Mercurial > repos > davidvanzessen > shm_csr

comparison wrapper.sh @ 43:77a7ac76c7b9 draft

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Uploaded
author davidvanzessen
date Tue, 11 Apr 2017 08:02:17 -0400
parents 1cf60ae234b4
children b66e8946ba75
comparison
equal deleted inserted replaced
42:1cf60ae234b4 43:77a7ac76c7b9
174 174
175 classes="IGA,IGA1,IGA2,IGG,IGG1,IGG2,IGG3,IGG4,IGM,IGE,unmatched" 175 classes="IGA,IGA1,IGA2,IGG,IGG1,IGG2,IGG3,IGG4,IGM,IGE,unmatched"
176 echo "R mutation analysis" 176 echo "R mutation analysis"
177 Rscript $dir/shm_csr.r $outdir/merged.txt $classes $outdir ${empty_region_filter} 2>&1 177 Rscript $dir/shm_csr.r $outdir/merged.txt $classes $outdir ${empty_region_filter} 2>&1
178 178
179 echo "---------------- plot_pdfs.r ----------------"
180 echo "---------------- plot_pdfs.r ----------------<br />" >> $log
181
182 echo "Rscript $dir/shm_csr.r $outdir/pdfplots.RData $outdir 2>&1"
183
184 Rscript $dir/plot_pdf.r "$outdir/pdfplots.RData" "$outdir" 2>&1
185
179 echo "---------------- shm_csr.py ----------------" 186 echo "---------------- shm_csr.py ----------------"
180 echo "---------------- shm_csr.py ----------------<br />" >> $log 187 echo "---------------- shm_csr.py ----------------<br />" >> $log
181 188
182 python $dir/shm_csr.py --input $outdir/merged.txt --genes $classes --empty_region_filter "${empty_region_filter}" --output $outdir/hotspot_analysis.txt 189 python $dir/shm_csr.py --input $outdir/merged.txt --genes $classes --empty_region_filter "${empty_region_filter}" --output $outdir/hotspot_analysis.txt
183 190
247 cat $outdir/mutations_${func}.txt $outdir/hotspot_analysis_${func}.txt > $outdir/data_${func}.txt 254 cat $outdir/mutations_${func}.txt $outdir/hotspot_analysis_${func}.txt > $outdir/data_${func}.txt
248 255
249 echo "---------------- pattern_plots.r ----------------" 256 echo "---------------- pattern_plots.r ----------------"
250 echo "---------------- pattern_plots.r ----------------<br />" >> $log 257 echo "---------------- pattern_plots.r ----------------<br />" >> $log
251 258
252 Rscript $dir/pattern_plots.r $outdir/data_${func}.txt $outdir/aid_motives $outdir/relative_mutations $outdir/abolute_mutations $outdir/shm_overview.txt 2>&1 259 Rscript $dir/pattern_plots.r $outdir/data_${func}.txt $outdir/aid_motives $outdir/relative_mutations $outdir/absolute_mutations $outdir/shm_overview.txt 2>&1
253 260
254 echo "<table class='pure-table pure-table-striped'>" >> $output 261 echo "<table class='pure-table pure-table-striped'>" >> $output
255 echo "<thead><tr><th>info</th>" >> $output 262 echo "<thead><tr><th>info</th>" >> $output
256 263
257 if [ "${class_filter}" != "101_101" ] ; then 264 if [ "${class_filter}" != "101_101" ] ; then
298 #echo "<a href='data_${func}.txt'>Download data</a>" >> $output 305 #echo "<a href='data_${func}.txt'>Download data</a>" >> $output
299 done 306 done
300 307
301 echo "<a href='aid_motives.pdf'><img src='aid_motives.png' /></a><br />" >> $output 308 echo "<a href='aid_motives.pdf'><img src='aid_motives.png' /></a><br />" >> $output
302 echo "<a href='relative_mutations.pdf'><img src='relative_mutations.png' /></a><br />" >> $output 309 echo "<a href='relative_mutations.pdf'><img src='relative_mutations.png' /></a><br />" >> $output
303 echo "<a href='abolute_mutations.pdf'><img src='abolute_mutations.png' /></a><br />" >> $output 310 echo "<a href='absolute_mutations.pdf'><img src='absolute_mutations.png' /></a><br />" >> $output
304 echo "<br />" >> $output 311 echo "<br />" >> $output
305 cat $dir/shm_overview.htm >> $output 312 cat $dir/shm_overview.htm >> $output
306 echo "</div>" >> $output #SHM overview tab end 313 echo "</div>" >> $output #SHM overview tab end
307 314
308 echo "---------------- images ----------------" 315 echo "---------------- images ----------------"
655 echo "<tr><td>Motif data per sequence ID</td><td><a href='motif_per_seq.txt' download='motif_per_seq.txt' >Download</a></td></tr>" >> $output 662 echo "<tr><td>Motif data per sequence ID</td><td><a href='motif_per_seq.txt' download='motif_per_seq.txt' >Download</a></td></tr>" >> $output
656 echo "<tr><td>Mutation data per sequence ID</td><td><a href='mutation_by_id.txt' download='mutation_by_id.txt' >Download</a></td></tr>" >> $output 663 echo "<tr><td>Mutation data per sequence ID</td><td><a href='mutation_by_id.txt' download='mutation_by_id.txt' >Download</a></td></tr>" >> $output
657 echo "<tr><td>Base count for every sequence</td><td><a href='base_overview.html'>View</a></td></tr>" >> $output 664 echo "<tr><td>Base count for every sequence</td><td><a href='base_overview.html'>View</a></td></tr>" >> $output
658 echo "<tr><td>The data used to generate the percentage of mutations in AID and pol eta motives plot</td><td><a href='aid_motives.txt' download='aid_motives.txt' >Download</a></td></tr>" >> $output 665 echo "<tr><td>The data used to generate the percentage of mutations in AID and pol eta motives plot</td><td><a href='aid_motives.txt' download='aid_motives.txt' >Download</a></td></tr>" >> $output
659 echo "<tr><td>The data used to generate the relative mutation patterns plot</td><td><a href='relative_mutations.txt' download='relative_mutations.txt' >Download</a></td></tr>" >> $output 666 echo "<tr><td>The data used to generate the relative mutation patterns plot</td><td><a href='relative_mutations.txt' download='relative_mutations.txt' >Download</a></td></tr>" >> $output
660 echo "<tr><td>The data used to generate the absolute mutation patterns plot</td><td><a href='absolute_mutations.txt' download='abolute_mutations.txt' >Download</a></td></tr>" >> $output 667 echo "<tr><td>The data used to generate the absolute mutation patterns plot</td><td><a href='absolute_mutations.txt' download='absolute_mutations.txt' >Download</a></td></tr>" >> $output
661 668
662 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>SHM Frequency</td></tr>" >> $output 669 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>SHM Frequency</td></tr>" >> $output
663 echo "<tr><td>The data generate the frequency scatter plot</td><td><a href='scatter.txt' download='scatter.txt' >Download</a></td></tr>" >> $output 670 echo "<tr><td>The data generate the frequency scatter plot</td><td><a href='scatter.txt' download='scatter.txt' >Download</a></td></tr>" >> $output
664 echo "<tr><td>The data used to generate the frequency by class plot</td><td><a href='frequency_ranges_classes.txt' download='frequency_ranges_classes.txt' >Download</a></td></tr>" >> $output 671 echo "<tr><td>The data used to generate the frequency by class plot</td><td><a href='frequency_ranges_classes.txt' download='frequency_ranges_classes.txt' >Download</a></td></tr>" >> $output
665 echo "<tr><td>The data for frequency by subclass</td><td><a href='frequency_ranges_subclasses.txt' download='frequency_ranges_subclasses.txt' >Download</a></td></tr>" >> $output 672 echo "<tr><td>The data for frequency by subclass</td><td><a href='frequency_ranges_subclasses.txt' download='frequency_ranges_subclasses.txt' >Download</a></td></tr>" >> $output