Mercurial > repos > davidvanzessen > mutation_analysis

comparison wrapper.sh @ 121:31cca6d3722a draft

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Uploaded
author davidvanzessen
date Wed, 17 Aug 2016 07:30:32 -0400
parents 613278c1bde0
children 3d64b3efd352
comparison
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120:613278c1bde0 121:31cca6d3722a
193 echo "---------------- sequence_overview.r ----------------" 193 echo "---------------- sequence_overview.r ----------------"
194 echo "---------------- sequence_overview.r ----------------<br />" >> $log 194 echo "---------------- sequence_overview.r ----------------<br />" >> $log
195 195
196 mkdir $outdir/sequence_overview 196 mkdir $outdir/sequence_overview
197 197
198 #Rscript $dir/sequence_overview.r $outdir/identified_genes.txt $PWD/sequences.txt $outdir/merged.txt $outdir/sequence_overview $classes $outdir/hotspot_analysis_sum.txt 2>&1
199 Rscript $dir/sequence_overview.r $outdir/before_unique_filter.txt $outdir/merged.txt $outdir/sequence_overview $classes $outdir/hotspot_analysis_sum.txt 2>&1 198 Rscript $dir/sequence_overview.r $outdir/before_unique_filter.txt $outdir/merged.txt $outdir/sequence_overview $classes $outdir/hotspot_analysis_sum.txt 2>&1
200 199
201 echo "<table border='1'>" > $outdir/base_overview.html 200 echo "<table border='1'>" > $outdir/base_overview.html
202 201
203 while IFS=$'\t' read ID class seq A C G T 202 while IFS=$'\t' read ID class seq A C G T
204 do 203 do
205 echo "<tr><td>$ID</td><td>$seq</td><td>$class</td><td>$A</td><td>$C</td><td>$G</td><td>$T</td></tr>" >> $outdir/base_overview.html 204 echo "<tr><td>$ID</td><td>$seq</td><td>$class</td><td>$A</td><td>$C</td><td>$G</td><td>$T</td></tr>" >> $outdir/base_overview.html
206 done < $outdir/sequence_overview/ntoverview.txt 205 done < $outdir/sequence_overview/ntoverview.txt
207 206
208 echo "<html><center><h1>$title</h1></center>" > $output 207 echo "<html><center><h1>$title</h1></center>" > $output
208 echo "<meta name='viewport' content='width=device-width, initial-scale=1'>" >> $output
209 echo "<script type='text/javascript' src='jquery-1.11.0.min.js'></script>" >> $output 209 echo "<script type='text/javascript' src='jquery-1.11.0.min.js'></script>" >> $output
210 echo "<script type='text/javascript' src='tabber.js'></script>" >> $output 210 echo "<script type='text/javascript' src='tabber.js'></script>" >> $output
211 echo "<script type='text/javascript' src='script.js'></script>" >> $output 211 echo "<script type='text/javascript' src='script.js'></script>" >> $output
212 echo "<link rel='stylesheet' type='text/css' href='style.css'>" >> $output 212 echo "<link rel='stylesheet' type='text/css' href='style.css'>" >> $output
213 213 echo "<link rel='stylesheet' href='http://yui.yahooapis.com/pure/0.6.0/pure-min.css'>" >> $output
214 #display the matched/unmatched for clearity
215 214
216 matched_count="`cat $outdir/merged.txt | grep -v 'unmatched' | tail -n +2 | wc -l`" 215 matched_count="`cat $outdir/merged.txt | grep -v 'unmatched' | tail -n +2 | wc -l`"
217 unmatched_count="`cat $outdir/unmatched.txt | tail -n +2 | wc -l`" 216 unmatched_count="`cat $outdir/unmatched.txt | tail -n +2 | wc -l`"
218 total_count=$((matched_count + unmatched_count)) 217 total_count=$((matched_count + unmatched_count))
219 perc_count=$((unmatched_count / total_count * 100)) 218 perc_count=$((unmatched_count / total_count * 100))
236 echo "---------------- $func table ----------------" 235 echo "---------------- $func table ----------------"
237 echo "---------------- $func table ----------------<br />" >> $log 236 echo "---------------- $func table ----------------<br />" >> $log
238 237
239 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
240 239
241 echo "<table border='1' width='100%'><caption><h3><a href='data_${func}.txt'>${func} table</a></h3></caption>" >> $output 240 echo "<table class='pure-table pure-table-striped'>" >> $output
242 echo "<tr><th>info</th>" >> $output 241 echo "<thead><tr><th>info</th>" >> $output
243 for gene in ${genes[@]} 242 for gene in ${genes[@]}
244 do 243 do
245 tmp=`cat $outdir/${gene}_${func}_n.txt` 244 tmp=`cat $outdir/${gene}_${func}_n.txt`
246 echo "<th><a href='matched_${gene}_${func}.txt'>${gene} (N = $tmp)</a></th>" >> $output 245 echo "<th><a href='matched_${gene}_${func}.txt'>${gene} (N = $tmp)</a></th>" >> $output
247 done 246 done
248 247
249 tmp=`cat $outdir/all_${func}_n.txt` 248 tmp=`cat $outdir/all_${func}_n.txt`
250 echo "<th><a href='matched_all_${func}.txt'>all (N = $tmp)</a></th>" >> $output 249 echo "<th><a href='matched_all_${func}.txt'>all (N = $tmp)</a></th>" >> $output
251 tmp=`cat $outdir/unmatched_${func}_n.txt` 250 tmp=`cat $outdir/unmatched_${func}_n.txt`
252 echo "<th><a href='unmatched.txt'>unmatched (N = ${unmatched_count})</a></th>" >> $output 251 echo "<th><a href='unmatched.txt'>unmatched (N = ${unmatched_count})</a></th><tr></thead>" >> $output
253 252
254 while IFS=, read name cax cay caz ca1x ca1y ca1z ca2x ca2y ca2z cgx cgy cgz cg1x cg1y cg1z cg2x cg2y cg2z cg3x cg3y cg3z cg4x cg4y cg4z cmx cmy cmz unx uny unz allx ally allz 253 while IFS=, read name cax cay caz ca1x ca1y ca1z ca2x ca2y ca2z cgx cgy cgz cg1x cg1y cg1z cg2x cg2y cg2z cg3x cg3y cg3z cg4x cg4y cg4z cmx cmy cmz unx uny unz allx ally allz
255 do 254 do
256 if [ "$name" == "FR S/R (ratio)" ] || [ "$name" == "CDR S/R (ratio)" ] ; then #meh 255 if [ "$name" == "FR S/R (ratio)" ] || [ "$name" == "CDR S/R (ratio)" ] ; then #meh
257 echo "<tr><td>$name</td><td>${cax}/${cay} (${caz})</td><td>${ca1x}/${ca1y} (${ca1z})</td><td>${ca2x}/${ca2y} (${ca2z})</td><td>${cgx}/${cgy} (${cgz})</td><td>${cg1x}/${cg1y} (${cg1z})</td><td>${cg2x}/${cg2y} (${cg2z})</td><td>${cg3x}/${cg3y} (${cg3z})</td><td>${cg4x}/${cg4y} (${cg4z})</td><td>${cmx}/${cmy} (${cmz})</td><td>${allx}/${ally} (${allz})</td></tr>" >> $output 256 echo "<tr><td>$name</td><td>${cax}/${cay} (${caz})</td><td>${ca1x}/${ca1y} (${ca1z})</td><td>${ca2x}/${ca2y} (${ca2z})</td><td>${cgx}/${cgy} (${cgz})</td><td>${cg1x}/${cg1y} (${cg1z})</td><td>${cg2x}/${cg2y} (${cg2z})</td><td>${cg3x}/${cg3y} (${cg3z})</td><td>${cg4x}/${cg4y} (${cg4z})</td><td>${cmx}/${cmy} (${cmz})</td><td>${allx}/${ally} (${allz})</td></tr>" >> $output
292 do 291 do
293 echo "<tr>" >> $output 292 echo "<tr>" >> $output
294 echo "<td><h1>${gene}</h1></td>" >> $output 293 echo "<td><h1>${gene}</h1></td>" >> $output
295 echo "<td><img src='transitions_heatmap_${gene}.png' /></td>" >> $output 294 echo "<td><img src='transitions_heatmap_${gene}.png' /></td>" >> $output
296 echo "<td><img src='transitions_stacked_${gene}.png' /></td>" >> $output 295 echo "<td><img src='transitions_stacked_${gene}.png' /></td>" >> $output
297 echo "<td><table border='1'>" >> $output 296 echo "<td><table class='pure-table transition-table pure-table-bordered'>" >> $output
298 while IFS=, read from a c g t 297 while IFS=, read from a c g t
299 do 298 do
300 echo "<tr><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output 299 echo "<tr><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
301 done < $outdir/transitions_${gene}_sum.txt 300 done < $outdir/transitions_${gene}_sum.txt
302 echo "</table></td>" >> $output 301 echo "</table></td>" >> $output
306 305
307 echo "<tr>" >> $output 306 echo "<tr>" >> $output
308 echo "<td><h1>All</h1></td>" >> $output 307 echo "<td><h1>All</h1></td>" >> $output
309 echo "<td><img src='transitions_heatmap_all.png' /></td>" >> $output 308 echo "<td><img src='transitions_heatmap_all.png' /></td>" >> $output
310 echo "<td><img src='transitions_stacked_all.png' /></td>" >> $output 309 echo "<td><img src='transitions_stacked_all.png' /></td>" >> $output
311 echo "<td><table border='1'>" >> $output 310 echo "<td><table class='pure-table transition-table pure-table-bordered'>" >> $output
312 while IFS=, read from a c g t 311 while IFS=, read from a c g t
313 do 312 do
314 echo "<tr><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output 313 echo "<tr><td>$from</td><td>$a</td><td>$c</td><td>$g</td><td>$t</td></tr>" >> $output
315 done < $outdir/transitions_all_sum.txt 314 done < $outdir/transitions_all_sum.txt
316 echo "</table></td>" >> $output 315 echo "</table></td>" >> $output
356 355
357 echo "</div>" >> $output #CSR tab end 356 echo "</div>" >> $output #CSR tab end
358 357
359 echo "<div class='tabbertab' title='Downloads'>" >> $output 358 echo "<div class='tabbertab' title='Downloads'>" >> $output
360 359
361 echo "<table border='1' width='700px'>" >> $output 360 echo "<table class='pure-table pure-table-striped'>" >> $output
361 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 362 echo "<tr><td>The complete dataset</td><td><a href='merged.txt'>Download</a></td></tr>" >> $output
363 echo "<tr><td>The alignment info on the unmatched sequences</td><td><a href='unmatched.txt'>Download</a></td></tr>" >> $output 363 echo "<tr><td>The alignment info on the unmatched sequences</td><td><a href='unmatched.txt'>Download</a></td></tr>" >> $output
364 echo "<tr><td>Motif data per sequence ID</td><td><a href='motif_per_seq.txt'>Download</a></td></tr>" >> $output 364 echo "<tr><td>Motif data per sequence ID</td><td><a href='motif_per_seq.txt'>Download</a></td></tr>" >> $output
365 echo "<tr><td>Mutation data per sequence ID</td><td><a href='mutation_by_id.txt'>Download</a></td></tr>" >> $output 365 echo "<tr><td>Mutation data per sequence ID</td><td><a href='mutation_by_id.txt'>Download</a></td></tr>" >> $output
366 echo "<tr><td>AA mutation data per sequence ID</td><td><a href='aa_id_mutations.txt'>Download</a></td></tr>" >> $output 366 echo "<tr><td>AA mutation data per sequence ID</td><td><a href='aa_id_mutations.txt'>Download</a></td></tr>" >> $output
367 echo "<tr><td>Absent AA location data per sequence ID</td><td><a href='absent_aa_id.txt'>Download</a></td></tr>" >> $output 367 echo "<tr><td>Absent AA location data per sequence ID</td><td><a href='absent_aa_id.txt'>Download</a></td></tr>" >> $output
368 echo "<tr><td>CDR1+FR2+CDR2+FR3+CDR3 sequences that show up more than once</td><td><a href='sequence_overview/index.html'>Download</a></td></tr>" >> $output 368 echo "<tr><td>CDR1+FR2+CDR2+FR3+CDR3 sequences that show up more than once</td><td><a href='sequence_overview/index.html'>Download</a></td></tr>" >> $output
369 echo "<tr><td>Base count for every sequence</td><td><a href='base_overview.html'>Download</a></td></tr>" >> $output 369 echo "<tr><td>Base count for every sequence</td><td><a href='base_overview.html'>Download</a></td></tr>" >> $output
370 echo "<tr><td>Baseline PDF (<href a='http://selection.med.yale.edu/baseline/'>http://selection.med.yale.edu/baseline/</a>)</td><td><a href='baseline.pdf'>Download</a></td></tr>" >> $output 370 echo "<tr><td>Baseline PDF (<a href='http://selection.med.yale.edu/baseline/'>http://selection.med.yale.edu/baseline/</a>)</td><td><a href='baseline.pdf'>Download</a></td></tr>" >> $output
371 echo "<tr><td>Baseline data</td><td><a href='baseline.txt'>Download</a></td></tr>" >> $output 371 echo "<tr><td>Baseline data</td><td><a href='baseline.txt'>Download</a></td></tr>" >> $output
372 echo "<tr><td>Baseline ca PDF</td><td><a href='baseline_ca.pdf'>Download</a></td></tr>" >> $output 372 echo "<tr><td>Baseline ca PDF</td><td><a href='baseline_ca.pdf'>Download</a></td></tr>" >> $output
373 echo "<tr><td>Baseline ca data</td><td><a href='baseline_ca.txt'>Download</a></td></tr>" >> $output 373 echo "<tr><td>Baseline ca data</td><td><a href='baseline_ca.txt'>Download</a></td></tr>" >> $output
374 echo "<tr><td>Baseline cg PDF</td><td><a href='baseline_cg.pdf'>Download</a></td></tr>" >> $output 374 echo "<tr><td>Baseline cg PDF</td><td><a href='baseline_cg.pdf'>Download</a></td></tr>" >> $output
375 echo "<tr><td>Baseline cg data</td><td><a href='baseline_cg.txt'>Download</a></td></tr>" >> $output 375 echo "<tr><td>Baseline cg data</td><td><a href='baseline_cg.txt'>Download</a></td></tr>" >> $output