Mercurial > repos > davidvanzessen > clonal_sequences_in_paired_samples
comparison wrapper.sh @ 2:8d562506f4f9 draft
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| author | davidvanzessen |
|---|---|
| date | Mon, 25 Aug 2014 03:38:07 -0400 |
| parents | c0110597898e |
| children | f9316f7676cc |
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| 1:c0110597898e | 2:8d562506f4f9 |
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| 36 echo "<div class='tabbertab' title='$patient'>" >> $html | 36 echo "<div class='tabbertab' title='$patient'>" >> $html |
| 37 echo "<div class='tabber'>" >> $html | 37 echo "<div class='tabber'>" >> $html |
| 38 echo "<div class='tabbertab' title='Data frequency'>" >> $html | 38 echo "<div class='tabbertab' title='Data frequency'>" >> $html |
| 39 echo "<table><tr><td style='vertical-align:top;'>" >> $html | 39 echo "<table><tr><td style='vertical-align:top;'>" >> $html |
| 40 echo "<table border = 1 class='result_table summary_table' id='summary_table_${patient}_freq'>" >> $html | 40 echo "<table border = 1 class='result_table summary_table' id='summary_table_${patient}_freq'>" >> $html |
| 41 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 | 41 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>Normalized Read Count $sample1</th><th>Number of sequences_$sample2</th><th>Normalized Read Count $sample2</th><th>Sum number of sequences $patient</th><th>Percentage of sequences ${patient}_both</th></thead>" >> $html |
| 42 echo "<tbody>" >> $html | 42 echo "<tbody>" >> $html |
| 43 while read locus j_segment v_segment cut_off_value both one read_count1 two read_count2 sum percent | 43 readsumtable="<table class='result_table summary_table'><thead><tr><th>Ig/TCR gene rearrangement type</th><th>Proximal gene segment</th><th>Distal gene segment</th><th>Total normalized read count for $sample1</th><th>Total normalized read count for $sample2</th></tr></thead>" |
| 44 while read locus j_segment v_segment cut_off_value both one read_count1 two read_count2 sum percent locusreadsum1 locusreadsum2 | |
| 44 do | 45 do |
| 45 if [ "$locus" != "$oldLocus" ] ; then | 46 if [ "$locus" != "$oldLocus" ] ; then |
| 46 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 | 47 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>" >> $html |
| 47 echo "<tr><td><b>$locus</b></td>" >> $html | 48 echo "<tr><td><b>$locus</b></td>" >> $html |
| 49 readsumtable="${readsumtable}<tr><td>$locus</td><td>$v_segment</td><td>$j_segment</td><td>$locusreadsum1</td><td>$locusreadsum2</td></tr>" | |
| 48 else | 50 else |
| 49 echo "<td></td>" >> $html | 51 echo "<td></td>" >> $html |
| 50 fi | 52 fi |
| 51 echo "<td>$v_segment</td>" >> $html | 53 echo "<td>$v_segment</td>" >> $html |
| 52 echo "<td>$j_segment</td>" >> $html | 54 echo "<td>$j_segment</td>" >> $html |
| 69 fi | 71 fi |
| 70 echo "<td>$read_count2</td>" >> $html | 72 echo "<td>$read_count2</td>" >> $html |
| 71 echo "<td>$sum</td>" >> $html | 73 echo "<td>$sum</td>" >> $html |
| 72 echo "<td>${percent}%</td>" >> $html | 74 echo "<td>${percent}%</td>" >> $html |
| 73 echo "</tr>" >> $html | 75 echo "</tr>" >> $html |
| 74 oldLocus="$locus" | 76 oldLocus="$locus" |
| 75 done < tmp.txt | 77 done < tmp.txt |
| 76 echo "</tbody></table>" >> $html | 78 echo "</tbody></table>" >> $html |
| 77 echo "</td><td style='vertical-align:top;'><div id='result_div_${patient}_freq'></div></td></tr></table></div>" >> $html | 79 echo "</td><td style='vertical-align:top;'><div id='result_div_${patient}_freq'></div></td></tr></table>" >> $html |
| 80 echo "${readsumtable}</table></div>" >> $html | |
| 78 echo "<div class='tabbertab' title='Graphs frequency'>" >> $html | 81 echo "<div class='tabbertab' title='Graphs frequency'>" >> $html |
| 79 echo "<a href='${patient}_freq.png'><img src='${patient}_freq.png' width='1280' height='720' /></a><br />" >> $html | 82 echo "<a href='${patient}_freq.png'><img src='${patient}_freq.png' width='1280' height='720' /></a><br />" >> $html |
| 80 echo "<a href='${patient}_freq_both.png'><img src='${patient}_freq_both.png' width='1280' height='720' /></a><br />" >> $html | 83 echo "<a href='${patient}_freq_both.png'><img src='${patient}_freq_both.png' width='1280' height='720' /></a><br />" >> $html |
| 81 echo "<a href='${patient}_percent_freq.png'><img src='${patient}_percent_freq.png' width='1280' height='720' /></a></div>" >> $html | 84 echo "<a href='${patient}_percent_freq.png'><img src='${patient}_percent_freq.png' width='1280' height='720' /></a></div>" >> $html |
| 82 | 85 |
| 84 echo "<div class='tabbertab' title='Data reads'>" >> $html | 87 echo "<div class='tabbertab' title='Data reads'>" >> $html |
| 85 echo "<table><tr><td style='vertical-align:top;'>" >> $html | 88 echo "<table><tr><td style='vertical-align:top;'>" >> $html |
| 86 echo "<table border = 1 class='result_table summary_table' id='summary_table_${patient}_reads'>" >> $html | 89 echo "<table border = 1 class='result_table summary_table' id='summary_table_${patient}_reads'>" >> $html |
| 87 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 | 90 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 |
| 88 echo "<tbody>" >> $html | 91 echo "<tbody>" >> $html |
| 89 while read locus j_segment v_segment cut_off_value both one read_count1 two read_count2 sum percent | 92 readsumtable="<table class='result_table summary_table'><thead><tr><th>Ig/TCR gene rearrangement type</th><th>Proximal gene segment</th><th>Distal gene segment</th><th>Total normalized read count for $sample1</th><th>Total normalized read count for $sample2</th></tr></thead>" |
| 93 while read locus j_segment v_segment cut_off_value both one read_count1 two read_count2 sum percent locusreadsum1 locusreadsum2 | |
| 90 do | 94 do |
| 91 if [ "$locus" != "$oldLocus" ] ; then | 95 if [ "$locus" != "$oldLocus" ] ; then |
| 92 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 | 96 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>" >> $html |
| 93 echo "<tr><td><b>$locus</b></td>" >> $html | 97 echo "<tr><td><b>$locus</b></td>" >> $html |
| 98 readsumtable="${readsumtable}<tr><td>$locus</td><td>$v_segment</td><td>$j_segment</td><td>$locusreadsum1</td><td>$locusreadsum2</td></tr>" | |
| 94 else | 99 else |
| 95 echo "<td></td>" >> $html | 100 echo "<td></td>" >> $html |
| 96 fi | 101 fi |
| 97 echo "<td>$v_segment</td>" >> $html | 102 echo "<td>$v_segment</td>" >> $html |
| 98 echo "<td>$j_segment</td>" >> $html | 103 echo "<td>$j_segment</td>" >> $html |
| 118 echo "<td>${percent}%</td>" >> $html | 123 echo "<td>${percent}%</td>" >> $html |
| 119 echo "</tr>" >> $html | 124 echo "</tr>" >> $html |
| 120 oldLocus="$locus" | 125 oldLocus="$locus" |
| 121 done < tmp.txt | 126 done < tmp.txt |
| 122 echo "</tbody></table>" >> $html | 127 echo "</tbody></table>" >> $html |
| 123 echo "</td><td style='vertical-align:top;'><div id='result_div_${patient}_reads'></div></td></tr></table></div>" >> $html | 128 echo "</td><td style='vertical-align:top;'><div id='result_div_${patient}_reads'></div></td></tr></table>" >> $html |
| 129 echo "${readsumtable}</table></div>" >> $html | |
| 124 echo "<div class='tabbertab' title='Graphs reads'>" >> $html | 130 echo "<div class='tabbertab' title='Graphs reads'>" >> $html |
| 125 echo "<a href='${patient}_reads.png'><img src='${patient}_reads.png' width='1280' height='720' /></a><br />" >> $html | 131 echo "<a href='${patient}_reads.png'><img src='${patient}_reads.png' width='1280' height='720' /></a><br />" >> $html |
| 126 echo "<a href='${patient}_reads_both.png'><img src='${patient}_reads_both.png' width='1280' height='720' /></a><br />" >> $html | 132 echo "<a href='${patient}_reads_both.png'><img src='${patient}_reads_both.png' width='1280' height='720' /></a><br />" >> $html |
| 127 echo "<a href='${patient}_percent_reads.png'><img src='${patient}_percent_reads.png' width='1280' height='720' /></a></div>" >> $html | 133 echo "<a href='${patient}_percent_reads.png'><img src='${patient}_percent_reads.png' width='1280' height='720' /></a></div>" >> $html |
| 128 echo "</div>" >> $html | 134 echo "</div>" >> $html |
| 129 echo "</div>" >> $html | 135 echo "</div>" >> $html |
| 130 done < patients.txt | 136 done < patients.txt |
| 131 echo "</div></html>" >> $html | 137 echo "</div></html>" >> $html |
| 132 rm tmp.txt | 138 rm tmp.txt |