--- a/wrapper.sh	Mon Aug 18 04:42:59 2014 -0400
+++ b/wrapper.sh	Wed Sep 10 10:33:29 2014 -0400
@@ -12,6 +12,8 @@
 cat $PWD/files/*/7_* > $PWD/mutationanalysis.txt
 cat $PWD/files/*/8_* > $PWD/mutationstats.txt
 cat $PWD/files/*/10_* > $PWD/hotspots.txt
+cp $dir/HS12RSS.txt $outdir/
+cp $dir/HS23RSS.txt $outdir/
 
 mkdir $outdir/identification/
 python $dir/gene_identification.py --input $PWD/summary.txt --outdir $outdir/identification/
@@ -25,6 +27,8 @@
 do
 	echo "Running $gene <br />" >> $output
 	mkdir $outdir/$gene
+	cp $dir/HS12RSS.txt $outdir/$gene/
+	cp $dir/HS23RSS.txt $outdir/$gene/
 	echo "Filtering input..." >> $output
 	Rscript $dir/filter.r $PWD/summary.txt $outdir/identification/${gene}.txt $outdir/$gene/summary.txt
 	Rscript $dir/filter.r $PWD/mutationanalysis.txt $outdir/identification/${gene}.txt $outdir/$gene/mutationanalysis.txt
@@ -45,6 +49,8 @@
 	cat $mutationtmp $hotspottmp > $tmp
 	paste $outdir/mutationandhotspot.txt -d, $tmp > $tmp2
 	cat $tmp2 > $outdir/mutationandhotspot.txt
+	rm $outdir/$gene/HS12RSS.txt
+	rm $outdir/$gene/HS23RSS.txt
 done
 
 Rscript --verbose $dir/mutation_analysis.r $PWD/mutationstats.txt $PWD/summary.txt $outdir/ 2>&1
@@ -98,10 +104,17 @@
 Rscript $dir/piechart.r "${ca1_n},${ca2_n}" "IgA1 - ${ca1_n},IgA2 - ${ca2_n}" "IgA (N = $ca_n)" $outdir/ca.png 2>&1
 Rscript $dir/piechart.r "${cg1_n},${cg2_n},${cg3_n},${cg4_n}" "IgG1 - ${cg1_n},IgG2 - ${cg2_n},IgG3 - ${cg3_n},IgG4 - ${cg4_n}" "IgG (N = $cg_n)" $outdir/cg.png 2>&1
 
+$dir/seqlogo -t "HS12RSS" -w 20 -h 5 -p -a -c -n -F PNG -f $outdir/weblogo_in_rs12.txt > $outdir/HS12.png 2>&1
+$dir/seqlogo -t "HS23RSS" -w 20 -h 5 -p -a -c -n -F PNG -f $outdir/weblogo_in_rs23.txt > $outdir/HS23.png 2>&1
+
+
 echo "<img src='all.png'/>" >> $output
 echo "<img src='ca.png'/>" >> $output
 echo "<img src='cg.png'/>" >> $output
 
+echo "<img src='HS12.png'/>" >> $output
+echo "<img src='HS23.png'/>" >> $output
+
 for gene in ${genes[@]}
 do
 	echo "<table border='1'><caption>$gene transition table</caption>" >> $output
@@ -120,3 +133,6 @@
 echo "</table>" >> $output
 
 echo "</html>" >> $output
+
+#rm $outdir/HS12RSS.txt
+#rm $outdir/HS23RSS.txt