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comparison mutspecStat_wrapper.sh @ 0:8c682b3a7c5b draft

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author iarc
date Tue, 19 Apr 2016 03:07:11 -0400
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-1:000000000000 0:8c682b3a7c5b
1 #!/bin/bash
2
3 #########################################
4 ### SPECIFY THE NUMBER OF CPU ###
5 #########################################
6 cpu=1
7
8
9
10
11
12 #########################################
13 ### Recover the arguments ###
14 #########################################
15 html=$1;shift
16 len_file_path=$1;shift
17 estimSign=$1;shift
18 parameters=$1;shift
19 working_dir=`pwd`
20
21
22
23 mkdir in
24 cd in
25
26 names=$(sed 's/\s/_/g' <<< $*)
27 names=$(sed 's/_\// \//g' <<< $names)
28 names=$(sed 's/_annotated//g' <<< $names)
29 names=$(sed 's/_filtered//g' <<< $names)
30 names=$(sed 's/\.txt_/_/' <<< $names)
31
32 for name in ${names}
33 do
34 file=$(sed 's/=/ /' <<< $name);
35 echo $file
36 ln -s $file
37 done
38 cd ..
39
40 output_dir=${html%%.*}_files
41
42
43 #########################################
44 ### Calculates the statistics ###
45 #########################################
46
47 perl $SCRIPT_PATH/mutspecStat.pl --outfile $output_dir \
48 --temp "$working_dir/temp" \
49 --pathRscript $SCRIPT_PATH \
50 $parameters \
51 $working_dir/in
52
53
54 #########################################
55 ### Estimate the number of signatures ###
56 #########################################
57 if [[ $estimSign > 0 ]]; then
58 Rscript $SCRIPT_PATH/R/estimateSign_Galaxy.r --input $output_dir/Mutational_Analysis/Figures/Input_NMF/Input_NMF_Count.txt --stop $estimSign --cpu $cpu --output $output_dir/Mutational_Analysis/Figures/Estimate_Number_Signatures.png 2>&1
59 fi
60
61
62 #########################################
63 ### Create css #
64 #########################################
65 css=$output_dir/Mutational_Analysis/style.css
66 echo ".legend{position:relative}.legend .legend-hidden{display:none;position:absolute;background-color:#fff;border:3px solid #03F;padding:3px;color:#000;font-size:1em;border-radius:10px;margin-top:-40px}.legend:hover .legend-hidden{display:block}" > $css
67
68
69
70 # HMTL page for the result of the tool
71 echo "<html>" >> $html
72 echo "<body>" >> $html
73
74 if [ -d $output_dir/Mutational_Analysis/Figures ]; then
75
76 echo "<center> <h2>Mutational spectra report summary</h2> </center>" >> $html
77
78 echo "<br/> Download the full report in Excel" >> $html
79
80 ## One report with all the samples. Specify the full path
81 if [[ -e "$output_dir/Mutational_Analysis/Report_Mutation_Spectra.xls" ]]
82 then
83 # Interpreted by Galaxy so don't need the full path
84 echo "<br/><a href="Mutational_Analysis/Report_Mutation_Spectra.xls">Report_Mutation_Spectra.xls</a>" >> $html
85 fi
86 ## One report for each samples
87 for file in $names
88 do
89 name=$(echo ${file}| cut -d"=" -f2)
90 name=${name%.*}
91
92 # One report for each samples
93 if [[ -e "$output_dir/Mutational_Analysis/Report_Mutation_Spectra-$name.xls" ]]
94 then
95 echo "<br/><a href="Mutational_Analysis/Report_Mutation_Spectra-$name.xls">Report_Mutation_Spectra-$name.xls</a>" >> $html
96 fi
97 done
98 ## One report for each samples: Pool_Data
99 if [[ $parameters =~ "--pooldata" ]]; then
100 if [[ -e "$output_dir/Mutational_Analysis/Report_Mutation_Spectra-Pool_Data.xls" ]]; then
101 echo "<br/><a href="Mutational_Analysis/Report_Mutation_Spectra-Pool_Data.xls">Report_Mutation_Spectra-Pool_Data.xls</a>" >> $html
102 fi
103 fi
104
105
106 ## Input file for NMF
107 if [[ -e "$output_dir/Mutational_Analysis/Figures/Input_NMF/Input_NMF_Count.txt" ]]
108 then
109 # Interpreted by Galaxy so don't need the full path
110 echo "<br/><br/> Download the input file for the tool mutSpec-NMF" >> $html
111 echo "<br/><a href="Mutational_Analysis/Figures/Input_NMF/Input_NMF_Count.txt">Input_NMF_Count.txt</a><br/>" >> $html
112 fi
113
114 ## Computed statistics for estimating the number of signatures
115 if [[ $estimSign > 0 ]]; then
116 echo "<br/> Link to the computed statistics for estimating the number of signatures <br/>" >> $html
117 if [[ -e "$output_dir/Mutational_Analysis/Figures/Estimate_Number_Signatures.png" ]]; then
118 outEstimateSign="$output_dir/Mutational_Analysis/EstimatingSignatures.html"
119 touch $outEstimateSign
120 echo "<a href='Mutational_Analysis/EstimatingSignatures.html'>Estimating the number of signatures</a><br/>" >> $html
121 echo "<br/> <center> <h2>Computed statistics for estimating the number of signatures</h2> </center> <br/>" >> $outEstimateSign
122 echo "Several approaches have been proposed to choose the optimal number of signatures to extract with NMF. <br/>
123 Brunet et al. 2004, proposed to take the first number of signature for which the cophenetic coefficient starts decreasing, <br/>
124 Hutchins et al. 2008, suggested to choose the first value where the RSS curve presents an inflection point. <br/>
125 Frigyesi et al. 2008, considered the smallest value at which the decrease in the RSS is lower than the decrease of the RSS obtained from random data. <br/><br/>
126 The estimation are based on Brunet’s algorithm computed from 50 runs for each value of signature to estimate. <br/> <br/>
127 The original data are shuffled for comparing the quality measures obtained with our data (Data x) and from randomized data (Data y). The curves for the actual data are in solid line, those for the randomized data are in dashed line. <br/> <br/>" >> $outEstimateSign
128 echo "<img src="Figures/Estimate_Number_Signatures.png width="1000""/><br/></td>" >> $outEstimateSign
129 else
130 echo "<br/>There is not enough mutations for estimating the number of signatures <br/>" >> $html
131 echo "Read the tool standard output for more detail<br/>" >> $html
132 fi
133 fi
134
135
136 ## HMTL Link to the samples
137 echo "<br/> Link to individual samples <br/>" >> $html
138 for file in $names
139 do
140 name=$(echo ${file}| cut -d"=" -f2)
141 name=${name%.*}
142 outfile="$output_dir/Mutational_Analysis/$name.html"
143 touch $outfile # Create an empty file named $outfile
144 echo "<a href='Mutational_Analysis/$name.html'>$name</a><br/>" >> $html
145
146 #-------------------------------------------------------------------------------------------------------------------------------------------------------------------------#
147 # INDIVIDUAL SAMPLES #
148 #-------------------------------------------------------------------------------------------------------------------------------------------------------------------------#
149 echo "<br/> <center> <h2>Mutational Spectra report for $name</h2> </center> <br/>" >> $outfile
150
151 echo "<html>" >> $outfile
152
153 echo "<head>" >> $outfile
154 echo "<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">" >> $outfile
155 # Link to the css style file for having a legend when we pass the mouse on the figures
156 echo "<link rel="stylesheet" href="style.css" />" >> $outfile
157 echo "</head>" >> $outfile
158
159 echo "<body>" >> $outfile
160
161 echo "<table>" >> $outfile
162 echo "<tr>" >> $outfile
163 echo "<th><h3>Overall mutation distribution</h3></th>" >> $outfile
164 echo "<th><h3>Impact on protein sequence</h3></th>" >> $outfile
165 echo "</tr><tr>" >> $outfile
166 echo "<td> <center> <a href="Figures/Overall_mutation_distribution/$name/$name-OverallMutationDistribution.txt">$name-OverallMutationDistribution.txt</a> </center> </td>" >> $outfile
167 echo "<td> <center> <a href="Figures/Impact_protein_sequence/$name/$name-DistributionExoFunc.txt">$name-DistributionExoFunc.txt</a> </center> </td>" >> $outfile
168 echo "</tr><tr>" >> $outfile
169
170 echo "<td>" >> $outfile
171 echo "<span class="legend"><img src="Figures/Overall_mutation_distribution/$name/$name-OverallMutationDistribution.png width="280""/>" >> $outfile
172 echo "<span class="legend-hidden">" >> $outfile
173 echo "<center><B>Overall Mutation Distribution</center></B><br/>Proportion of all mutation types (total count are indicated in parenthesis). For indels the counts are based on annotation retrieved from the database ExonicFunc.refGene<br/>" >> $outfile
174 echo "</td>" >> $outfile
175 echo "<td>" >> $outfile
176 echo "<span class="legend"><img src="Figures/Impact_protein_sequence/$name/$name-DistributionExoFunc.png width="400""/>" >> $outfile
177 echo "<span class="legend-hidden">" >> $outfile
178 echo "<center><B>Graph 1. Impact on protein sequence</center></B><br/>Impact of all mutations (SBS and Indel) on the protein sequence based on the ExonicFunc.refGene annotation<br/>" >> $outfile
179 echo "</td>" >> $outfile
180
181 echo "</tr>" >> $outfile
182 echo "</table>" >> $outfile
183
184 echo "<br/><br/>" >> $outfile
185
186
187 echo "<table>" >> $outfile
188 echo "<tr>" >> $outfile
189 echo "<th><h3>SBS distribution</h3></th>" >> $outfile
190 echo "<th><h3>Stranded distribution of SBS</h3></th>" >> $outfile
191 echo "</tr><tr>" >> $outfile
192 echo "<td> <center> <a href="Figures/SBS_distribution/$name/$name-SBS_distribution.txt">$name-SBS_distribution.txt</a> </center> </td>" >> $outfile
193 echo "<td> <center> <a href="Figures/Stranded_Analysis/$name/$name-StrandBias.txt">$name-StrandBias.txt</a> </center> </td>" >> $outfile
194 echo "</tr><tr>" >> $outfile
195
196 echo "<td>" >> $outfile
197 echo "<span class="legend"><img src="Figures/SBS_distribution/$name/$name-SBS_distribution.png width="550""/>" >> $outfile
198 echo "<span class="legend-hidden">" >> $outfile
199 echo "<center><B>Graph 2. SBS distribution</center></B><br/>Proportion of each type of single base substitution (SBS)<br/>" >> $outfile
200 echo "</td>" >> $outfile
201 echo "<td>" >> $outfile
202 echo "<span class="legend"><img src="Figures/Stranded_Analysis/$name/$name-StrandBias.png width="400""/>" >> $outfile
203 echo "<span class="legend-hidden">" >> $outfile
204 echo "<center><B>Graph 3. Stranded distribution of SBS</center></B><br/>Count of the six substitution types on the transcribed and non-transcribed strand<br/>" >> $outfile
205 echo "</td>" >> $outfile
206
207 echo "</tr>" >> $outfile
208 echo "</table>" >> $outfile
209
210
211 echo "<br/><br/>" >> $outfile
212
213
214 ######################################################
215 # Trinucleotide sequence context of SBS on genomic #
216 ######################################################
217 echo "<table>" >> $outfile
218 echo "<h3>Trinucleotide sequence context of SBS on the genomic sequence</h3>" >> $outfile
219 echo "<tr>" >> $outfile
220 echo "<td> <center> <a href="Figures/Trinucleotide_Sequence_Context/$name/$name-MutationSpectraPercent-Genomic.txt">$name-MutationSpectraPercent.txt</a> </center> </td>" >> $outfile
221 echo "<td> <center> <a href="Figures/Trinucleotide_Sequence_Context/$name/$name-HeatmapPercent-Genomic.txt">$name-HeatmapPercent-Genomic.txt</a> </center> </td>" >> $outfile
222 echo "</tr><tr>" >> $outfile
223
224 echo "<td>" >> $outfile
225 echo "<span class="legend"><img src="Figures/Trinucleotide_Sequence_Context/$name/$name-MutationSpectraPercent-Genomic.png width="1000""/>" >> $outfile
226 echo "<span class="legend-hidden">" >> $outfile
227 echo "<center><B>Panel 1. Trinucleotide sequence context of SBS on the genomic sequence</center></B><br/>Proportion of the six substitution types with their trinucleotide sequence context (total number of mutation is shown in parenthesis)<br/>" >> $outfile
228 echo "</td>" >> $outfile
229 echo "<td>" >> $outfile
230 echo "<span class="legend"><img src="Figures/Trinucleotide_Sequence_Context/$name/$name-HeatmapPercent-Genomic.png width="250""/>" >> $outfile
231 echo "<span class="legend-hidden">" >> $outfile
232 echo "<center><B>Panel 1. Trinucleotide sequence context of SBS on the genomic sequence</center></B><br/>Proportion of the six substitution types with their trinucleotide sequence context<br/>" >> $outfile
233 echo "</td>" >> $outfile
234
235 echo "</tr>" >> $outfile
236 echo "</table>" >> $outfile
237
238
239 echo "<br/><br/>" >> $outfile
240
241
242 ##############################################################
243 # Trinucleotide sequence context of SBS on coding sequence #
244 ##############################################################
245 echo "<table>" >> $outfile
246 echo "<h3>Stranded analysis of trinucleotide sequence context of SBS</h3>" >> $outfile
247 echo "<tr>" >> $outfile
248 echo "<td> <center> <a href="Figures/Stranded_Analysis/$name/$name-StrandedSignaturePercent.txt">$name-StrandedSignaturePercent.txt</a> </center> </td>" >> $outfile
249 echo "</tr><tr>" >> $outfile
250
251 echo "<td>" >> $outfile
252 echo "<span class="legend"><img src="Figures/Stranded_Analysis/$name/$name-StrandedSignaturePercent.png width="1300""/>" >> $outfile
253 echo "<span class="legend-hidden">" >> $outfile
254 echo "<center><B>Panel 2. Stranded analysis of trinucleotide sequence context of SBS</center></B><br/>Proportion of SBS with their trinucleotide context considering the non-transcribed and transcribed strand<br/>" >> $outfile
255 echo "</td>" >> $outfile
256 echo "</tr>" >> $outfile
257 echo "</table>" >> $outfile
258
259 echo "<br/><br/>" >> $outfile
260
261
262 #############################################
263 # Sequence logo generated with Weblogo3 #
264 #############################################
265 echo "<table>" >> $outfile
266 echo "<h3>Wider sequence context with Weblogo3</h3>" >> $outfile
267 # Legende de la figure : Panel 3. Wider sequence context on genomic strand generated with Weblogo3
268
269 # C>A
270 echo "<tr>" >> $outfile
271 if [[ ! -e "$output_dir/Mutational_Analysis/Figures/WebLogo/$name/$name-CA-Probability.png" ]]; then
272 echo "<td>WARNING: No sequence for C>A </br> </td>" >> $outfile
273 else
274 echo "<td><a href="Figures/WebLogo/$name/$name-CA.fa">$name-CA.fa</a><br/>" >> $outfile
275 echo "<img src="Figures/WebLogo/$name/$name-CA-Probability.png"/><br/></td>" >> $outfile
276 fi
277 # C>G
278 if [[ ! -e "$output_dir/Mutational_Analysis/Figures/WebLogo/$name/$name-CG-Probability.png" ]]; then
279 echo "<td> WARNING: No sequence for C>G </br> </td>" >> $outfile
280 else
281 echo "<td><a href="Figures/WebLogo/$name/$name-CG.fa">$name-CG.fa</a><br/>" >> $outfile
282 echo "<img src="Figures/WebLogo/$name/$name-CG-Probability.png"/><br/></td>" >> $outfile
283 fi
284 # C>T
285 if [[ ! -e "$output_dir/Mutational_Analysis/Figures/WebLogo/$name/$name-CT-Probability.png" ]]; then
286 echo "<td> WARNING: No sequence for C>T </br> </td>" >> $outfile
287 else
288 echo "<td><a href="Figures/WebLogo/$name/$name-CT.fa">$name-CT.fa</a><br/>" >> $outfile
289 echo "<img src="Figures/WebLogo/$name/$name-CT-Probability.png"/><br/></td>" >> $outfile
290 fi
291 echo "</tr>" >> $outfile
292
293 # T>A
294 echo "<tr>" >> $outfile
295 if [[ ! -e "$output_dir/Mutational_Analysis/Figures/WebLogo/$name/$name-TA-Probability.png" ]]; then
296 echo "<td>WARNING: No sequence for T>A </br> </td>" >> $outfile
297 else
298 echo "<td><a href="Figures/WebLogo/$name/$name-TA.fa">$name-TA.fa</a><br/>" >> $outfile
299 echo "<img src="Figures/WebLogo/$name/$name-TA-Probability.png"/><br/></td>" >> $outfile
300 fi
301 # T>C
302 if [[ ! -e "$output_dir/Mutational_Analysis/Figures/WebLogo/$name/$name-TC-Probability.png" ]]; then
303 echo "<td>WARNING: No sequence for T>C </br> </td>" >> $outfile
304 else
305 echo "<td><a href="Figures/WebLogo/$name/$name-TC.fa">$name-TC.fa</a><br/>" >> $outfile
306 echo "<img src="Figures/WebLogo/$name/$name-TC-Probability.png"/><br/></td>" >> $outfile
307 fi
308 # T>G
309 if [[ ! -e "$output_dir/Mutational_Analysis/Figures/WebLogo/$name/$name-TG-Probability.png" ]]; then
310 echo "<td>WARNING: No sequence for T>G </br> </td>" >> $outfile
311 else
312 echo "<td><a href="Figures/WebLogo/$name/$name-TG.fa">$name-TG.fa</a><br/>" >> $outfile
313 echo "<img src="Figures/WebLogo/$name/$name-TG-Probability.png"/><br/></td>" >> $outfile
314 fi
315 echo "</tr>" >> $outfile
316
317 echo "</table>" >> $outfile
318
319 echo "</body></html>" >> $outfile
320
321 done
322
323 #-------------------------------------------------------------------------------------------------------------------------------------------------------------------------#
324 # POOL DATA #
325 #-------------------------------------------------------------------------------------------------------------------------------------------------------------------------#
326 ## HMTL Link to Pool_Data
327 if [[ $parameters =~ "--pooldata" ]]; then
328 outfilePoolData="$output_dir/Mutational_Analysis/Pool_Data.html"
329 touch $outfilePoolData # Create an empty file named $outfile
330 echo "<a href='Mutational_Analysis/Pool_Data.html'>Pool_Data</a><br/>" >> $html
331
332
333 echo "<br/> <center> <h2>Mutational Spectra report for Pool_Data</h2> </center> <br/>" >> $outfilePoolData
334 echo "<html>" >> $outfilePoolData
335
336 echo "<head>" >> $outfilePoolData
337 echo "<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">" >> $outfilePoolData
338 # Link to the css style file for having a legend when we pass the mouse on the figures
339 echo "<link rel="stylesheet" href="style.css" />" >> $outfilePoolData
340 echo "</head>" >> $outfilePoolData
341
342 echo "<body>" >> $outfilePoolData
343
344 echo "<table>" >> $outfilePoolData
345 echo "<tr>" >> $outfilePoolData
346 echo "<th><h3>Overall mutation distribution</h3></th>" >> $outfilePoolData
347 echo "<th><h3>Impact on protein sequence</h3></th>" >> $outfilePoolData
348 echo "</tr><tr>" >> $outfilePoolData
349 echo "<td> <center> <a href="Figures/Overall_mutation_distribution/Pool_Data/Pool_Data-OverallMutationDistribution.txt">Pool_Data-OverallMutationDistribution.txt</a> </center> </td>" >> $outfilePoolData
350 echo "<td> <center> <a href="Figures/Impact_protein_sequence/Pool_Data/Pool_Data-DistributionExoFunc.txt">Pool_Data-DistributionExoFunc.txt</a> </center> </td>" >> $outfilePoolData
351 echo "</tr><tr>" >> $outfilePoolData
352
353 echo "<td>" >> $outfilePoolData
354 echo "<span class="legend"><img src="Figures/Overall_mutation_distribution/Pool_Data/Pool_Data-OverallMutationDistribution.png width="280""/>" >> $outfilePoolData
355 echo "<span class="legend-hidden">" >> $outfilePoolData
356 echo "<center><B>Overall Mutation Distribution</center></B><br/>Proportion of all mutation types (total count are indicated in parenthesis). For indels the counts are based on annotation retrieved from the database ExonicFunc.refGene<br/>" >> $outfilePoolData
357 echo "</td>" >> $outfilePoolData
358 echo "<td>" >> $outfilePoolData
359 echo "<span class="legend"><img src="Figures/Impact_protein_sequence/Pool_Data/Pool_Data-DistributionExoFunc.png width="400""/>" >> $outfilePoolData
360 echo "<span class="legend-hidden">" >> $outfilePoolData
361 echo "<center><B>Graph 1. Impact on protein sequence</center></B><br/>Impact of all mutations (SBS and Indel) on the protein sequence based on the ExonicFunc.refGene annotation<br/>" >> $outfilePoolData
362 echo "</td>" >> $outfilePoolData
363
364 echo "</tr>" >> $outfilePoolData
365 echo "</table>" >> $outfilePoolData
366
367 echo "<br/><br/>" >> $outfilePoolData
368
369
370 echo "<table>" >> $outfilePoolData
371 echo "<tr>" >> $outfilePoolData
372 echo "<th><h3>SBS distribution</h3></th>" >> $outfilePoolData
373 echo "<th><h3>Stranded distribution of SBS</h3></th>" >> $outfilePoolData
374 echo "</tr><tr>" >> $outfilePoolData
375 echo "<td> <center> <a href="Figures/SBS_distribution/Pool_Data/Pool_Data-SBS_distribution.txt">Pool_Data-SBS_distribution.txt</a> </center> </td>" >> $outfilePoolData
376 echo "<td> <center> <a href="Figures/Stranded_Analysis/Pool_Data/Pool_Data-StrandBias.txt">Pool_Data-StrandBias.txt</a> </center> </td>" >> $outfilePoolData
377 echo "</tr><tr>" >> $outfilePoolData
378
379 echo "<td>" >> $outfilePoolData
380 echo "<span class="legend"><img src="Figures/SBS_distribution/Pool_Data/Pool_Data-SBS_distribution.png width="550""/>" >> $outfilePoolData
381 echo "<span class="legend-hidden">" >> $outfilePoolData
382 echo "<center><B>Graph 2. SBS distribution</center></B><br/>Proportion of each type of single base substitution (SBS)<br/>" >> $outfilePoolData
383 echo "</td>" >> $outfilePoolData
384 echo "<td>" >> $outfilePoolData
385 echo "<span class="legend"><img src="Figures/Stranded_Analysis/Pool_Data/Pool_Data-StrandBias.png width="400""/>" >> $outfilePoolData
386 echo "<span class="legend-hidden">" >> $outfilePoolData
387 echo "<center><B>Graph 3. Stranded distribution of SBS</center></B><br/>Count of the six substitution types on the transcribed and non-transcribed strand<br/>" >> $outfilePoolData
388 echo "</td>" >> $outfilePoolData
389
390 echo "</tr>" >> $outfilePoolData
391 echo "</table>" >> $outfilePoolData
392
393
394 echo "<br/><br/>" >> $outfilePoolData
395
396
397 ##########################################################
398 # Trinucleotide sequence context of SBS on genomic: Pool #
399 ##########################################################
400 echo "<table>" >> $outfilePoolData
401 echo "<h3>Trinucleotide sequence context of SBS on the genomic sequence</h3>" >> $outfilePoolData
402 echo "<tr>" >> $outfilePoolData
403 echo "<td> <center> <a href="Figures/Trinucleotide_Sequence_Context/Pool_Data/Pool_Data-MutationSpectraPercent-Genomic.txt">Pool_Data-MutationSpectraPercent.txt</a> </center> </td>" >> $outfilePoolData
404 echo "<td> <center> <a href="Figures/Trinucleotide_Sequence_Context/Pool_Data/Pool_Data-HeatmapPercent-Genomic.txt">Pool_Data-HeatmapPercent-Genomic.txt</a> </center> </td>" >> $outfilePoolData
405 echo "</tr><tr>" >> $outfilePoolData
406
407 echo "<td>" >> $outfilePoolData
408 echo "<span class="legend"><img src="Figures/Trinucleotide_Sequence_Context/Pool_Data/Pool_Data-MutationSpectraPercent-Genomic.png width="1000""/>" >> $outfilePoolData
409 echo "<span class="legend-hidden">" >> $outfilePoolData
410 echo "<center><B>Panel 1. Trinucleotide sequence context of SBS on the genomic sequence</center></B><br/>Proportion of the six substitution types with their trinucleotide sequence context (total number of mutation is shown in parenthesis)<br/>" >> $outfilePoolData
411 echo "</td>" >> $outfilePoolData
412 echo "<td>" >> $outfilePoolData
413 echo "<span class="legend"><img src="Figures/Trinucleotide_Sequence_Context/Pool_Data/Pool_Data-HeatmapPercent-Genomic.png width="250""/>" >> $outfilePoolData
414 echo "<span class="legend-hidden">" >> $outfilePoolData
415 echo "<center><B>Panel 1. Trinucleotide sequence context of SBS on the genomic sequence</center></B><br/>Proportion of the six substitution types with their trinucleotide sequence context<br/>" >> $outfilePoolData
416 echo "</td>" >> $outfilePoolData
417
418 echo "</tr>" >> $outfilePoolData
419 echo "</table>" >> $outfilePoolData
420
421
422 echo "<br/><br/>" >> $outfilePoolData
423
424
425 ##################################################################
426 # Trinucleotide sequence context of SBS on coding sequence: Pool #
427 ##################################################################
428 echo "<table>" >> $outfilePoolData
429 echo "<h3>Stranded analysis of trinucleotide sequence context of SBS</h3>" >> $outfilePoolData
430 echo "<tr>" >> $outfilePoolData
431 echo "<td> <center> <a href="Figures/Stranded_Analysis/Pool_Data/Pool_Data-StrandedSignaturePercent.txt">Pool_Data-StrandedSignaturePercent.txt</a> </center> </td>" >> $outfilePoolData
432 echo "</tr><tr>" >> $outfilePoolData
433
434 echo "<td>" >> $outfilePoolData
435 echo "<span class="legend"><img src="Figures/Stranded_Analysis/Pool_Data/Pool_Data-StrandedSignaturePercent.png width="1300""/>" >> $outfilePoolData
436 echo "<span class="legend-hidden">" >> $outfilePoolData
437 echo "<center><B>Panel 2. Stranded analysis of trinucleotide sequence context of SBS</center></B><br/>Proportion of SBS with their trinucleotide context considering the non-transcribed and transcribed strand<br/>" >> $outfilePoolData
438 echo "</td>" >> $outfilePoolData
439 echo "</tr>" >> $outfilePoolData
440 echo "</table>" >> $outfilePoolData
441
442 echo "<br/><br/>" >> $outfilePoolData
443
444 #####################################################
445 # Sequence logo generated with Weblogo3: Pool #
446 #####################################################
447 echo "<table>" >> $outfilePoolData
448 echo "<h3>Sequence logo generated with Weblogo3</h3>" >> $outfilePoolData
449 # C>A
450 echo "<tr>" >> $outfilePoolData
451 if [[ ! -e "$output_dir/Mutational_Analysis/Figures/WebLogo/Pool_Data/Pool_Data-CA-Probability.png" ]]; then
452 echo "<td>WARNING: No sequence for C>A </br> </td>" >> $outfilePoolData
453 else
454 echo "<td><a href="Figures/WebLogo/Pool_Data/Pool_Data-CA.fa">Pool_Data-CA.fa</a><br/>" >> $outfilePoolData
455 echo "<img src="Figures/WebLogo/Pool_Data/Pool_Data-CA-Probability.png"/><br/></td>" >> $outfilePoolData
456 fi
457 # C>G
458 if [[ ! -e "$output_dir/Mutational_Analysis/Figures/WebLogo/Pool_Data/Pool_Data-CG-Probability.png" ]]; then
459 echo "<td>WARNING: No sequence for C>G </br> </td>" >> $outfilePoolData
460 else
461 echo "<td><a href="Figures/WebLogo/Pool_Data/Pool_Data-CG.fa">Pool_Data-CG.fa</a><br/>" >> $outfilePoolData
462 echo "<img src="Figures/WebLogo/Pool_Data/Pool_Data-CG-Probability.png"/><br/></td>" >> $outfilePoolData
463 fi
464 # C>T
465 if [[ ! -e "$output_dir/Mutational_Analysis/Figures/WebLogo/Pool_Data/Pool_Data-CT-Probability.png" ]]; then
466 echo "<td>WARNING: No sequence for C>T </br> </td>" >> $outfilePoolData
467 else
468 echo "<td><a href="Figures/WebLogo/Pool_Data/Pool_Data-CT.fa">Pool_Data-CT.fa</a><br/>" >> $outfilePoolData
469 echo "<img src="Figures/WebLogo/Pool_Data/Pool_Data-CT-Probability.png"/><br/></td>" >> $outfilePoolData
470 fi
471 echo "</tr>" >> $outfilePoolData
472
473 # T>A
474 echo "<tr>" >> $outfilePoolData
475 if [[ ! -e "$output_dir/Mutational_Analysis/Figures/WebLogo/Pool_Data/Pool_Data-TA-Probability.png" ]]; then
476 echo "<td>WARNING: No sequence for T>A </br> </td>" >> $outfilePoolData
477 else
478 echo "<td><a href="Figures/WebLogo/Pool_Data/Pool_Data-TA.fa">Pool_Data-TA.fa</a><br/>" >> $outfilePoolData
479 echo "<img src="Figures/WebLogo/Pool_Data/Pool_Data-TA-Probability.png"/><br/></td>" >> $outfilePoolData
480 fi
481 # T>C
482 if [[ ! -e "$output_dir/Mutational_Analysis/Figures/WebLogo/Pool_Data/Pool_Data-TC-Probability.png" ]]; then
483 echo "<td>WARNING: No sequence for T>C </br> </td>" >> $outfilePoolData
484 else
485 echo "<td><a href="Figures/WebLogo/Pool_Data/Pool_Data-TC.fa">Pool_Data-TC.fa</a><br/>" >> $outfilePoolData
486 echo "<img src="Figures/WebLogo/Pool_Data/Pool_Data-TC-Probability.png"/><br/></td>" >> $outfilePoolData
487 fi
488 # T>G
489 if [[ ! -e "$output_dir/Mutational_Analysis/Figures/WebLogo/Pool_Data/Pool_Data-TG-Probability.png" ]]; then
490 echo "<td>WARNING: No sequence for T>G </br> </td>" >> $outfilePoolData
491 else
492 echo "<td><a href="Figures/WebLogo/Pool_Data/Pool_Data-TG.fa">Pool_Data-TG.fa</a><br/>" >> $outfilePoolData
493 echo "<img src="Figures/WebLogo/Pool_Data/Pool_Data-TG-Probability.png"/><br/></td>" >> $outfilePoolData
494 fi
495 echo "</tr>" >> $outfilePoolData
496 echo "</table>" >> $outfilePoolData
497
498 echo "</body></html>" >> $outfilePoolData
499
500 fi # End if --poolData
501
502 fi # End if [ -d $output_dir/Mutational_Analysis/Figures ]
503
504 echo "</body></html>" >> $html
505
506 exit 0
507