#!/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_ca=$9
naive_output_cg=${10}
naive_output_cm=${11}
filter_unique=${12}
class_filter=${13}
empty_region_filter=${14}
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 $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

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

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


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 $tmp

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

classes="IGA,IGA1,IGA2,IGG,IGG1,IGG2,IGG3,IGG4,IGM,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" $outdir/ 2>&1
if [ -e "$outdir/aa_histogram_.png" ]; then
        mv $outdir/aa_histogram_.png $outdir/aa_histogram.png
        mv $outdir/aa_histogram_.txt $outdir/aa_histogram.txt
fi

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

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 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'>" >> $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 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 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>${allx}/${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>${allz}%</td><td>${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} (${cmz}%)</td><td>${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 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'>" >> $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'>" >> $output

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

for gene in ${genes[@]}
do
	echo "<tr>" >> $output
	echo "<td><h1>${gene}</h1></td>" >> $output
	echo "<td><img src='transitions_heatmap_${gene}.png' /></td>" >> $output
	echo "<td><img src='transitions_stacked_${gene}.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 < $outdir/transitions_${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 [ -a $outdir/aa_histogram.png ]
then
	echo "<img src='aa_histogram.png'/><br />" >> $output
	echo "<img src='aa_histogram_IGA.png'/><br />" >> $output
	echo "<img src='aa_histogram_IGG.png'/><br />" >> $output
	echo "<img src='aa_histogram_IGM.png'/><br />" >> $output
fi

echo "<embed src='baseline.pdf' width='700px' height='1000px'>" >> $output
echo "<embed src='baseline_IGA.pdf' width='700px' height='1000px'>" >> $output
echo "<embed src='baseline_IGG.pdf' width='700px' height='1000px'>" >> $output
echo "<embed src='baseline_IGM.pdf' width='700px' height='1000px'>" >> $output

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

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

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

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

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

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

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

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

echo "<div class='tabbertab' title='Overview'>" >> $output
cat "$outdir/sequence_overview/index.html" >> $output
echo "</div>" >> $output


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

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

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='data_sum.txt' download='data_sum.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='transition_all_sum.txt' download='transition_all_sum.txt' >Download</a></td></tr>" >> $output
echo "<tr><td>The data for the 'IGA' transition plot</td><td><a href='transition_IGA_sum.txt' download='transition_all_sum.txt' >Download</a></td></tr>" >> $output
echo "<tr><td>The data for the 'IGA1' transition plot</td><td><a href='transition_IGA1_sum.txt' download='transition_IGA1_sum.txt' >Download</a></td></tr>" >> $output
echo "<tr><td>The data for the 'IGA1' transition plot</td><td><a href='transition_IGA1_sum.txt' download='transition_IGA1_sum.txt' >Download</a></td></tr>" >> $output
echo "<tr><td>The data for the 'IGG' transition plot</td><td><a href='transition_IGG_sum.txt' download='transition_IGG_sum.txt' >Download</a></td></tr>" >> $output
echo "<tr><td>The data for the 'IGG1' transition plot</td><td><a href='transition_IGG1_sum.txt' download='transition_IGG1_sum.txt' >Download</a></td></tr>" >> $output
echo "<tr><td>The data for the 'IGG2' transition plot</td><td><a href='transition_IGG2_sum.txt' download='transition_IGG2_sum.txt' >Download</a></td></tr>" >> $output
echo "<tr><td>The data for the 'IGG3' transition plot</td><td><a href='transition_IGG3_sum.txt' download='transition_IGG3_sum.txt' >Download</a></td></tr>" >> $output
echo "<tr><td>The data for the 'IGG4' transition plot</td><td><a href='transition_IGG4_sum.txt' download='transition_IGG4_sum.txt' >Download</a></td></tr>" >> $output
echo "<tr><td>The data for the 'IGM' transition plot</td><td><a href='transition_IGM_sum.txt' download='transition_IGM_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>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 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 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 "</table>" >> $output

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

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

echo "</html>" >> $output

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/IMGT-reference-seqs-IGHV-2015-11-05.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/IMGT-reference-seqs-IGHV-2015-11-05.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:-" $outdir/new_IMGT_IGG.txz "cg" "$dir/baseline/IMGT-reference-seqs-IGHV-2015-11-05.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/IMGT-reference-seqs-IGHV-2015-11-05.fa" "$outdir/baseline_IGM.pdf" "Sequence.ID" "$outdir/baseline_IGM.txt"
else
	echo "No IGM sequences" > "$outdir/baseline_IGM.txt"
fi

cd $tmp

echo "Cleaning up *.RData files"
find $outdir/baseline -name "*.RData" -type f -delete

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

if [[ "$naive_output" != "None" ]]
then
	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}
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