Mercurial > repos > davidvanzessen > mutation_analysis

comparison wrapper.sh @ 124:4a93146f87aa draft

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Uploaded
author davidvanzessen
date Mon, 22 Aug 2016 09:11:17 -0400
parents 0453ea4d9f14
children e87dcca14bd6
comparison
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123:0453ea4d9f14 124:4a93146f87aa
235 echo "---------------- $func table ----------------" 235 echo "---------------- $func table ----------------"
236 echo "---------------- $func table ----------------<br />" >> $log 236 echo "---------------- $func table ----------------<br />" >> $log
237 237
238 cat $outdir/mutations_${func}.txt $outdir/hotspot_analysis_${func}.txt > $outdir/data_${func}.txt 238 cat $outdir/mutations_${func}.txt $outdir/hotspot_analysis_${func}.txt > $outdir/data_${func}.txt
239 239
240 echo "---------------- pattern_plots.r ----------------"
241 echo "---------------- pattern_plots.r ----------------<br />" >> $log
242
243 Rscript $dir/pattern_plots.r $outdir/data_${func}.txt $outdir/plot1 $outdir/plot2 $outdir/plot3 2>&1
244
240 echo "<table class='pure-table pure-table-striped'>" >> $output 245 echo "<table class='pure-table pure-table-striped'>" >> $output
241 echo "<thead><tr><th>info</th>" >> $output 246 echo "<thead><tr><th>info</th>" >> $output
242 for gene in ${genes[@]} 247 for gene in ${genes[@]}
243 do 248 do
244 tmp=`cat $outdir/${gene}_${func}_n.txt` 249 tmp=`cat $outdir/${gene}_${func}_n.txt`
259 fi 264 fi
260 done < $outdir/data_${func}.txt 265 done < $outdir/data_${func}.txt
261 echo "</table>" >> $output 266 echo "</table>" >> $output
262 #echo "<a href='data_${func}.txt'>Download data</a>" >> $output 267 #echo "<a href='data_${func}.txt'>Download data</a>" >> $output
263 done 268 done
269
270 echo "<img src='plot1.png' /><br />" >> $output
271 echo "<img src='plot2.png' /><br />" >> $output
272 echo "<img src='plot3.png' /><br />" >> $output
264 273
265 echo "</div>" >> $output #SHM overview tab end 274 echo "</div>" >> $output #SHM overview tab end
266 275
267 echo "---------------- images ----------------" 276 echo "---------------- images ----------------"
268 echo "---------------- images ----------------<br />" >> $log 277 echo "---------------- images ----------------<br />" >> $log
359 368
360 echo "<table class='pure-table pure-table-striped'>" >> $output 369 echo "<table class='pure-table pure-table-striped'>" >> $output
361 echo "<thead><tr><th>info</th><th>link</th></tr></thead>" >> $output 370 echo "<thead><tr><th>info</th><th>link</th></tr></thead>" >> $output
362 echo "<tr><td>The complete dataset</td><td><a href='merged.txt'>Download</a></td></tr>" >> $output 371 echo "<tr><td>The complete dataset</td><td><a href='merged.txt'>Download</a></td></tr>" >> $output
363 echo "<tr><td>The SHM Overview table as a dataset</td><td><a href='data_sum.txt'>Download</a></td></tr>" >> $output 372 echo "<tr><td>The SHM Overview table as a dataset</td><td><a href='data_sum.txt'>Download</a></td></tr>" >> $output
373 echo "<tr><td>The data used to generate the first SHM Overview plot</td><td><a href='plot1.txt'>Download</a></td></tr>" >> $output
374 echo "<tr><td>The data used to generate the sexond SHM Overview plot</td><td><a href='plot2.txt'>Download</a></td></tr>" >> $output
375 echo "<tr><td>The data used to generate the third SHM Overview plot</td><td><a href='plot3.txt'>Download</a></td></tr>" >> $output
364 echo "<tr><td>The alignment info on the unmatched sequences</td><td><a href='unmatched.txt'>Download</a></td></tr>" >> $output 376 echo "<tr><td>The alignment info on the unmatched sequences</td><td><a href='unmatched.txt'>Download</a></td></tr>" >> $output
365 echo "<tr><td>Motif data per sequence ID</td><td><a href='motif_per_seq.txt'>Download</a></td></tr>" >> $output 377 echo "<tr><td>Motif data per sequence ID</td><td><a href='motif_per_seq.txt'>Download</a></td></tr>" >> $output
366 echo "<tr><td>Mutation data per sequence ID</td><td><a href='mutation_by_id.txt'>Download</a></td></tr>" >> $output 378 echo "<tr><td>Mutation data per sequence ID</td><td><a href='mutation_by_id.txt'>Download</a></td></tr>" >> $output
367 echo "<tr><td>AA mutation data per sequence ID</td><td><a href='aa_id_mutations.txt'>Download</a></td></tr>" >> $output 379 echo "<tr><td>AA mutation data per sequence ID</td><td><a href='aa_id_mutations.txt'>Download</a></td></tr>" >> $output
368 echo "<tr><td>Absent AA location data per sequence ID</td><td><a href='absent_aa_id.txt'>Download</a></td></tr>" >> $output 380 echo "<tr><td>Absent AA location data per sequence ID</td><td><a href='absent_aa_id.txt'>Download</a></td></tr>" >> $output