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comparison wrapper.sh @ 21:d980e2493657 draft

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author davidvanzessen
date Mon, 23 Feb 2015 10:23:14 -0500
parents 58a28427930e
children 0940835d259c
comparison
equal deleted inserted replaced
20:d938aef60589 21:d980e2493657
182 tail -n+2 ${patient}_freq.txt | sed "s/>//" > tmp.txt 182 tail -n+2 ${patient}_freq.txt | sed "s/>//" > tmp.txt
183 echo "<div class='tabber'>" >> "$html" 183 echo "<div class='tabber'>" >> "$html"
184 echo "<div class='tabbertab' title='Data frequency'>" >> "$html" 184 echo "<div class='tabbertab' title='Data frequency'>" >> "$html"
185 echo "<table><tr><td style='vertical-align:top;'>" >> "$html" 185 echo "<table><tr><td style='vertical-align:top;'>" >> "$html"
186 echo "<table border = 1 class='result_table summary_table' id='summary_table_${patient}_freq'>" >> "$html" 186 echo "<table border = 1 class='result_table summary_table' id='summary_table_${patient}_freq'>" >> "$html"
187 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" 187 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>" >> "$html"
188 echo "<tbody>" >> "$html" 188 echo "<tbody>" >> "$html"
189 while read locus j_segment v_segment cut_off_value all one read_count1 two read_count2 three read_count3 189 while read locus j_segment v_segment cut_off_value all one two three one_two one_three two_three
190 do 190 do
191 if [ "$locus" != "$oldLocus" ] ; then 191 if [ "$locus" != "$oldLocus" ] ; then
192 echo "<tr><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr>" >> "$html" 192 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>" >> "$html"
193 echo "<tr><td><b>$locus</b></td>" >> "$html" 193 echo "<tr><td><b>$locus</b></td>" >> "$html"
194 else 194 else
204 fi 204 fi
205 if [ "$one" != "0" ] && [ "$cut_off_value" != "0" ] ; then 205 if [ "$one" != "0" ] && [ "$cut_off_value" != "0" ] ; then
206 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${locus}_${cut_off_value}.txt\", \"$patient\", \"freq\")'>$one</td>" >> "$html" 206 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${locus}_${cut_off_value}.txt\", \"$patient\", \"freq\")'>$one</td>" >> "$html"
207 else 207 else
208 echo "<td>$one</td>" >> "$html" 208 echo "<td>$one</td>" >> "$html"
209 fi 209 fi
210 echo "<td>$read_count1</td>" >> "$html"
211 if [ "$two" != "0" ] && [ "$cut_off_value" != "0" ] ; then 210 if [ "$two" != "0" ] && [ "$cut_off_value" != "0" ] ; then
212 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample2}_${locus}_${cut_off_value}.txt\", \"$patient\", \"freq\")'>$two</td>" >> "$html" 211 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample2}_${locus}_${cut_off_value}.txt\", \"$patient\", \"freq\")'>$two</td>" >> "$html"
213 else 212 else
214 echo "<td>$two</td>" >> "$html" 213 echo "<td>$two</td>" >> "$html"
215 fi 214 fi
216 echo "<td>$read_count2</td>" >> "$html"
217 if [ "$three" != "0" ] && [ "$cut_off_value" != "0" ] ; then 215 if [ "$three" != "0" ] && [ "$cut_off_value" != "0" ] ; then
218 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample3}_${locus}_${cut_off_value}.txt\", \"$patient\", \"freq\")'>$three</td>" >> "$html" 216 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample3}_${locus}_${cut_off_value}.txt\", \"$patient\", \"freq\")'>$three</td>" >> "$html"
219 else 217 else
220 echo "<td>$three</td>" >> "$html" 218 echo "<td>$three</td>" >> "$html"
221 fi 219 fi
222 echo "<td>$read_count3</td>" >> "$html" 220
221 if [ "${one_two}" != "0" ] && [ "$cut_off_value" != "0" ] ; then
222 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${sample2}_${locus}_${cut_off_value}.txt\", \"$patient\", \"freq\")'>${one_two}</td>" >> "$html"
223 else
224 echo "<td>${one_two}</td>" >> "$html"
225 fi
226 if [ "${one_three}" != "0" ] && [ "$cut_off_value" != "0" ] ; then
227 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${sample3}_${locus}_${cut_off_value}.txt\", \"$patient\", \"freq\")'>${one_three}</td>" >> "$html"
228 else
229 echo "<td>${one_three}</td>" >> "$html"
230 fi
231 if [ "${two_three}" != "0" ] && [ "$cut_off_value" != "0" ] ; then
232 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample2}_${sample3}_${locus}_${cut_off_value}.txt\", \"$patient\", \"freq\")'>${two_three}</td>" >> "$html"
233 else
234 echo "<td>${two_three}</td>" >> "$html"
235 fi
236
223 echo "</tr>" >> "$html" 237 echo "</tr>" >> "$html"
224 oldLocus="$locus" 238 oldLocus="$locus"
225 done < tmp.txt 239 done < tmp.txt
226 echo "</tbody></table>" >> "$html" 240 echo "</tbody></table>" >> "$html"
227 echo "</td><td style='vertical-align:top;'><div id='result_div_${patient}_freq'></div></td></tr></table>" >> "$html" 241 echo "</td><td style='vertical-align:top;'><div id='result_div_${patient}_freq'></div></td></tr></table>" >> "$html"
232 246
233 tail -n+2 ${patient}_reads.txt | sed "s/>//" > tmp.txt 247 tail -n+2 ${patient}_reads.txt | sed "s/>//" > tmp.txt
234 echo "<div class='tabbertab' title='Data reads'>" >> "$html" 248 echo "<div class='tabbertab' title='Data reads'>" >> "$html"
235 echo "<table><tr><td style='vertical-align:top;'>" >> "$html" 249 echo "<table><tr><td style='vertical-align:top;'>" >> "$html"
236 echo "<table border = 1 class='result_table summary_table' id='summary_table_${patient}_reads'>" >> "$html" 250 echo "<table border = 1 class='result_table summary_table' id='summary_table_${patient}_reads'>" >> "$html"
237 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" 251 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>" >> "$html"
238 echo "<tbody>" >> "$html" 252 echo "<tbody>" >> "$html"
239 while read locus j_segment v_segment cut_off_value all one read_count1 two read_count2 three read_count3 253 while read locus j_segment v_segment cut_off_value all one two three one_two one_three two_three
240 do 254 do
241 if [ "$locus" != "$oldLocus" ] ; then 255 if [ "$locus" != "$oldLocus" ] ; then
242 echo "<tr><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr>" >> "$html" 256 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>" >> "$html"
243 echo "<tr><td><b>$locus</b></td>" >> "$html" 257 echo "<tr><td><b>$locus</b></td>" >> "$html"
244 else 258 else
255 if [ "$one" != "0" ] && [ "$cut_off_value" != "0" ] ; then 269 if [ "$one" != "0" ] && [ "$cut_off_value" != "0" ] ; then
256 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${locus}_${cut_off_value}.txt\", \"$patient\", \"reads\")'>$one</td>" >> "$html" 270 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${locus}_${cut_off_value}.txt\", \"$patient\", \"reads\")'>$one</td>" >> "$html"
257 else 271 else
258 echo "<td>$one</td>" >> "$html" 272 echo "<td>$one</td>" >> "$html"
259 fi 273 fi
260 echo "<td>$read_count1</td>" >> "$html"
261 if [ "$two" != "0" ] && [ "$cut_off_value" != "0" ] ; then 274 if [ "$two" != "0" ] && [ "$cut_off_value" != "0" ] ; then
262 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample2}_${locus}_${cut_off_value}.txt\", \"$patient\", \"reads\")'>$two</td>" >> "$html" 275 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample2}_${locus}_${cut_off_value}.txt\", \"$patient\", \"reads\")'>$two</td>" >> "$html"
263 else 276 else
264 echo "<td>$two</td>" >> "$html" 277 echo "<td>$two</td>" >> "$html"
265 fi 278 fi
266 echo "<td>$read_count2</td>" >> "$html"
267 if [ "$three" != "0" ] && [ "$cut_off_value" != "0" ] ; then 279 if [ "$three" != "0" ] && [ "$cut_off_value" != "0" ] ; then
268 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample3}_${locus}_${cut_off_value}.txt\", \"$patient\", \"reads\")'>$three</td>" >> "$html" 280 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample3}_${locus}_${cut_off_value}.txt\", \"$patient\", \"reads\")'>$three</td>" >> "$html"
269 else 281 else
270 echo "<td>$three</td>" >> "$html" 282 echo "<td>$three</td>" >> "$html"
271 fi 283 fi
272 echo "<td>$read_count3</td>" >> "$html" 284
285 if [ "${one_two}" != "0" ] && [ "$cut_off_value" != "0" ] ; then
286 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${sample2}_${locus}_${cut_off_value}.txt\", \"$patient\", \"reads\")'>${one_two}</td>" >> "$html"
287 else
288 echo "<td>${one_two}</td>" >> "$html"
289 fi
290 if [ "${one_three}" != "0" ] && [ "$cut_off_value" != "0" ] ; then
291 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${sample3}_${locus}_${cut_off_value}.txt\", \"$patient\", \"reads\")'>${one_three}</td>" >> "$html"
292 else
293 echo "<td>${one_three}</td>" >> "$html"
294 fi
295 if [ "${two_three}" != "0" ] && [ "$cut_off_value" != "0" ] ; then
296 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample2}_${sample3}_${locus}_${cut_off_value}.txt\", \"$patient\", \"reads\")'>${two_three}</td>" >> "$html"
297 else
298 echo "<td>${two_three}</td>" >> "$html"
299 fi
300
273 echo "</tr>" >> "$html" 301 echo "</tr>" >> "$html"
274 oldLocus="$locus" 302 oldLocus="$locus"
275 done < tmp.txt 303 done < tmp.txt
276 echo "</tbody></table>" >> "$html" 304 echo "</tbody></table>" >> "$html"
277 echo "</td><td style='vertical-align:top;'><div id='result_div_${patient}_reads'></div></td></tr></table>" >> "$html" 305 echo "</td><td style='vertical-align:top;'><div id='result_div_${patient}_reads'></div></td></tr></table>" >> "$html"