--- a/wrapper.sh	Mon May 30 10:11:20 2016 -0400
+++ b/wrapper.sh	Tue May 31 08:30:50 2016 -0400
@@ -21,6 +21,8 @@
 
 echo "unpacking IMGT file"
 
+
+
 type="`file $input`"
 if [[ "$type" == *"Zip archive"* ]] ; then
 	echo "Zip archive"
@@ -41,8 +43,6 @@
 cat `find $PWD/files/ -name "8_*"` > $PWD/mutationstats.txt
 cat `find $PWD/files/ -name "10_*"` > $PWD/hotspots.txt
 
-
-
 #cat $PWD/files/*/1_* > $PWD/summary.txt
 #cat $PWD/files/*/3_* > $PWD/sequences.txt
 #cat $PWD/files/*/5_* > $PWD/aa.txt
@@ -56,22 +56,17 @@
 echo "${BLASTN_DIR}"
 
 echo "identification ($method)"
-echo "identification ($method)<br />" >> $output
-
-echo "blast or custom"
+echo "---------------- identification ($method) ----------------"
+echo "---------------- identification ($method) ----------------<br />" >> $output
 
 if [[ "${method}" == "custom" ]] ; then
-	echo "custom"
 	python $dir/gene_identification.py --input $PWD/summary.txt --output $outdir/identified_genes.txt
 else
-	echo "blast"
 	ID_index=$(cat $PWD/summary.txt | grep -o -P ".+Sequence ID" | grep -o -P "\t" | wc -l)
 	ID_index=$((ID_index+1))
 	sequence_index=$(cat $PWD/summary.txt | grep -o -P ".+\tSequence" | grep -o -P "\t" | wc -l)
 	sequence_index=$((sequence_index+1))
 	
-	echo "$ID_index ${sequence_index}"
-	
 	cat $PWD/summary.txt | tail -n+2 | cut -f ${ID_index},${sequence_index} | awk '{print ">" $1 "\n" $2}' > $PWD/sequences.fasta
 	
 	echo -e "qseqid\tsseqid\tpident\tlength\tmismatch\tgapopen\tqstart\tqend\tsstart\tsend\tevalue\tbitscore" > $outdir/identified_genes.txt
@@ -110,6 +105,7 @@
 mkdir $outdir/sequence_overview
 
 Rscript $dir/sequence_overview.r $outdir/identified_genes.txt $PWD/sequences.txt $outdir/merged.txt $outdir/sequence_overview $classes $outdir/hotspot_analysis_sum.txt 2>&1
+#Rscript $dir/sequence_overview.r $outdir/before_unique_filter.txt $outdir/sequence_overview $classes $outdir/hotspot_analysis_sum.txt 2>&1
 
 echo "<table border='1'>" > $outdir/base_overview.html
 
@@ -153,7 +149,7 @@
 	tmp=`cat $outdir/unmatched_${func}_n.txt`
 	echo "<th><a href='unmatched.txt'>unmatched (N = ${unmatched_count})</a></th>" >> $output
 	tmp=`cat $outdir/all_${func}_n.txt`
-	echo "<th><a href='matched_${func}_all.txt'>all (N = $tmp)</a></th>" >> $output
+	echo "<th><a href='matched_all_${func}.txt'>all (N = $tmp)</a></th>" >> $output
 
 	while IFS=, read name cax cay caz ca1x ca1y ca1z ca2x ca2y ca2z cgx cgy cgz cg1x cg1y cg1z cg2x cg2y cg2z cg3x cg3y cg3z cg4x cg4y cg4z cmx cmy cmz unx uny unz allx ally allz
 	do