comparison wrapper.sh @ 1:75853bceec00 draft

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0:ed6885c85660

		singles+=( "$patient" )
	fi
	oldLocus=""
	sample1="$(echo ${sample1} | tr -d '\r' | tr -d '\n')"
	sample2="$(echo ${sample2} | tr -d '\r' | tr -d '\n')"
	tail -n+2 ${patient}_freq.txt | sed "s/>//" > tmp.txt
	echo "<div class='tabber'>" >> "$html"
	echo "<div class='tabbertab' title='Data frequency'>" >> "$html"
	echo "<table><tr><td style='vertical-align:top;'>" >> "$html"
	echo "<table border = 1 class='result_table summary_table' id='summary_table_${patient}_freq'>" >> "$html"
	echo "<thead><th>Ig/TCR gene rearrangement type</th><th>Proximal gene segment</th><th>Distal gene segment</th><th>Cut off value</th><th>Number of sequences ${patient}_Both</th><th>Number of sequences_$sample1</th><th>Read Count $sample1</th><th>Number of sequences_$sample2</th><th>Read Count $sample2</th><th>Sum number of sequences $patient</th><th>Percentage of sequences ${patient}_both</th></thead>" >> "$html"

	echo "<a href='${patient}_freq.png'><img src='${patient}_freq.png' width='1280' height='720' /></a><br />" >> "$html"
	echo "<a href='${patient}_freq_both.png'><img src='${patient}_freq_both.png' width='1280' height='720' /></a><br />" >> "$html"
	echo "<a href='${patient}_percent_freq.png'><img src='${patient}_percent_freq.png' width='1280' height='720' /></a></div>" >> "$html"
	echo "${scatterplot_tab}</tr></table></div>" >> "$html"
	
	tail -n+2 ${patient}_reads.txt | sed "s/>//" > tmp.txt
	echo "<div class='tabbertab' title='Data reads'>" >> "$html"
	echo "<table><tr><td style='vertical-align:top;'>" >> "$html"
	echo "<table border = 1 class='result_table summary_table' id='summary_table_${patient}_reads'>" >> "$html"
	echo "<thead><th>Ig/TCR gene rearrangement type</th><th>Proximal gene segment</th><th>Distal gene segment</th><th>Cut off value</th><th>Number of sequences ${patient}_Both</th><th>Number of sequences_$sample1</th><th>Read Count $sample1</th><th>Number of sequences_$sample2</th><th>Read Count $sample2</th><th>Sum number of sequences $patient</th><th>Percentage of sequences ${patient}_both</th></thead>" >> "$html"
	echo "<tbody>" >> "$html"

	sample3="$(echo ${sample3} | tr -d '\r' | tr -d '\n')"
	patient="${sample1}_${sample2}_${sample3}"
	echo "$patient"
	html="${patient}.html"
	echo "<tr><td><a href='${patient}.html'>$patient</a></td></tr>" >> "index.html"
	echo "$header" > $html
	oldLocus=""
	tail -n+2 ${patient}_freq.txt | sed "s/>//" > tmp.txt
	echo "<div class='tabber'>" >> "$html"
	echo "<div class='tabbertab' title='Data frequency'>" >> "$html"
	echo "<table><tr><td style='vertical-align:top;'>" >> "$html"
	echo "<table border = 1 class='result_table summary_table' id='summary_table_${patient}_freq'>" >> "$html"
	echo "<thead><th>Ig/TCR gene rearrangement type</th><th>Proximal gene segment</th><th>Distal gene segment</th><th>Cut off value</th><th>Number of sequences ${patient}_All</th><th>Number of sequences_$sample1</th><th>Number of sequences_$sample2</th><th>Number of sequences_$sample3</th><th>Number of sequences_${sample1}_${sample2}</th><th>Number of sequences_${sample1}_${sample3}</th><th>Number of sequences_${sample2}_${sample3}</th></thead>" >> "$html"

	echo "<div class='tabbertab' title='Graphs frequency'>" >> "$html"
	echo "<a href='${patient}_freq_total_all.png'><img src='${patient}_freq_total_all.png' width='1280' height='720' /></a><br />" >> "$html"
	echo "<a href='${patient}_freq_indiv_all.png'><img src='${patient}_freq_indiv_all.png' width='1280' height='720' /></a><br /></div>" >> "$html"
	echo "${scatterplot_tab}</tr></table></div>" >> "$html"
	
	tail -n+2 ${patient}_reads.txt | sed "s/>//" > tmp.txt
	echo "<div class='tabbertab' title='Data reads'>" >> "$html"
	echo "<table><tr><td style='vertical-align:top;'>" >> "$html"
	echo "<table border = 1 class='result_table summary_table' id='summary_table_${patient}_reads'>" >> "$html"
	echo "<thead><th>Ig/TCR gene rearrangement type</th><th>Proximal gene segment</th><th>Distal gene segment</th><th>Cut off value</th><th>Number of sequences ${patient}_All</th><th>Number of sequences_$sample1</th><th>Number of sequences_$sample2</th><th>Number of sequences_$sample3</th><th>Number of sequences_${sample1}_${sample2}</th><th>Number of sequences_${sample1}_${sample3}</th><th>Number of sequences_${sample2}_${sample3}</th></thead>" >> "$html"
	echo "<tbody>" >> "$html"

1:75853bceec00

		singles+=( "$patient" )
	fi
	oldLocus=""
	sample1="$(echo ${sample1} | tr -d '\r' | tr -d '\n')"
	sample2="$(echo ${sample2} | tr -d '\r' | tr -d '\n')"
	tail -n+2 "${patient}_freq.txt" | sed "s/>//" > tmp.txt
	echo "<div class='tabber'>" >> "$html"
	echo "<div class='tabbertab' title='Data frequency'>" >> "$html"
	echo "<table><tr><td style='vertical-align:top;'>" >> "$html"
	echo "<table border = 1 class='result_table summary_table' id='summary_table_${patient}_freq'>" >> "$html"
	echo "<thead><th>Ig/TCR gene rearrangement type</th><th>Proximal gene segment</th><th>Distal gene segment</th><th>Cut off value</th><th>Number of sequences ${patient}_Both</th><th>Number of sequences_$sample1</th><th>Read Count $sample1</th><th>Number of sequences_$sample2</th><th>Read Count $sample2</th><th>Sum number of sequences $patient</th><th>Percentage of sequences ${patient}_both</th></thead>" >> "$html"

	echo "<a href='${patient}_freq.png'><img src='${patient}_freq.png' width='1280' height='720' /></a><br />" >> "$html"
	echo "<a href='${patient}_freq_both.png'><img src='${patient}_freq_both.png' width='1280' height='720' /></a><br />" >> "$html"
	echo "<a href='${patient}_percent_freq.png'><img src='${patient}_percent_freq.png' width='1280' height='720' /></a></div>" >> "$html"
	echo "${scatterplot_tab}</tr></table></div>" >> "$html"
	
	tail -n+2 "${patient}_reads.txt" | sed "s/>//" > tmp.txt
	echo "<div class='tabbertab' title='Data reads'>" >> "$html"
	echo "<table><tr><td style='vertical-align:top;'>" >> "$html"
	echo "<table border = 1 class='result_table summary_table' id='summary_table_${patient}_reads'>" >> "$html"
	echo "<thead><th>Ig/TCR gene rearrangement type</th><th>Proximal gene segment</th><th>Distal gene segment</th><th>Cut off value</th><th>Number of sequences ${patient}_Both</th><th>Number of sequences_$sample1</th><th>Read Count $sample1</th><th>Number of sequences_$sample2</th><th>Read Count $sample2</th><th>Sum number of sequences $patient</th><th>Percentage of sequences ${patient}_both</th></thead>" >> "$html"
	echo "<tbody>" >> "$html"

	sample3="$(echo ${sample3} | tr -d '\r' | tr -d '\n')"
	patient="${sample1}_${sample2}_${sample3}"
	echo "$patient"
	html="${patient}.html"
	echo "<tr><td><a href='${patient}.html'>$patient</a></td></tr>" >> "index.html"
	echo "$header" > "$html"
	oldLocus=""
	tail -n+2 "${patient}_freq.txt" | sed "s/>//" > tmp.txt
	echo "<div class='tabber'>" >> "$html"
	echo "<div class='tabbertab' title='Data frequency'>" >> "$html"
	echo "<table><tr><td style='vertical-align:top;'>" >> "$html"
	echo "<table border = 1 class='result_table summary_table' id='summary_table_${patient}_freq'>" >> "$html"
	echo "<thead><th>Ig/TCR gene rearrangement type</th><th>Proximal gene segment</th><th>Distal gene segment</th><th>Cut off value</th><th>Number of sequences ${patient}_All</th><th>Number of sequences_$sample1</th><th>Number of sequences_$sample2</th><th>Number of sequences_$sample3</th><th>Number of sequences_${sample1}_${sample2}</th><th>Number of sequences_${sample1}_${sample3}</th><th>Number of sequences_${sample2}_${sample3}</th></thead>" >> "$html"

	echo "<div class='tabbertab' title='Graphs frequency'>" >> "$html"
	echo "<a href='${patient}_freq_total_all.png'><img src='${patient}_freq_total_all.png' width='1280' height='720' /></a><br />" >> "$html"
	echo "<a href='${patient}_freq_indiv_all.png'><img src='${patient}_freq_indiv_all.png' width='1280' height='720' /></a><br /></div>" >> "$html"
	echo "${scatterplot_tab}</tr></table></div>" >> "$html"
	
	tail -n+2 "${patient}_reads.txt" | sed "s/>//" > tmp.txt
	echo "<div class='tabbertab' title='Data reads'>" >> "$html"
	echo "<table><tr><td style='vertical-align:top;'>" >> "$html"
	echo "<table border = 1 class='result_table summary_table' id='summary_table_${patient}_reads'>" >> "$html"
	echo "<thead><th>Ig/TCR gene rearrangement type</th><th>Proximal gene segment</th><th>Distal gene segment</th><th>Cut off value</th><th>Number of sequences ${patient}_All</th><th>Number of sequences_$sample1</th><th>Number of sequences_$sample2</th><th>Number of sequences_$sample3</th><th>Number of sequences_${sample1}_${sample2}</th><th>Number of sequences_${sample1}_${sample3}</th><th>Number of sequences_${sample2}_${sample3}</th></thead>" >> "$html"
	echo "<tbody>" >> "$html"