Mercurial > repos > davidvanzessen > clonal_sequences_in_paired_samples
comparison wrapper.sh @ 31:ce8bd23d0335 draft
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author | davidvanzessen |
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date | Tue, 02 Jun 2015 05:26:52 -0400 |
parents | 45554fd15511 |
children | d592dab2fca1 |
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30:45554fd15511 | 31:ce8bd23d0335 |
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195 echo "<div class='tabbertab' title='Data frequency'>" >> "$html" | 195 echo "<div class='tabbertab' title='Data frequency'>" >> "$html" |
196 echo "<table><tr><td style='vertical-align:top;'>" >> "$html" | 196 echo "<table><tr><td style='vertical-align:top;'>" >> "$html" |
197 echo "<table border = 1 class='result_table summary_table' id='summary_table_${patient}_freq'>" >> "$html" | 197 echo "<table border = 1 class='result_table summary_table' id='summary_table_${patient}_freq'>" >> "$html" |
198 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" | 198 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>" >> "$html" |
199 echo "<tbody>" >> "$html" | 199 echo "<tbody>" >> "$html" |
200 scatterplot_tab="<div class='tabbertab' title='Scatter Plots Frequency'>" | 200 scatterplot_tab="<div class='tabbertab' title='Scatter Plots Frequency'><table border='0'><tr>" |
201 while read locus j_segment v_segment cut_off_value all one two three one_two one_three two_three | 201 while read locus j_segment v_segment cut_off_value all one two three one_two one_three two_three |
202 do | 202 do |
203 if [ "$locus" != "$oldLocus" ] ; then | 203 if [ "$locus" != "$oldLocus" ] ; then |
204 echo "<tr><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr>" >> "$html" | 204 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>" >> "$html" |
205 echo "<tr><td><b>$locus</b></td>" >> "$html" | 205 echo "<tr><td><b>$locus</b></td>" >> "$html" |
247 fi | 247 fi |
248 | 248 |
249 echo "</tr>" >> "$html" | 249 echo "</tr>" >> "$html" |
250 oldLocus="$locus" | 250 oldLocus="$locus" |
251 if [ "${cut_off_value}" == "0" ] ; then | 251 if [ "${cut_off_value}" == "0" ] ; then |
252 scatterplot_tab="${scatterplot_tab}<img src='${sample1}_${sample2}_${sample3}_freq_${locus}_scatter.png' /><br />" | 252 scatterplot_tab="${scatterplot_tab}<td><img src='${sample1}_${sample2}_${sample3}_freq_${locus}_scatter.png' /></td>" |
253 fi | 253 fi |
254 done < tmp.txt | 254 done < tmp.txt |
255 echo "</tbody></table>" >> "$html" | 255 echo "</tbody></table>" >> "$html" |
256 echo "</td><td style='vertical-align:top;'><div id='result_div_${patient}_freq'></div></td></tr></table>" >> "$html" | 256 echo "</td><td style='vertical-align:top;'><div id='result_div_${patient}_freq'></div></td></tr></table>" >> "$html" |
257 echo "</div>" >> "$html" | 257 echo "</div>" >> "$html" |
258 echo "<div class='tabbertab' title='Graphs frequency'>" >> "$html" | 258 echo "<div class='tabbertab' title='Graphs frequency'>" >> "$html" |
259 echo "<a href='${patient}_freq_total_all.png'><img src='${patient}_freq_total_all.png' width='1280' height='720' /></a><br />" >> "$html" | 259 echo "<a href='${patient}_freq_total_all.png'><img src='${patient}_freq_total_all.png' width='1280' height='720' /></a><br />" >> "$html" |
260 echo "<a href='${patient}_freq_indiv_all.png'><img src='${patient}_freq_indiv_all.png' width='1280' height='720' /></a><br /></div>" >> "$html" | 260 echo "<a href='${patient}_freq_indiv_all.png'><img src='${patient}_freq_indiv_all.png' width='1280' height='720' /></a><br /></div>" >> "$html" |
261 echo "${scatterplot_tab}</div>" >> "$html" | 261 echo "${scatterplot_tab}</tr></table></div>" >> "$html" |
262 | 262 |
263 tail -n+2 ${patient}_reads.txt | sed "s/>//" > tmp.txt | 263 tail -n+2 ${patient}_reads.txt | sed "s/>//" > tmp.txt |
264 echo "<div class='tabbertab' title='Data reads'>" >> "$html" | 264 echo "<div class='tabbertab' title='Data reads'>" >> "$html" |
265 echo "<table><tr><td style='vertical-align:top;'>" >> "$html" | 265 echo "<table><tr><td style='vertical-align:top;'>" >> "$html" |
266 echo "<table border = 1 class='result_table summary_table' id='summary_table_${patient}_reads'>" >> "$html" | 266 echo "<table border = 1 class='result_table summary_table' id='summary_table_${patient}_reads'>" >> "$html" |
267 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" | 267 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>" >> "$html" |
268 echo "<tbody>" >> "$html" | 268 echo "<tbody>" >> "$html" |
269 scatterplot_tab="<div class='tabbertab' title='Scatter Plots Reads'>" | 269 scatterplot_tab="<div class='tabbertab' title='Scatter Plots Reads'><table border='0'><tr>" |
270 while read locus j_segment v_segment cut_off_value all one two three one_two one_three two_three | 270 while read locus j_segment v_segment cut_off_value all one two three one_two one_three two_three |
271 do | 271 do |
272 if [ "$locus" != "$oldLocus" ] ; then | 272 if [ "$locus" != "$oldLocus" ] ; then |
273 echo "<tr><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr>" >> "$html" | 273 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>" >> "$html" |
274 echo "<tr><td><b>$locus</b></td>" >> "$html" | 274 echo "<tr><td><b>$locus</b></td>" >> "$html" |
316 fi | 316 fi |
317 | 317 |
318 echo "</tr>" >> "$html" | 318 echo "</tr>" >> "$html" |
319 oldLocus="$locus" | 319 oldLocus="$locus" |
320 if [ "${cut_off_value}" == "0" ] ; then | 320 if [ "${cut_off_value}" == "0" ] ; then |
321 scatterplot_tab="${scatterplot_tab}<img src='${sample1}_${sample2}_${sample3}_reads_${locus}_scatter.png' /><br />" | 321 scatterplot_tab="${scatterplot_tab}<td><img src='${sample1}_${sample2}_${sample3}_reads_${locus}_scatter.png' /></td>" |
322 fi | 322 fi |
323 done < tmp.txt | 323 done < tmp.txt |
324 echo "</tbody></table>" >> "$html" | 324 echo "</tbody></table>" >> "$html" |
325 echo "</td><td style='vertical-align:top;'><div id='result_div_${patient}_reads'></div></td></tr></table>" >> "$html" | 325 echo "</td><td style='vertical-align:top;'><div id='result_div_${patient}_reads'></div></td></tr></table>" >> "$html" |
326 echo "</div>" >> "$html" | 326 echo "</div>" >> "$html" |
327 echo "<div class='tabbertab' title='Graphs reads'>" >> "$html" | 327 echo "<div class='tabbertab' title='Graphs reads'>" >> "$html" |
328 echo "<a href='${patient}_reads_total_all.png'><img src='${patient}_reads_total_all.png' width='1280' height='720' /></a><br />" >> "$html" | 328 echo "<a href='${patient}_reads_total_all.png'><img src='${patient}_reads_total_all.png' width='1280' height='720' /></a><br />" >> "$html" |
329 echo "<a href='${patient}_reads_indiv_all.png'><img src='${patient}_reads_indiv_all.png' width='1280' height='720' /></a><br /></div>" >> "$html" | 329 echo "<a href='${patient}_reads_indiv_all.png'><img src='${patient}_reads_indiv_all.png' width='1280' height='720' /></a><br /></div>" >> "$html" |
330 echo "${scatterplot_tab}</div>" >> "$html" | 330 echo "${scatterplot_tab}</tr></table></div>" >> "$html" |
331 echo "</div>" >> "$html" | 331 echo "</div>" >> "$html" |
332 echo "</div>" >> "$html" | 332 echo "</div>" >> "$html" |
333 echo "</html>" >> "$html" | 333 echo "</html>" >> "$html" |
334 done < triplets.txt | 334 done < triplets.txt |
335 rm tmp.txt | 335 rm tmp.txt |