--- a/wrapper.sh	Thu Nov 05 10:16:32 2015 -0500
+++ b/wrapper.sh	Mon Nov 09 07:21:09 2015 -0500
@@ -9,6 +9,7 @@
 include_fr1=$6
 functionality=$7
 unique=$8
+naive_output=$9
 mkdir $outdir
 
 type="`file $input`"
@@ -25,6 +26,7 @@
 
 cat $PWD/files/*/1_* > $PWD/summary.txt
 cat $PWD/files/*/3_* > $PWD/sequences.txt
+cat $PWD/files/*/5_* > $PWD/aa.txt
 cat $PWD/files/*/6_* > $PWD/junction.txt
 cat $PWD/files/*/7_* > $PWD/mutationanalysis.txt
 cat $PWD/files/*/8_* > $PWD/mutationstats.txt
@@ -134,5 +136,25 @@
 
 echo "</html>" >> $output
 
+
+#optional output for naive
+
+if [[ "$naive_output" != "None" ]]
+then
+	echo "naive_output: $naive_output"
+	python $dir/imgt_loader.py --summ $PWD/summary.txt --aa $PWD/aa.txt --junction $PWD/junction.txt --output $naive_output
+	Rscript $dir/naive_output.r $naive_output $outdir/merged.txt $naive_output 2>&1
+fi
+
+
+
+
+
+
+
+
+
+
+
 #rm $outdir/HS12RSS.txt
 #rm $outdir/HS23RSS.txt