] ; then
+		echo "<tr><td>V-D</td><td><img src='circosVD_${sample}.png' width='700' height='700'/></td></tr>" >> $outputFile
+	fi
+	echo "<tr><td>V-J</td><td><img src='circosVJ_${sample}.png' width='700' height='700'/></td></tr>" >> $outputFile
+	if [[ "$useD" == "true" ]] ; then
+		echo "<tr><td>D-J</td><td><img src='circosDJ_${sample}.png' width='700' height='700'/></td></tr>" >> $outputFile
+	fi
+	echo "<center></table></div>" >> $outputFile
+	count=$((count+1))
+done
+echo "</div></div>" >> $outputFile
+
 #echo "<div class='tabbertab' title='Interactive'><svg class='chart'></svg><script src='http://d3js.org/d3.v3.min.js'></script></div>" >> $outputFile
 
 hasReplicateColumn="$(if head -n 1 $inputFile | grep -q 'Replicate'; then echo 'Yes'; else echo 'No'; fi)"