Mercurial > repos > davidvanzessen > clonal_sequences_in_paired_samples

comparison wrapper.sh @ 31:ce8bd23d0335 draft

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Uploaded
author davidvanzessen
date Tue, 02 Jun 2015 05:26:52 -0400
parents 45554fd15511
children d592dab2fca1
comparison
equal deleted inserted replaced
30:45554fd15511 31:ce8bd23d0335
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