#!/bin/bash
#set -e
dir="$(cd "$(dirname "$0")" && pwd)"
input=$1
method=$2
log=$3 #becomes the main html page at the end
outdir=$4
output="$outdir/index.html" #copied to $log location at the end
title="$5"
include_fr1=$6
functionality=$7
unique=$8
naive_output=$9
naive_output_ca=${10}
naive_output_cg=${11}
naive_output_cm=${12}
naive_output_ce=${13}
naive_output_all=${14}
filter_unique=${15}
class_filter=${16}
empty_region_filter=${17}
fast=${18}
mkdir $outdir

tar -xzf $dir/style.tar.gz -C $outdir

echo "---------------- read parameters ----------------"
echo "---------------- read parameters ----------------<br />" > $log

echo "unpacking IMGT file"

type="`file $input`"
if [[ "$type" == *"Zip archive"* ]] ; then
	echo "Zip archive"
	echo "unzip $input -d $PWD/files/"
	unzip $input -d $PWD/files/
elif [[ "$type" == *"XZ compressed data"* ]] ; then
	echo "ZX archive"
	echo "tar -xJf $input -C $PWD/files/"
	mkdir -p "$PWD/files/$title"
	tar -xJf $input -C "$PWD/files/$title"
fi

cat "`find $PWD/files/ -name "1_*"`" > $PWD/summary.txt
cat "`find $PWD/files/ -name "3_*"`" > $PWD/sequences.txt
cat "`find $PWD/files/ -name "5_*"`" > $PWD/aa.txt
cat "`find $PWD/files/ -name "6_*"`" > $PWD/junction.txt
cat "`find $PWD/files/ -name "7_*"`" > $PWD/mutationanalysis.txt
cat "`find $PWD/files/ -name "8_*"`" > $PWD/mutationstats.txt
cat "`find $PWD/files/ -name "10_*"`" > $PWD/hotspots.txt

if [[ ${#BLASTN_DIR} -ge 5 ]] ; then
	echo "On server, using BLASTN_DIR env: ${BLASTN_DIR}"
else
	BLASTN_DIR="/home/galaxy/Downloads/ncbi-blast-2.4.0+/bin"
	echo "Dev Galaxy set BLASTN_DIR to: ${BLASTN_DIR}"
fi

echo "---------------- class identification ----------------"
echo "---------------- class identification ----------------<br />" >> $log

python $dir/gene_identification.py --input $PWD/summary.txt --output $outdir/identified_genes.txt

echo "---------------- merge_and_filter.r ----------------"
echo "---------------- merge_and_filter.r ----------------<br />" >> $log

Rscript $dir/merge_and_filter.r $PWD/summary.txt $PWD/sequences.txt $PWD/mutationanalysis.txt $PWD/mutationstats.txt $PWD/hotspots.txt $PWD/aa.txt $outdir/identified_genes.txt $outdir/merged.txt $outdir/before_unique_filter.txt $outdir/unmatched.txt $method $functionality $unique ${filter_unique} ${class_filter} ${empty_region_filter} 2>&1

if [[ "$fast" == "no" ]] ; then

	echo "---------------- creating new IMGT zips ----------------"
	echo "---------------- creating new IMGT zips ----------------<br />" >> $log

	mkdir $outdir/new_IMGT

	cat `find $PWD/files/ -name "1_*"` > "$outdir/new_IMGT/1_Summary.txt"
	cat `find $PWD/files/ -name "2_*"` > "$outdir/new_IMGT/2_IMGT-gapped-nt-sequences.txt"
	cat `find $PWD/files/ -name "3_*"` > "$outdir/new_IMGT/3_Nt-sequences.txt"
	cat `find $PWD/files/ -name "4_*"` > "$outdir/new_IMGT/4_IMGT-gapped-AA-sequences.txt"
	cat `find $PWD/files/ -name "5_*"` > "$outdir/new_IMGT/5_AA-sequences.txt"
	cat `find $PWD/files/ -name "6_*"` > "$outdir/new_IMGT/6_Junction.txt"
	cat `find $PWD/files/ -name "7_*"` > "$outdir/new_IMGT/7_V-REGION-mutation-and-AA-change-table.txt"
	cat `find $PWD/files/ -name "8_*"` > "$outdir/new_IMGT/8_V-REGION-nt-mutation-statistics.txt"
	cat `find $PWD/files/ -name "9_*"` > "$outdir/new_IMGT/9_V-REGION-AA-change-statistics.txt"
	cat `find $PWD/files/ -name "10_*"` > "$outdir/new_IMGT/10_V-REGION-mutation-hotspots.txt"

	mkdir $outdir/new_IMGT_IGA
	cp $outdir/new_IMGT/* $outdir/new_IMGT_IGA

	mkdir $outdir/new_IMGT_IGA1
	cp $outdir/new_IMGT/* $outdir/new_IMGT_IGA1

	mkdir $outdir/new_IMGT_IGA2
	cp $outdir/new_IMGT/* $outdir/new_IMGT_IGA2

	mkdir $outdir/new_IMGT_IGG
	cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG

	mkdir $outdir/new_IMGT_IGG1
	cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG1

	mkdir $outdir/new_IMGT_IGG2
	cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG2

	mkdir $outdir/new_IMGT_IGG3
	cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG3

	mkdir $outdir/new_IMGT_IGG4
	cp $outdir/new_IMGT/* $outdir/new_IMGT_IGG4

	mkdir $outdir/new_IMGT_IGM
	cp $outdir/new_IMGT/* $outdir/new_IMGT_IGM

	mkdir $outdir/new_IMGT_IGE
	cp $outdir/new_IMGT/* $outdir/new_IMGT_IGE

	Rscript $dir/new_imgt.r $outdir/new_IMGT/ $outdir/merged.txt "-" 2>&1

	Rscript $dir/new_imgt.r $outdir/new_IMGT_IGA/ $outdir/merged.txt "IGA" 2>&1
	Rscript $dir/new_imgt.r $outdir/new_IMGT_IGA1/ $outdir/merged.txt "IGA1" 2>&1
	Rscript $dir/new_imgt.r $outdir/new_IMGT_IGA2/ $outdir/merged.txt "IGA2" 2>&1

	Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG/ $outdir/merged.txt "IGG" 2>&1
	Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG1/ $outdir/merged.txt "IGG1" 2>&1
	Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG2/ $outdir/merged.txt "IGG2" 2>&1
	Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG3/ $outdir/merged.txt "IGG3" 2>&1
	Rscript $dir/new_imgt.r $outdir/new_IMGT_IGG4/ $outdir/merged.txt "IGG4" 2>&1

	Rscript $dir/new_imgt.r $outdir/new_IMGT_IGM/ $outdir/merged.txt "IGM" 2>&1

	Rscript $dir/new_imgt.r $outdir/new_IMGT_IGE/ $outdir/merged.txt "IGE" 2>&1


	tmp="$PWD"
	cd $outdir/new_IMGT/ #tar weirdness...
	tar -cJf ../new_IMGT.txz *

	cd $outdir/new_IMGT_IGA/
	tar -cJf ../new_IMGT_IGA.txz *

	cd $outdir/new_IMGT_IGA1/
	tar -cJf ../new_IMGT_IGA1.txz *

	cd $outdir/new_IMGT_IGA2/
	tar -cJf ../new_IMGT_IGA2.txz *

	cd $outdir/new_IMGT_IGG/
	tar -cJf ../new_IMGT_IGG.txz *

	cd $outdir/new_IMGT_IGG1/
	tar -cJf ../new_IMGT_IGG1.txz *

	cd $outdir/new_IMGT_IGG2/
	tar -cJf ../new_IMGT_IGG2.txz *

	cd $outdir/new_IMGT_IGG3/
	tar -cJf ../new_IMGT_IGG3.txz *

	cd $outdir/new_IMGT_IGG4/
	tar -cJf ../new_IMGT_IGG4.txz *

	cd $outdir/new_IMGT_IGM/
	tar -cJf ../new_IMGT_IGM.txz *

	cd $outdir/new_IMGT_IGE/
	tar -cJf ../new_IMGT_IGE.txz *

	cd $tmp
fi

echo "---------------- shm_csr.r ----------------"
echo "---------------- shm_csr.r ----------------<br />" >> $log

classes="IGA,IGA1,IGA2,IGG,IGG1,IGG2,IGG3,IGG4,IGM,IGE,unmatched"
echo "R mutation analysis"
Rscript $dir/shm_csr.r $outdir/merged.txt $classes $outdir ${empty_region_filter} 2>&1

echo "---------------- shm_csr.py ----------------"
echo "---------------- shm_csr.py ----------------<br />" >> $log

python $dir/shm_csr.py --input $outdir/merged.txt --genes $classes --empty_region_filter "${empty_region_filter}" --output $outdir/hotspot_analysis.txt

echo "---------------- aa_histogram.r ----------------"
echo "---------------- aa_histogram.r ----------------<br />" >> $log

Rscript $dir/aa_histogram.r $outdir/aa_id_mutations.txt $outdir/absent_aa_id.txt "IGA,IGG,IGM,IGE" $outdir/ 2>&1
if [ -e "$outdir/aa_histogram_.png" ]; then
        mv $outdir/aa_histogram_.png $outdir/aa_histogram.png
        mv $outdir/aa_histogram_.txt $outdir/aa_histogram.txt
        mv $outdir/aa_histogram_absent_.txt $outdir/aa_histogram_absent.txt
        mv $outdir/aa_histogram_count_.txt $outdir/aa_histogram_count.txt
        mv $outdir/aa_histogram_sum_.txt $outdir/aa_histogram_sum.txt
fi

genes=(IGA IGA1 IGA2 IGG IGG1 IGG2 IGG3 IGG4 IGM IGE)

funcs=(sum mean median)
funcs=(sum)

echo "---------------- sequence_overview.r ----------------"
echo "---------------- sequence_overview.r ----------------<br />" >> $log

mkdir $outdir/sequence_overview

Rscript $dir/sequence_overview.r $outdir/before_unique_filter.txt $outdir/merged.txt $outdir/sequence_overview $classes $outdir/hotspot_analysis_sum.txt ${empty_region_filter} 2>&1

echo "<table border='1'>" > $outdir/base_overview.html

while IFS=$'\t' read ID class seq A C G T
do
	echo "<tr><td>$ID</td><td>$seq</td><td>$class</td><td>$A</td><td>$C</td><td>$G</td><td>$T</td></tr>" >> $outdir/base_overview.html
done < $outdir/sequence_overview/ntoverview.txt

echo "<html><center><h1>$title</h1></center>" > $output
echo "<meta name='viewport' content='width=device-width, initial-scale=1'>" >> $output
echo "<script type='text/javascript' src='jquery-1.11.0.min.js'></script>" >> $output
echo "<script type='text/javascript' src='tabber.js'></script>" >> $output
echo "<script type='text/javascript' src='script.js'></script>" >> $output
echo "<link rel='stylesheet' type='text/css' href='style.css'>" >> $output
echo "<link rel='stylesheet' type='text/css' href='pure-min.css'>" >> $output

matched_count="`cat $outdir/merged.txt | grep -v 'unmatched' | tail -n +2 | wc -l`"
unmatched_count="`cat $outdir/unmatched.txt | tail -n +2 | wc -l`"
total_count=$((matched_count + unmatched_count))
perc_count=$((unmatched_count / total_count * 100))
perc_count=`bc -l <<< "scale=2; ${unmatched_count} / ${total_count} * 100"`
perc_count=`bc -l <<< "scale=2; (${unmatched_count} / ${total_count} * 100 ) / 1"`

echo "<center><h2>Total: ${total_count}</h2></center>" >> $output
echo "<center><h2>Matched: ${matched_count} Unmatched: ${unmatched_count}</h2></center>" >> $output
echo "<center><h2>Percentage unmatched: ${perc_count}</h2></center>" >> $output

echo "---------------- main tables ----------------"
echo "---------------- main tables ----------------<br />" >> $log

echo "<div class='tabber'>" >> $output
echo "<div class='tabbertab' title='SHM Overview' style='width: 3000px;'>" >> $output

for func in ${funcs[@]}
do
	
	echo "---------------- $func table ----------------"
	echo "---------------- $func table ----------------<br />" >> $log
	
	cat $outdir/mutations_${func}.txt $outdir/hotspot_analysis_${func}.txt > $outdir/data_${func}.txt
	
	echo "---------------- pattern_plots.r ----------------"
	echo "---------------- pattern_plots.r ----------------<br />" >> $log

	Rscript $dir/pattern_plots.r $outdir/data_${func}.txt $outdir/plot1 $outdir/plot2 $outdir/plot3 $outdir/shm_overview.txt 2>&1
	
	echo "<table class='pure-table pure-table-striped'>" >> $output
	echo "<thead><tr><th>info</th>" >> $output
	
	if [ "${class_filter}" != "101_101" ] ; then
	
		for gene in ${genes[@]}
		do
			tmp=`cat $outdir/${gene}_${func}_n.txt`
			echo "<th><a href='matched_${gene}_${func}.txt'>${gene} (N = $tmp)</a></th>" >> $output
		done
		
		tmp=`cat $outdir/all_${func}_n.txt`
		echo "<th><a href='matched_all_${func}.txt'>all (N = $tmp)</a></th>" >> $output
		tmp=`cat $outdir/unmatched_${func}_n.txt`
		echo "<th><a href='unmatched.txt'>unmatched (N = ${unmatched_count})</a></th><tr></thead>" >> $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 cex cey cez unx uny unz allx ally allz 
		do
			if [ "$name" == "FR R/S (ratio)" ] || [ "$name" == "CDR R/S (ratio)" ] ; then #meh
				echo "<tr><td>$name</td><td>${cax}/${cay} (${caz})</td><td>${ca1x}/${ca1y} (${ca1z})</td><td>${ca2x}/${ca2y} (${ca2z})</td><td>${cgx}/${cgy} (${cgz})</td><td>${cg1x}/${cg1y} (${cg1z})</td><td>${cg2x}/${cg2y} (${cg2z})</td><td>${cg3x}/${cg3y} (${cg3z})</td><td>${cg4x}/${cg4y} (${cg4z})</td><td>${cmx}/${cmy} (${cmz})</td><td>${cex}/${cey} (${cez})</td><td>${allx}/${ally} (${allz})</td><td>${unx}/${uny} (${unz})</td></tr>" >> $output
			elif [ "$name" == "Median of Number of Mutations (%)" ] ; then
				echo "<tr><td>$name</td><td>${caz}%</td><td>${ca1z}%</td><td>${ca2z}%</td><td>${cgz}%</td><td>${cg1z}%</td><td>${cg2z}%</td><td>${cg3z}%</td><td>${cg4z}%</td><td>${cmz}%</td><td>${cez}%</td><td>${allz}%</td><td>${unz}%</td></tr>" >> $output
			else
				echo "<tr><td>$name</td><td>${cax}/${cay} (${caz}%)</td><td>${ca1x}/${ca1y} (${ca1z}%)</td><td>${ca2x}/${ca2y} (${ca2z}%)</td><td>${cgx}/${cgy} (${cgz}%)</td><td>${cg1x}/${cg1y} (${cg1z}%)</td><td>${cg2x}/${cg2y} (${cg2z}%)</td><td>${cg3x}/${cg3y} (${cg3z}%)</td><td>${cg4x}/${cg4y} (${cg4z}%)</td><td>${cmx}/${cmy} (${cmz}%)</td><td>${cex}/${cey} (${cez}%)</td><td>${allx}/${ally} (${allz}%)</td><td>${unx}/${uny} (${unz}%)</td></tr>" >> $output
			fi
		done < $outdir/data_${func}.txt
		
	else
		tmp=`cat $outdir/all_${func}_n.txt`
		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 cex cey cez unx uny unz allx ally allz
		do
			if [ "$name" == "FR R/S (ratio)" ] || [ "$name" == "CDR R/S (ratio)" ] ; then #meh
				echo "<tr><td>$name</td><td>${allx}/${ally}</td></tr>" >> $output
			elif [ "$name" == "Median of Number of Mutations (%)" ] ; then
				echo "<tr><td>$name</td><td>${allz}%</td></tr>" >> $output
			else
				echo "<tr><td>$name</td><td>${allx}/${ally} (${allz}%)</td></tr>" >> $output
			fi
		done < $outdir/data_${func}.txt
		
	fi
	echo "</table>" >> $output
	#echo "<a href='data_${func}.txt'>Download data</a>" >> $output
done

echo "<img src='plot1.png' /><br />" >> $output
echo "<img src='plot2.png' /><br />" >> $output
echo "<img src='plot3.png' /><br />" >> $output

echo "</div>" >> $output #SHM overview tab end

echo "---------------- images ----------------"
echo "---------------- images ----------------<br />" >> $log

echo "<div class='tabbertab' title='SHM Frequency' style='width: 3000px;'>" >> $output

if [ -a $outdir/scatter.png ]
then
	echo "<img src='scatter.png'/><br />" >> $output
fi
if [ -a $outdir/frequency_ranges.png ]
then
	echo "<img src='frequency_ranges.png'/><br />" >> $output
fi

echo "</div>" >> $output #SHM frequency tab end

echo "<div class='tabbertab' title='Transition tables' style='width: 3000px;'>" >> $output

echo "<table border='0'>" >> $output

for gene in ${genes[@]}
do
	echo "<tr>" >> $output
	echo "<td><h1>${gene}</h1></td>" >> $output
	
	if [ -e $outdir/transitions_heatmap_${gene}.png ]
	then
		echo "<td><img src='transitions_heatmap_${gene}.png' /></td>" >> $output
	else
		echo "<td></td>" >> $output
	fi
	
	if [ -e $outdir/transitions_stacked_${gene}.png ]
	then
		echo "<td><img src='transitions_stacked_${gene}.png' /></td>" >> $output
	else
		echo "<td></td>" >> $output
	fi
	
	echo "<td><table style='border-left-width: 1;' class='pure-table transition-table pure-table-bordered'>" >> $output
	echo "<tr><td></td><td colspan="5"><center>To</center></td></tr>" >> $output
	first="true"
	while IFS=, read from a c g t
		do
			if [ "$first" == "true" ] ; then
				echo "<tr><td rowspan='5'>From</td><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
				first="false"
			else
				echo "<tr><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
			fi
	done < $outdir/transitions_${gene}_sum.txt
	echo "</table></td>" >> $output
	
	echo "</tr>" >> $output
done

echo "<tr>" >> $output
echo "<td><h1>All</h1></td>" >> $output
echo "<td><img src='transitions_heatmap_all.png' /></td>" >> $output
echo "<td><img src='transitions_stacked_all.png' /></td>" >> $output
echo "<td><table style='border-left-width: 1;' class='pure-table transition-table pure-table-bordered'>" >> $output
echo "<tr><td></td><td colspan="5"><center>To</center></td></tr>" >> $output
first="true"
while IFS=, read from a c g t
	do
		if [ "$first" == "true" ] ; then
			echo "<tr><td rowspan='5'>From</td><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
			first="false"
		else
			echo "<tr><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
		fi
done < $outdir/transitions_all_sum.txt
echo "</table></td>" >> $output

echo "</tr>" >> $output

echo "</table>" >> $output

echo "</div>" >> $output #transition tables tab end

echo "<div class='tabbertab' title='Antigen Selection'>" >> $output

if [ -e $outdir/aa_histogram.png ]
then
	echo "<img src='aa_histogram.png'/><br />" >> $output
fi

if [ -e $outdir/aa_histogram_IGA.png ]
then
	echo "<img src='aa_histogram_IGA.png'/><br />" >> $output
fi

if [ -e $outdir/aa_histogram_IGG.png ]
then
	echo "<img src='aa_histogram_IGG.png'/><br />" >> $output
fi

if [ -e $outdir/aa_histogram_IGM.png ]
then
	echo "<img src='aa_histogram_IGM.png'/><br />" >> $output
fi

if [ -e $outdir/aa_histogram_IGE.png ]
then
	echo "<img src='aa_histogram_IGE.png'/><br />" >> $output
fi



if [[ "$fast" == "no" ]] ; then

	echo "---------------- baseline ----------------"
	echo "---------------- baseline ----------------<br />" >> $log
	tmp="$PWD"

	mkdir $outdir/baseline


	mkdir $outdir/baseline/IGA_IGG_IGM
	if [[ $(wc -l < $outdir/new_IMGT/1_Summary.txt) -gt "1" ]]; then
		cd $outdir/baseline/IGA_IGG_IGM
		bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT.txz "IGA_IGG_IGM" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline.pdf" "Sequence.ID" "$outdir/baseline.txt"	
	else
		echo "No sequences" > "$outdir/baseline.txt"
	fi

	mkdir $outdir/baseline/IGA
	if [[ $(wc -l < $outdir/new_IMGT_IGA/1_Summary.txt) -gt "1" ]]; then
		cd $outdir/baseline/IGA
		bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_IGA.txz "IGA" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGA.pdf" "Sequence.ID" "$outdir/baseline_IGA.txt"
	else
		echo "No IGA sequences" > "$outdir/baseline_IGA.txt"
	fi

	mkdir $outdir/baseline/IGG
	if [[ $(wc -l < $outdir/new_IMGT_IGG/1_Summary.txt) -gt "1" ]]; then
		cd $outdir/baseline/IGG
		bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_IGG.txz "IGG" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGG.pdf" "Sequence.ID" "$outdir/baseline_IGG.txt"
	else
		echo "No IGG sequences" > "$outdir/baseline_IGG.txt"
	fi

	mkdir $outdir/baseline/IGM
	if [[ $(wc -l < $outdir/new_IMGT_IGM/1_Summary.txt) -gt "1" ]]; then
		cd $outdir/baseline/IGM
		bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_IGM.txz "IGM" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGM.pdf" "Sequence.ID" "$outdir/baseline_IGM.txt"
	else
		echo "No IGM sequences" > "$outdir/baseline_IGM.txt"
	fi

	mkdir $outdir/baseline/IGE
	if [[ $(wc -l < $outdir/new_IMGT_IGE/1_Summary.txt) -gt "1" ]]; then
		cd $outdir/baseline/IGE
		bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_IGE.txz "IGE" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGE.pdf" "Sequence.ID" "$outdir/baseline_IGE.txt"
	else
		echo "No IGE sequences" > "$outdir/baseline_IGE.txt"
	fi

	cd $tmp

	echo "Cleaning up *.RData files"
	find $outdir/baseline -name "*.RData" -type f -delete
	
	if [ -e $outdir/baseline.pdf ]
	then
		echo "<embed src='baseline.pdf' width='700px' height='1000px'>" >> $output
	fi

	if [ -e $outdir/baseline_IGA.pdf ]
	then
		echo "<embed src='baseline_IGA.pdf' width='700px' height='1000px'>" >> $output
	fi

	if [ -e $outdir/baseline_IGG.pdf ]
	then
		echo "<embed src='baseline_IGG.pdf' width='700px' height='1000px'>" >> $output
	fi

	if [ -e $outdir/baseline_IGM.pdf ]
	then
		echo "<embed src='baseline_IGM.pdf' width='700px' height='1000px'>" >> $output
	fi

	if [ -e $outdir/baseline_IGE.pdf ]
	then
		echo "<embed src='baseline_IGE.pdf' width='700px' height='1000px'>" >> $output
	fi
fi

echo "</div>" >> $output #antigen selection tab end

echo "<div class='tabbertab' title='CSR'>" >> $output #CSR tab

if [ -e $outdir/IGA.png ] 
then
	echo "<img src='IGA.png'/><br />" >> $output
fi
if [ -e $outdir/IGG.png ]
then
	echo "<img src='IGG.png'/><br />" >> $output
fi

echo "</div>" >> $output #CSR tab end

if [[ "$fast" == "no" ]] ; then

	echo "---------------- change-o MakeDB ----------------"

	mkdir $outdir/change_o

	tmp="$PWD"

	cd $outdir/change_o

	bash $dir/change_o/makedb.sh $outdir/new_IMGT.txz false false false $outdir/change_o/change-o-db.txt
	bash $dir/change_o/define_clones.sh bygroup $outdir/change_o/change-o-db.txt gene first ham none min complete 3.0 $outdir/change_o/change-o-db-defined_clones.txt $outdir/change_o/change-o-defined_clones-summary.txt

	Rscript $dir/merge.r $outdir/change_o/change-o-db-defined_clones.txt $outdir/merged.txt "all" "Sequence.ID,best_match" "SEQUENCE_ID" "Sequence.ID" $outdir/change_o/change-o-db-defined_clones.txt 2>&1

	echo "Rscript $dir/merge.r $outdir/change_o/change-o-db-defined_clones.txt $outdir/$outdir/merged.txt 'all' 'Sequence.ID,best_match' 'Sequence.ID' 'Sequence.ID' '\t' $outdir/change_o/change-o-db-defined_clones.txt 2>&1"

	if [[ $(wc -l < $outdir/new_IMGT_IGA/1_Summary.txt) -gt "1" ]]; then
		bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGA.txz false false false $outdir/change_o/change-o-db-IGA.txt
		bash $dir/change_o/define_clones.sh bygroup $outdir/change_o/change-o-db-IGA.txt gene first ham none min complete 3.0 $outdir/change_o/change-o-db-defined_clones-IGA.txt $outdir/change_o/change-o-defined_clones-summary-IGA.txt
	else
		echo "No IGA sequences" > "$outdir/change_o/change-o-db-defined_clones-IGA.txt"
		echo "No IGA sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGA.txt"
	fi

	if [[ $(wc -l < $outdir/new_IMGT_IGG/1_Summary.txt) -gt "1" ]]; then
		bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGG.txz false false false $outdir/change_o/change-o-db-IGG.txt
		bash $dir/change_o/define_clones.sh bygroup $outdir/change_o/change-o-db-IGG.txt gene first ham none min complete 3.0 $outdir/change_o/change-o-db-defined_clones-IGG.txt $outdir/change_o/change-o-defined_clones-summary-IGG.txt
	else
		echo "No IGG sequences" > "$outdir/change_o/change-o-db-defined_clones-IGG.txt"
		echo "No IGG sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGG.txt"
	fi

	if [[ $(wc -l < $outdir/new_IMGT_IGM/1_Summary.txt) -gt "1" ]]; then
		bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGM.txz false false false $outdir/change_o/change-o-db-IGM.txt
		bash $dir/change_o/define_clones.sh bygroup $outdir/change_o/change-o-db-IGM.txt gene first ham none min complete 3.0 $outdir/change_o/change-o-db-defined_clones-IGM.txt $outdir/change_o/change-o-defined_clones-summary-IGM.txt
	else
		echo "No IGM sequences" > "$outdir/change_o/change-o-db-defined_clones-IGM.txt"
		echo "No IGM sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGM.txt"
	fi

	if [[ $(wc -l < $outdir/new_IMGT_IGE/1_Summary.txt) -gt "1" ]]; then
		bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGE.txz false false false $outdir/change_o/change-o-db-IGE.txt
		bash $dir/change_o/define_clones.sh bygroup $outdir/change_o/change-o-db-IGE.txt gene first ham none min complete 3.0 $outdir/change_o/change-o-db-defined_clones-IGE.txt $outdir/change_o/change-o-defined_clones-summary-IGE.txt
	else
		echo "No IGE sequences" > "$outdir/change_o/change-o-db-defined_clones-IGE.txt"
		echo "No IGE sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGE.txt"
	fi

	PWD="$tmp"

	echo "<div class='tabbertab' title='Clonality'>" >> $output #clonality tab

	function clonality_table {
		local infile=$1
		local outfile=$2
		
		echo "<table class='pure-table pure-table-striped'>" >> $outfile
		echo "<thead><tr><th>Clone size</th><th>Nr of clones</th><th>Nr of sequences</th></tr></thead>" >> $outfile
		
		first='true'
		
		while read size clones seqs
		do
			if [[ "$first" == "true" ]]; then
				first="false"
				continue
			fi
			echo "<tr><td>$size</td><td>$clones</td><td>$seqs</td></tr>" >> $outfile
		done < $infile
		
		echo "</table>" >> $outfile
	}
	echo "<div class='tabber'>" >> $output

	echo "<div class='tabbertab' title='All'>" >> $output
	clonality_table $outdir/change_o/change-o-defined_clones-summary.txt $output
	echo "</div>" >> $output

	echo "<div class='tabbertab' title='IGA'>" >> $output
	clonality_table $outdir/change_o/change-o-defined_clones-summary-IGA.txt $output
	echo "</div>" >> $output

	echo "<div class='tabbertab' title='IGG'>" >> $output
	clonality_table $outdir/change_o/change-o-defined_clones-summary-IGG.txt $output
	echo "</div>" >> $output

	echo "<div class='tabbertab' title='IGM'>" >> $output
	clonality_table $outdir/change_o/change-o-defined_clones-summary-IGM.txt $output
	echo "</div>" >> $output

	echo "<div class='tabbertab' title='IGE'>" >> $output
	clonality_table $outdir/change_o/change-o-defined_clones-summary-IGM.txt $output
	echo "</div>" >> $output

	echo "<div class='tabbertab' title='Overlap'>" >> $output
	cat "$outdir/sequence_overview/index.html" | sed "s%href='\(.*\).html%href='sequence_overview/\1.html%g" >> $output # rewrite href to 'sequence_overview/..."
	echo "</div>" >> $output


	echo "</div>" >> $output #clonality tabber end

	echo "</div>" >> $output #clonality tab end

fi

echo "<div class='tabbertab' title='Downloads'>" >> $output

echo "<table class='pure-table pure-table-striped'>" >> $output
echo "<thead><tr><th>info</th><th>link</th></tr></thead>" >> $output
echo "<tr><td>The complete dataset</td><td><a href='merged.txt' download='merged.txt' >Download</a></td></tr>" >> $output
echo "<tr><td>The filtered dataset</td><td><a href='filtered.txt' download='filtered.txt' >Download</a></td></tr>" >> $output
echo "<tr><td>The alignment info on the unmatched sequences</td><td><a href='unmatched.txt' download='unmatched.txt' >Download</a></td></tr>" >> $output

echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>SHM Overview</td></tr>" >> $output
echo "<tr><td>The SHM Overview table as a dataset</td><td><a href='shm_overview.txt' download='shm_overview.txt' >Download</a></td></tr>" >> $output
echo "<tr><td>Motif data per sequence ID</td><td><a href='motif_per_seq.txt' download='motif_per_seq.txt' >Download</a></td></tr>" >> $output
echo "<tr><td>Mutation data per sequence ID</td><td><a href='mutation_by_id.txt' download='mutation_by_id.txt' >Download</a></td></tr>" >> $output
echo "<tr><td>Base count for every sequence</td><td><a href='base_overview.html'>View</a></td></tr>" >> $output
echo "<tr><td>The data used to generate the RGYW/WRCY and TW/WA plot</td><td><a href='plot1.txt' download='plot1.txt' >Download</a></td></tr>" >> $output
echo "<tr><td>The data used to generate the relative transition and transversion plot</td><td><a href='plot2.txt' download='plot2.txt' >Download</a></td></tr>" >> $output
echo "<tr><td>The data used to generate the absolute transition and transversion plot</td><td><a href='plot3.txt' download='plot3.txt' >Download</a></td></tr>" >> $output

echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>SHM Frequency</td></tr>" >> $output
echo "<tr><td>The data  generate the frequency scatter plot</td><td><a href='scatter.txt' download='scatter.txt' >Download</a></td></tr>" >> $output
echo "<tr><td>The data used to generate the frequency by class plot</td><td><a href='frequency_ranges_classes.txt' download='frequency_ranges_classes.txt' >Download</a></td></tr>" >> $output
echo "<tr><td>The data for frequency by subclass</td><td><a href='frequency_ranges_subclasses.txt' download='frequency_ranges_subclasses.txt' >Download</a></td></tr>" >> $output

echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Transition Tables</td></tr>" >> $output
echo "<tr><td>The data for the 'all' transition plot</td><td><a href='transitions_all_sum.txt' download='transitions_all_sum.txt' >Download</a></td></tr>" >> $output
echo "<tr><td>The data for the 'IGA' transition plot</td><td><a href='transitions_IGA_sum.txt' download='transitions_all_sum.txt' >Download</a></td></tr>" >> $output
echo "<tr><td>The data for the 'IGA1' transition plot</td><td><a href='transitions_IGA1_sum.txt' download='transitions_IGA1_sum.txt' >Download</a></td></tr>" >> $output
echo "<tr><td>The data for the 'IGA2' transition plot</td><td><a href='transitions_IGA2_sum.txt' download='transitions_IGA2_sum.txt' >Download</a></td></tr>" >> $output
echo "<tr><td>The data for the 'IGG' transition plot</td><td><a href='transitions_IGG_sum.txt' download='transitions_IGG_sum.txt' >Download</a></td></tr>" >> $output
echo "<tr><td>The data for the 'IGG1' transition plot</td><td><a href='transitions_IGG1_sum.txt' download='transitions_IGG1_sum.txt' >Download</a></td></tr>" >> $output
echo "<tr><td>The data for the 'IGG2' transition plot</td><td><a href='transitions_IGG2_sum.txt' download='transitions_IGG2_sum.txt' >Download</a></td></tr>" >> $output
echo "<tr><td>The data for the 'IGG3' transition plot</td><td><a href='transitions_IGG3_sum.txt' download='transitions_IGG3_sum.txt' >Download</a></td></tr>" >> $output
echo "<tr><td>The data for the 'IGG4' transition plot</td><td><a href='transitions_IGG4_sum.txt' download='transitions_IGG4_sum.txt' >Download</a></td></tr>" >> $output
echo "<tr><td>The data for the 'IGM' transition plot</td><td><a href='transitions_IGM_sum.txt' download='transitions_IGM_sum.txt' >Download</a></td></tr>" >> $output
echo "<tr><td>The data for the 'IGE' transition plot</td><td><a href='transitions_IGE_sum.txt' download='transitions_IGE_sum.txt' >Download</a></td></tr>" >> $output

echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Antigen Selection</td></tr>" >> $output
echo "<tr><td>AA mutation data per sequence ID</td><td><a href='aa_id_mutations.txt' download='aa_id_mutations.txt' >Download</a></td></tr>" >> $output
echo "<tr><td>Absent AA location data per sequence ID</td><td><a href='absent_aa_id.txt' download='absent_aa_id.txt' >Download</a></td></tr>" >> $output

echo "<tr><td>The data used to generate the aa mutation frequency plot</td><td><a href='aa_histogram_sum.txt' download='aa_histogram_sum.txt' >Download</a></td></tr>" >> $output
echo "<tr><td>The data used to generate the aa mutation frequency plot for IGA</td><td><a href='aa_histogram_sum_IGA.txt' download='aa_histogram_sum_IGA.txt' >Download</a></td></tr>" >> $output
echo "<tr><td>The data used to generate the aa mutation frequency plot for IGG</td><td><a href='aa_histogram_sum_IGG.txt' download='aa_histogram_sum_IGG.txt' >Download</a></td></tr>" >> $output
echo "<tr><td>The data used to generate the aa mutation frequency plot for IGM</td><td><a href='aa_histogram_sum_IGM.txt' download='aa_histogram_sum_IGM.txt' >Download</a></td></tr>" >> $output
echo "<tr><td>The data used to generate the aa mutation frequency plot for IGE</td><td><a href='aa_histogram_sum_IGE.txt' download='aa_histogram_sum_IGE.txt' >Download</a></td></tr>" >> $output

echo "<tr><td>Baseline PDF (<a href='http://selection.med.yale.edu/baseline/'>http://selection.med.yale.edu/baseline/</a>)</td><td><a href='baseline.pdf' download='baseline.pdf' >Download</a></td></tr>" >> $output
echo "<tr><td>Baseline data</td><td><a href='baseline.txt' download='baseline.txt' >Download</a></td></tr>" >> $output
echo "<tr><td>Baseline IGA PDF</td><td><a href='baseline_IGA.pdf' download='baseline_IGA.pdf' >Download</a></td></tr>" >> $output
echo "<tr><td>Baseline IGA data</td><td><a href='baseline_IGA.txt' download='baseline_IGA.txt' >Download</a></td></tr>" >> $output
echo "<tr><td>Baseline IGG PDF</td><td><a href='baseline_IGG.pdf' download='baseline_IGG.pdf' >Download</a></td></tr>" >> $output
echo "<tr><td>Baseline IGG data</td><td><a href='baseline_IGG.txt' download='baseline_IGG.txt' >Download</a></td></tr>" >> $output
echo "<tr><td>Baseline IGM PDF</td><td><a href='baseline_IGM.pdf' download='baseline_IGM.pdf' >Download</a></td></tr>" >> $output
echo "<tr><td>Baseline IGM data</td><td><a href='baseline_IGM.txt' download='baseline_IGM.txt' >Download</a></td></tr>" >> $output
echo "<tr><td>Baseline IGE PDF</td><td><a href='baseline_IGE.pdf' download='baseline_IGE.pdf' >Download</a></td></tr>" >> $output
echo "<tr><td>Baseline IGE data</td><td><a href='baseline_IGE.txt' download='baseline_IGE.txt' >Download</a></td></tr>" >> $output

echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>CSR</td></tr>" >> $output
echo "<tr><td>The data for the CSR IGA pie plot</td><td><a href='IGA_pie.txt' download='IGA_pie.txt' >Download</a></td></tr>" >> $output
echo "<tr><td>The data for the CSR IGG pie plot</td><td><a href='IGG_pie.txt' download='IGG_pie.txt' >Download</a></td></tr>" >> $output

echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Clonality</td></tr>" >> $output
echo "<tr><td>Sequence overlap between subclasses</td><td><a href='sequence_overview/index.html'>View</a></td></tr>" >> $output
echo "<tr><td>The Change-O DB file with defined clones and subclass annotation</td><td><a href='change_o/change-o-db-defined_clones.txt' download='change_o/change-o-db-defined_clones.txt' >Download</a></td></tr>" >> $output
echo "<tr><td>The Change-O DB defined clones summary file</td><td><a href='change_o/change-o-defined_clones-summary.txt' download='change_o/change-o-defined_clones-summary.txt' >Download</a></td></tr>" >> $output
echo "<tr><td>The Change-O DB file with defined clones of IGA</td><td><a href='change_o/change-o-db-defined_clones-IGA.txt' download='change_o/change-o-db-defined_clones-IGA.txt' >Download</a></td></tr>" >> $output
echo "<tr><td>The Change-O DB defined clones summary file of IGA</td><td><a href='change_o/change-o-defined_clones-summary-IGA.txt' download='change_o/change-o-defined_clones-summary-IGA.txt' >Download</a></td></tr>" >> $output
echo "<tr><td>The Change-O DB file with defined clones of IGG</td><td><a href='change_o/change-o-db-defined_clones-IGG.txt' download='change_o/change-o-db-defined_clones-IGG.txt' >Download</a></td></tr>" >> $output
echo "<tr><td>The Change-O DB defined clones summary file of IGG</td><td><a href='change_o/change-o-defined_clones-summary-IGG.txt' download='change_o/change-o-defined_clones-summary-IGG.txt' >Download</a></td></tr>" >> $output
echo "<tr><td>The Change-O DB file with defined clones of IGM</td><td><a href='change_o/change-o-db-defined_clones-IGM.txt' download='change_o/change-o-db-defined_clones-IGM.txt' >Download</a></td></tr>" >> $output
echo "<tr><td>The Change-O DB defined clones summary file of IGM</td><td><a href='change_o/change-o-defined_clones-summary-IGM.txt' download='change_o/change-o-defined_clones-summary-IGM.txt' >Download</a></td></tr>" >> $output
echo "<tr><td>The Change-O DB file with defined clones of IGE</td><td><a href='change_o/change-o-db-defined_clones-IGE.txt' download='change_o/change-o-db-defined_clones-IGE.txt' >Download</a></td></tr>" >> $output
echo "<tr><td>The Change-O DB defined clones summary file of IGE</td><td><a href='change_o/change-o-defined_clones-summary-IGE.txt' download='change_o/change-o-defined_clones-summary-IGE.txt' >Download</a></td></tr>" >> $output

echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Filtered IMGT output files</td></tr>" >> $output
echo "<tr><td>An IMGT archive with just the matched and filtered sequences</td><td><a href='new_IMGT.txz' download='new_IMGT.txz' >Download</a></td></tr>" >> $output
echo "<tr><td>An IMGT archive with just the matched and filtered IGA sequences</td><td><a href='new_IMGT_IGA.txz' download='new_IMGT_IGA.txz' >Download</a></td></tr>" >> $output
echo "<tr><td>An IMGT archive with just the matched and filtered IGA1 sequences</td><td><a href='new_IMGT_IGA1.txz' download='new_IMGT_IGA1.txz' >Download</a></td></tr>" >> $output
echo "<tr><td>An IMGT archive with just the matched and filtered IGA2 sequences</td><td><a href='new_IMGT_IGA2.txz' download='new_IMGT_IGA2.txz' >Download</a></td></tr>" >> $output
echo "<tr><td>An IMGT archive with just the matched and filtered IGG sequences</td><td><a href='new_IMGT_IGG.txz' download='new_IMGT_IGG.txz' >Download</a></td></tr>" >> $output
echo "<tr><td>An IMGT archive with just the matched and filtered IGG1 sequences</td><td><a href='new_IMGT_IGG1.txz' download='new_IMGT_IGG1.txz' >Download</a></td></tr>" >> $output
echo "<tr><td>An IMGT archive with just the matched and filtered IGG2 sequences</td><td><a href='new_IMGT_IGG2.txz' download='new_IMGT_IGG2.txz' >Download</a></td></tr>" >> $output
echo "<tr><td>An IMGT archive with just the matched and filtered IGG3 sequences</td><td><a href='new_IMGT_IGG3.txz' download='new_IMGT_IGG3.txz' >Download</a></td></tr>" >> $output
echo "<tr><td>An IMGT archive with just the matched and filtered IGG4 sequences</td><td><a href='new_IMGT_IGG4.txz' download='new_IMGT_IGG4.txz' >Download</a></td></tr>" >> $output
echo "<tr><td>An IMGT archive with just the matched and filtered IGM sequences</td><td><a href='new_IMGT_IGM.txz' download='new_IMGT_IGM.txz' >Download</a></td></tr>" >> $output
echo "<tr><td>An IMGT archive with just the matched and filtered IGE sequences</td><td><a href='new_IMGT_IGE.txz' download='new_IMGT_IGE.txz' >Download</a></td></tr>" >> $output

echo "</table>" >> $output

echo "</div>" >> $output #downloads tab end

echo "</div>" >> $output #tabs end 

echo "</html>" >> $output


echo "---------------- naive_output.r ----------------"
echo "---------------- naive_output.r ----------------<br />" >> $log

if [[ "$naive_output" == "yes" ]]
then
	echo "output naive output"
	if [[ "${class_filter}" == "101_101" ]]
	then
		echo "copy new_IMGT.txz to ${naive_output_all}"
		cp $outdir/new_IMGT.txz ${naive_output_all}
	else
		echo "copy for classes"
		cp $outdir/new_IMGT_IGA.txz ${naive_output_ca}
		cp $outdir/new_IMGT_IGG.txz ${naive_output_cg}
		cp $outdir/new_IMGT_IGM.txz ${naive_output_cm}
		cp $outdir/new_IMGT_IGE.txz ${naive_output_ce}
	fi
fi

echo "</table>" >> $outdir/base_overview.html

mv $log $outdir/log.html

echo "<html><center><h1><a href='index.html'>Click here for the results</a></h1>Tip: Open it in a new tab (middle mouse button or right mouse button -> 'open in new tab' on the link above)<br />" > $log
echo "<table border = 1>" >> $log
echo "<thead><tr><th>Info</th><th>Sequences</th><th>Percentage</th></tr></thead>" >> $log
tIFS="$TMP"
IFS=$'\t'
while read step seq perc
	do
		echo "<tr>" >> $log
		echo "<td>$step</td>" >> $log
		echo "<td>$seq</td>" >> $log
		echo "<td>${perc}%</td>" >> $log
		echo "</tr>" >> $log
done < $outdir/filtering_steps.txt
echo "</table border></center></html>" >> $log

IFS="$tIFS"


echo "---------------- Done! ----------------"
echo "---------------- Done! ----------------<br />" >> $outdir/log.html