Mercurial > repos > davidvanzessen > clonal_sequences_in_paired_samples
comparison wrapper.sh @ 30:45554fd15511 draft
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| author | davidvanzessen |
|---|---|
| date | Tue, 26 May 2015 10:37:51 -0400 |
| parents | 5ab17bdf2530 |
| children | ce8bd23d0335 |
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| 29:5ab17bdf2530 | 30:45554fd15511 |
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| 50 echo "<div class='tabbertab' title='Data frequency'>" >> "$html" | 50 echo "<div class='tabbertab' title='Data frequency'>" >> "$html" |
| 51 echo "<table><tr><td style='vertical-align:top;'>" >> "$html" | 51 echo "<table><tr><td style='vertical-align:top;'>" >> "$html" |
| 52 echo "<table border = 1 class='result_table summary_table' id='summary_table_${patient}_freq'>" >> "$html" | 52 echo "<table border = 1 class='result_table summary_table' id='summary_table_${patient}_freq'>" >> "$html" |
| 53 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" | 53 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" |
| 54 echo "<tbody>" >> "$html" | 54 echo "<tbody>" >> "$html" |
| 55 scatterplot_tab="<div class='tabbertab' title='Scatter Plots Reads'>" | 55 scatterplot_tab="<div class='tabbertab' title='Scatter Plots Frequency'><table border='0'><tr>" |
| 56 while read locus j_segment v_segment cut_off_value both one read_count1 two read_count2 sum percent locusreadsum1 locusreadsum2 | 56 while read locus j_segment v_segment cut_off_value both one read_count1 two read_count2 sum percent locusreadsum1 locusreadsum2 |
| 57 do | 57 do |
| 58 if [ "$locus" != "$oldLocus" ] ; then | 58 if [ "$locus" != "$oldLocus" ] ; then |
| 59 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>" >> "$html" | 59 echo "<tr><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr>" >> "$html" |
| 60 echo "<tr><td><b>$locus</b></td>" >> "$html" | 60 echo "<tr><td><b>$locus</b></td>" >> "$html" |
| 84 echo "<td>$sum</td>" >> "$html" | 84 echo "<td>$sum</td>" >> "$html" |
| 85 echo "<td>${percent}%</td>" >> "$html" | 85 echo "<td>${percent}%</td>" >> "$html" |
| 86 echo "</tr>" >> "$html" | 86 echo "</tr>" >> "$html" |
| 87 oldLocus="$locus" | 87 oldLocus="$locus" |
| 88 if [ "${cut_off_value}" == "0" ] ; then | 88 if [ "${cut_off_value}" == "0" ] ; then |
| 89 scatterplot_tab="${scatterplot_tab}<img src='${patient}_${sample1}_${sample2}_freq_${locus}_scatter.png' /><br />" | 89 scatterplot_tab="${scatterplot_tab}<td><img src='${patient}_${sample1}_${sample2}_freq_${locus}_scatter.png' /></td>" |
| 90 fi | 90 fi |
| 91 done < tmp.txt | 91 done < tmp.txt |
| 92 echo "</tbody></table>" >> "$html" | 92 echo "</tbody></table>" >> "$html" |
| 93 echo "</td><td style='vertical-align:top;'><div id='result_div_${patient}_freq'></div></td></tr></table>" >> "$html" | 93 echo "</td><td style='vertical-align:top;'><div id='result_div_${patient}_freq'></div></td></tr></table>" >> "$html" |
| 94 echo "</div>" >> "$html" | 94 echo "</div>" >> "$html" |
| 95 echo "<div class='tabbertab' title='Graphs frequency'>" >> "$html" | 95 echo "<div class='tabbertab' title='Graphs frequency'>" >> "$html" |
| 96 echo "<a href='${patient}_freq.png'><img src='${patient}_freq.png' width='1280' height='720' /></a><br />" >> "$html" | 96 echo "<a href='${patient}_freq.png'><img src='${patient}_freq.png' width='1280' height='720' /></a><br />" >> "$html" |
| 97 echo "<a href='${patient}_freq_both.png'><img src='${patient}_freq_both.png' width='1280' height='720' /></a><br />" >> "$html" | 97 echo "<a href='${patient}_freq_both.png'><img src='${patient}_freq_both.png' width='1280' height='720' /></a><br />" >> "$html" |
| 98 echo "<a href='${patient}_percent_freq.png'><img src='${patient}_percent_freq.png' width='1280' height='720' /></a></div>" >> "$html" | 98 echo "<a href='${patient}_percent_freq.png'><img src='${patient}_percent_freq.png' width='1280' height='720' /></a></div>" >> "$html" |
| 99 echo "${scatterplot_tab}</div>" >> "$html" | 99 echo "${scatterplot_tab}</tr></table></div>" >> "$html" |
| 100 | 100 |
| 101 tail -n+2 ${patient}_reads.txt | sed "s/>//" > tmp.txt | 101 tail -n+2 ${patient}_reads.txt | sed "s/>//" > tmp.txt |
| 102 echo "<div class='tabbertab' title='Data reads'>" >> "$html" | 102 echo "<div class='tabbertab' title='Data reads'>" >> "$html" |
| 103 echo "<table><tr><td style='vertical-align:top;'>" >> "$html" | 103 echo "<table><tr><td style='vertical-align:top;'>" >> "$html" |
| 104 echo "<table border = 1 class='result_table summary_table' id='summary_table_${patient}_reads'>" >> "$html" | 104 echo "<table border = 1 class='result_table summary_table' id='summary_table_${patient}_reads'>" >> "$html" |
| 105 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" | 105 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" |
| 106 echo "<tbody>" >> "$html" | 106 echo "<tbody>" >> "$html" |
| 107 scatterplot_tab="<div class='tabbertab' title='Scatter Plots Frequency'>" | 107 scatterplot_tab="<div class='tabbertab' title='Scatter Plots Reads'><table border='0'><tr>" |
| 108 while read locus j_segment v_segment cut_off_value both one read_count1 two read_count2 sum percent locusreadsum1 locusreadsum2 | 108 while read locus j_segment v_segment cut_off_value both one read_count1 two read_count2 sum percent locusreadsum1 locusreadsum2 |
| 109 do | 109 do |
| 110 if [ "$locus" != "$oldLocus" ] ; then | 110 if [ "$locus" != "$oldLocus" ] ; then |
| 111 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>" >> "$html" | 111 echo "<tr><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr>" >> "$html" |
| 112 echo "<tr><td><b>$locus</b></td>" >> "$html" | 112 echo "<tr><td><b>$locus</b></td>" >> "$html" |
| 136 echo "<td>$sum</td>" >> "$html" | 136 echo "<td>$sum</td>" >> "$html" |
| 137 echo "<td>${percent}%</td>" >> "$html" | 137 echo "<td>${percent}%</td>" >> "$html" |
| 138 echo "</tr>" >> "$html" | 138 echo "</tr>" >> "$html" |
| 139 oldLocus="$locus" | 139 oldLocus="$locus" |
| 140 if [ "${cut_off_value}" == "0" ] ; then | 140 if [ "${cut_off_value}" == "0" ] ; then |
| 141 scatterplot_tab="${scatterplot_tab}<img src='${patient}_${sample1}_${sample2}_reads_${locus}_scatter.png' /><br />" | 141 scatterplot_tab="${scatterplot_tab}<td><img src='${patient}_${sample1}_${sample2}_reads_${locus}_scatter.png' /></td>" |
| 142 fi | 142 fi |
| 143 done < tmp.txt | 143 done < tmp.txt |
| 144 echo "</tbody></table>" >> "$html" | 144 echo "</tbody></table>" >> "$html" |
| 145 echo "</td><td style='vertical-align:top;'><div id='result_div_${patient}_reads'></div></td></tr></table>" >> "$html" | 145 echo "</td><td style='vertical-align:top;'><div id='result_div_${patient}_reads'></div></td></tr></table>" >> "$html" |
| 146 echo "</div>" >> "$html" | 146 echo "</div>" >> "$html" |
| 147 echo "<div class='tabbertab' title='Graphs reads'>" >> "$html" | 147 echo "<div class='tabbertab' title='Graphs reads'>" >> "$html" |
| 148 echo "<a href='${patient}_reads.png'><img src='${patient}_reads.png' width='1280' height='720' /></a><br />" >> "$html" | 148 echo "<a href='${patient}_reads.png'><img src='${patient}_reads.png' width='1280' height='720' /></a><br />" >> "$html" |
| 149 echo "<a href='${patient}_reads_both.png'><img src='${patient}_reads_both.png' width='1280' height='720' /></a><br />" >> "$html" | 149 echo "<a href='${patient}_reads_both.png'><img src='${patient}_reads_both.png' width='1280' height='720' /></a><br />" >> "$html" |
| 150 echo "<a href='${patient}_percent_reads.png'><img src='${patient}_percent_reads.png' width='1280' height='720' /></a></div>" >> "$html" | 150 echo "<a href='${patient}_percent_reads.png'><img src='${patient}_percent_reads.png' width='1280' height='720' /></a></div>" >> "$html" |
| 151 echo "${scatterplot_tab}</div>" >> "$html" | 151 echo "${scatterplot_tab}</tr></table></div>" >> "$html" |
| 152 echo "</div>" >> "$html" | 152 echo "</div>" >> "$html" |
| 153 echo "</div>" >> "$html" | 153 echo "</div>" >> "$html" |
| 154 echo "</html>" >> "$html" | 154 echo "</html>" >> "$html" |
| 155 done < patients.txt | 155 done < patients.txt |
| 156 | 156 |