Mercurial > repos > davidvanzessen > clonal_sequences_in_paired_samples

comparison wrapper.sh @ 7:68c6c7624ffc draft

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author davidvanzessen
date Thu, 18 Sep 2014 08:56:44 -0400
parents f11df36f43bb
children fa240d1c57a9
comparison
equal deleted inserted replaced
6:8313c6cc65c5 7:68c6c7624ffc
7 min_cells=$5 7 min_cells=$5
8 8
9 dir="$(cd "$(dirname "$0")" && pwd)" 9 dir="$(cd "$(dirname "$0")" && pwd)"
10 mkdir $outputDir 10 mkdir $outputDir
11 11
12 echo "testtestsetset" > $outputFile
13 12
14 Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputFile $min_freq $min_cells 2>&1 13 Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputFile $min_freq $min_cells 2>&1
15 cp $dir/jquery-1.11.0.min.js $outputDir 14 cp $dir/jquery-1.11.0.min.js $outputDir
16 cp $dir/script.js $outputDir 15 cp $dir/script.js $outputDir
17 cp $dir/style.css $outputDir 16 cp $dir/style.css $outputDir
141 echo "<a href='${patient}_percent_reads.png'><img src='${patient}_percent_reads.png' width='1280' height='720' /></a></div>" >> $html 140 echo "<a href='${patient}_percent_reads.png'><img src='${patient}_percent_reads.png' width='1280' height='720' /></a></div>" >> $html
142 echo "</div>" >> $html 141 echo "</div>" >> $html
143 echo "</div>" >> $html 142 echo "</div>" >> $html
144 echo "</html>" >> $html 143 echo "</html>" >> $html
145 done < patients.txt 144 done < patients.txt
146 rm tmp.txt
147 145
148 html="index.html" 146 html="index.html"
149 echo "<html>" > $html 147 echo "<html>" > $html
150 echo "<table>" >> $html 148 echo "<table>" >> $html
151 echo "<tr><td><b>Singles:</b></td></tr>" >> $html 149 echo "<tr><td><b>Singles:</b></td></tr>" >> $html
168 do 166 do
169 echo "<tr><td><a href='${patient}.html'>$patient</a></td></tr>" >> $html 167 echo "<tr><td><a href='${patient}.html'>$patient</a></td></tr>" >> $html
170 done 168 done
171 echo "<tr><td><b>Triplets:</b></td></tr>" >> $html 169 echo "<tr><td><b>Triplets:</b></td></tr>" >> $html
172 170
171 while read sample1 sample2 sample3
172 do
173 sample1="$(echo ${sample1} | tr -d '\r' | tr -d '\n')"
174 sample2="$(echo ${sample2} | tr -d '\r' | tr -d '\n')"
175 sample3="$(echo ${sample3} | tr -d '\r' | tr -d '\n')"
176 patient="${sample1}_${sample2}_${sample3}"
177 echo "$patient"
178 html="${patient}.html"
179 echo "<tr><td><a href='${patient}.html'>$patient</a></td></tr>" >> "index.html"
180 echo "$header" > $html
181 oldLocus=""
182 tail -n+2 ${patient}_freq.txt | sed "s/>//" > tmp.txt
183 echo "<div class='tabber'>" >> $html
184 echo "<div class='tabbertab' title='Data frequency'>" >> $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
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
188 echo "<tbody>" >> $html
189 while read locus j_segment v_segment cut_off_value all one read_count1 two read_count2 three read_count3
190 do
191 if [ "$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>" >> $html
193 echo "<tr><td><b>$locus</b></td>" >> $html
194 else
195 echo "<td></td>" >> $html
196 fi
197 echo "<td>$v_segment</td>" >> $html
198 echo "<td>$j_segment</td>" >> $html
199 echo "<td>>$cut_off_value</td>" >> $html
200 if [ "$all" != "0" ] ; then
201 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${sample2}_${sample3}_${locus}_${cut_off_value}.txt\", \"$patient\", \"freq\")'>$all</td>" >> $html
202 else
203 echo "<td>$all</td>" >> $html
204 fi
205 if [ "$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>" >> $html
207 else
208 echo "<td>$one</td>" >> $html
209 fi
210 echo "<td>$read_count1</td>" >> $html
211 if [ "$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>" >> $html
213 else
214 echo "<td>$two</td>" >> $html
215 fi
216 echo "<td>$read_count2</td>" >> $html
217 if [ "$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>" >> $html
219 else
220 echo "<td>$three</td>" >> $html
221 fi
222 echo "<td>$read_count3</td>" >> $html
223 echo "</tr>" >> $html
224 oldLocus="$locus"
225 done < tmp.txt
226 echo "</tbody></table>" >> $html
227 echo "</td><td style='vertical-align:top;'><div id='result_div_${patient}_freq'></div></td></tr></table>" >> $html
228 echo "</div>" >> $html
229 echo "<div class='tabbertab' title='Graphs frequency'>" >> $html
230 echo "<a href='${patient}_reads_total_all.png'><img src='${patient}_reads.png' width='1280' height='720' /></a><br />" >> $html
231 echo "<a href='${patient}_reads_indiv_all.png'><img src='${patient}_reads_all.png' width='1280' height='720' /></a><br />" >> $html
232
233 tail -n+2 ${patient}_reads.txt | sed "s/>//" > tmp.txt
234 echo "<div class='tabbertab' title='Data reads'>" >> $html
235 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
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
238 echo "<tbody>" >> $html
239 while read locus j_segment v_segment cut_off_value all one read_count1 two read_count2 three read_count3
240 do
241 if [ "$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>" >> $html
243 echo "<tr><td><b>$locus</b></td>" >> $html
244 else
245 echo "<td></td>" >> $html
246 fi
247 echo "<td>$v_segment</td>" >> $html
248 echo "<td>$j_segment</td>" >> $html
249 echo "<td>>$cut_off_value</td>" >> $html
250 if [ "$all" != "0" ] ; then
251 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${sample2}_${sample3}_${locus}_${cut_off_value}.txt\", \"$patient\", \"reads\")'>$all</td>" >> $html
252 else
253 echo "<td>$all</td>" >> $html
254 fi
255 if [ "$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>" >> $html
257 else
258 echo "<td>$one</td>" >> $html
259 fi
260 echo "<td>$read_count1</td>" >> $html
261 if [ "$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>" >> $html
263 else
264 echo "<td>$two</td>" >> $html
265 fi
266 echo "<td>$read_count2</td>" >> $html
267 if [ "$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>" >> $html
269 else
270 echo "<td>$three</td>" >> $html
271 fi
272 echo "<td>$read_count3</td>" >> $html
273 echo "</tr>" >> $html
274 oldLocus="$locus"
275 done < tmp.txt
276 echo "</tbody></table>" >> $html
277 echo "</td><td style='vertical-align:top;'><div id='result_div_${patient}_reads'></div></td></tr></table>" >> $html
278 echo "</div>" >> $html
279 echo "<div class='tabbertab' title='Graphs reads'>" >> $html
280 echo "<a href='${patient}_reads_total_all.png'><img src='${patient}_reads.png' width='1280' height='720' /></a><br />" >> $html
281 echo "<a href='${patient}_reads_indiv_all.png'><img src='${patient}_reads_all.png' width='1280' height='720' /></a><br />" >> $html
282 echo "</div>" >> $html
283 echo "</div>" >> $html
284 echo "</html>" >> $html
285 done < triplets.txt
286 rm tmp.txt
287
288
289 html="index.html"
290
173 echo "</table>" >> $html 291 echo "</table>" >> $html
174 echo "</html>" >> $html 292 echo "</html>" >> $html
175 293