Mercurial > repos > davidvanzessen > clonal_sequences_in_paired_samples
changeset 21:d980e2493657 draft
Uploaded
author | davidvanzessen |
---|---|
date | Mon, 23 Feb 2015 10:23:14 -0500 |
parents | d938aef60589 |
children | b662fdc7eff4 |
files | wrapper.sh |
diffstat | 1 files changed, 39 insertions(+), 11 deletions(-) [+] |
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--- a/wrapper.sh Mon Feb 23 10:22:59 2015 -0500 +++ b/wrapper.sh Mon Feb 23 10:23:14 2015 -0500 @@ -184,9 +184,9 @@ 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>Read Count $sample1</th><th>Number of sequences_$sample2</th><th>Read Count $sample2</th><th>Number of sequences_$sample3</th><th>Read Count $sample3</th></thead>" >> "$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" - while read locus j_segment v_segment cut_off_value all one read_count1 two read_count2 three read_count3 + while read locus j_segment v_segment cut_off_value all one two three one_two one_three two_three do if [ "$locus" != "$oldLocus" ] ; then echo "<tr><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr>" >> "$html" @@ -206,20 +206,34 @@ echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${locus}_${cut_off_value}.txt\", \"$patient\", \"freq\")'>$one</td>" >> "$html" else echo "<td>$one</td>" >> "$html" - fi - echo "<td>$read_count1</td>" >> "$html" + fi if [ "$two" != "0" ] && [ "$cut_off_value" != "0" ] ; then echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample2}_${locus}_${cut_off_value}.txt\", \"$patient\", \"freq\")'>$two</td>" >> "$html" else echo "<td>$two</td>" >> "$html" fi - echo "<td>$read_count2</td>" >> "$html" if [ "$three" != "0" ] && [ "$cut_off_value" != "0" ] ; then echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample3}_${locus}_${cut_off_value}.txt\", \"$patient\", \"freq\")'>$three</td>" >> "$html" else echo "<td>$three</td>" >> "$html" fi - echo "<td>$read_count3</td>" >> "$html" + + if [ "${one_two}" != "0" ] && [ "$cut_off_value" != "0" ] ; then + echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${sample2}_${locus}_${cut_off_value}.txt\", \"$patient\", \"freq\")'>${one_two}</td>" >> "$html" + else + echo "<td>${one_two}</td>" >> "$html" + fi + if [ "${one_three}" != "0" ] && [ "$cut_off_value" != "0" ] ; then + echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${sample3}_${locus}_${cut_off_value}.txt\", \"$patient\", \"freq\")'>${one_three}</td>" >> "$html" + else + echo "<td>${one_three}</td>" >> "$html" + fi + if [ "${two_three}" != "0" ] && [ "$cut_off_value" != "0" ] ; then + echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample2}_${sample3}_${locus}_${cut_off_value}.txt\", \"$patient\", \"freq\")'>${two_three}</td>" >> "$html" + else + echo "<td>${two_three}</td>" >> "$html" + fi + echo "</tr>" >> "$html" oldLocus="$locus" done < tmp.txt @@ -234,9 +248,9 @@ 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>Read Count $sample1</th><th>Number of sequences_$sample2</th><th>Read Count $sample2</th><th>Number of sequences_$sample3</th><th>Read Count $sample3</th></thead>" >> "$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" - while read locus j_segment v_segment cut_off_value all one read_count1 two read_count2 three read_count3 + while read locus j_segment v_segment cut_off_value all one two three one_two one_three two_three do if [ "$locus" != "$oldLocus" ] ; then echo "<tr><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr>" >> "$html" @@ -257,19 +271,33 @@ else echo "<td>$one</td>" >> "$html" fi - echo "<td>$read_count1</td>" >> "$html" if [ "$two" != "0" ] && [ "$cut_off_value" != "0" ] ; then echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample2}_${locus}_${cut_off_value}.txt\", \"$patient\", \"reads\")'>$two</td>" >> "$html" else echo "<td>$two</td>" >> "$html" fi - echo "<td>$read_count2</td>" >> "$html" if [ "$three" != "0" ] && [ "$cut_off_value" != "0" ] ; then echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample3}_${locus}_${cut_off_value}.txt\", \"$patient\", \"reads\")'>$three</td>" >> "$html" else echo "<td>$three</td>" >> "$html" fi - echo "<td>$read_count3</td>" >> "$html" + + if [ "${one_two}" != "0" ] && [ "$cut_off_value" != "0" ] ; then + echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${sample2}_${locus}_${cut_off_value}.txt\", \"$patient\", \"reads\")'>${one_two}</td>" >> "$html" + else + echo "<td>${one_two}</td>" >> "$html" + fi + if [ "${one_three}" != "0" ] && [ "$cut_off_value" != "0" ] ; then + echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${sample3}_${locus}_${cut_off_value}.txt\", \"$patient\", \"reads\")'>${one_three}</td>" >> "$html" + else + echo "<td>${one_three}</td>" >> "$html" + fi + if [ "${two_three}" != "0" ] && [ "$cut_off_value" != "0" ] ; then + echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample2}_${sample3}_${locus}_${cut_off_value}.txt\", \"$patient\", \"reads\")'>${two_three}</td>" >> "$html" + else + echo "<td>${two_three}</td>" >> "$html" + fi + echo "</tr>" >> "$html" oldLocus="$locus" done < tmp.txt