Mercurial > repos > davidvanzessen > mutation_analysis

comparison wrapper.sh @ 125:e87dcca14bd6 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author davidvanzessen
date Mon, 29 Aug 2016 03:28:49 -0400
parents 4a93146f87aa
children ffd5462da9d1
comparison
equal deleted inserted replaced
124:4a93146f87aa 125:e87dcca14bd6
372 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 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 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 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
376 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
377
377 echo "<tr><td>Motif data per sequence ID</td><td><a href='motif_per_seq.txt'>Download</a></td></tr>" >> $output 378 echo "<tr><td>Motif data per sequence ID</td><td><a href='motif_per_seq.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 379 echo "<tr><td>Mutation data per sequence ID</td><td><a href='mutation_by_id.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 380 echo "<tr><td>AA mutation data per sequence ID</td><td><a href='aa_id_mutations.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 381 echo "<tr><td>Absent AA location data per sequence ID</td><td><a href='absent_aa_id.txt'>Download</a></td></tr>" >> $output
381 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 382 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
383
382 echo "<tr><td>Base count for every sequence</td><td><a href='base_overview.html'>Download</a></td></tr>" >> $output 384 echo "<tr><td>Base count for every sequence</td><td><a href='base_overview.html'>Download</a></td></tr>" >> $output
385
383 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 386 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
384 echo "<tr><td>Baseline data</td><td><a href='baseline.txt'>Download</a></td></tr>" >> $output 387 echo "<tr><td>Baseline data</td><td><a href='baseline.txt'>Download</a></td></tr>" >> $output
385 echo "<tr><td>Baseline ca PDF</td><td><a href='baseline_ca.pdf'>Download</a></td></tr>" >> $output 388 echo "<tr><td>Baseline ca PDF</td><td><a href='baseline_ca.pdf'>Download</a></td></tr>" >> $output
386 echo "<tr><td>Baseline ca data</td><td><a href='baseline_ca.txt'>Download</a></td></tr>" >> $output 389 echo "<tr><td>Baseline ca data</td><td><a href='baseline_ca.txt'>Download</a></td></tr>" >> $output
387 echo "<tr><td>Baseline cg PDF</td><td><a href='baseline_cg.pdf'>Download</a></td></tr>" >> $output 390 echo "<tr><td>Baseline cg PDF</td><td><a href='baseline_cg.pdf'>Download</a></td></tr>" >> $output
388 echo "<tr><td>Baseline cg data</td><td><a href='baseline_cg.txt'>Download</a></td></tr>" >> $output 391 echo "<tr><td>Baseline cg data</td><td><a href='baseline_cg.txt'>Download</a></td></tr>" >> $output
389 echo "<tr><td>Baseline cm PDF</td><td><a href='baseline_cm.pdf'>Download</a></td></tr>" >> $output 392 echo "<tr><td>Baseline cm PDF</td><td><a href='baseline_cm.pdf'>Download</a></td></tr>" >> $output
390 echo "<tr><td>Baseline cm data</td><td><a href='baseline_cm.txt'>Download</a></td></tr>" >> $output 393 echo "<tr><td>Baseline cm data</td><td><a href='baseline_cm.txt'>Download</a></td></tr>" >> $output
394
391 echo "<tr><td>An IMGT archive with just the matched and filtered sequences</td><td><a href='new_IMGT.txz'>Download</a></td></tr>" >> $output 395 echo "<tr><td>An IMGT archive with just the matched and filtered sequences</td><td><a href='new_IMGT.txz'>Download</a></td></tr>" >> $output
392 echo "<tr><td>An IMGT archive with just the matched and filtered ca sequences</td><td><a href='new_IMGT_ca.txz'>Download</a></td></tr>" >> $output 396 echo "<tr><td>An IMGT archive with just the matched and filtered ca sequences</td><td><a href='new_IMGT_ca.txz'>Download</a></td></tr>" >> $output
393 echo "<tr><td>An IMGT archive with just the matched and filtered ca1 sequences</td><td><a href='new_IMGT_ca1.txz'>Download</a></td></tr>" >> $output 397 echo "<tr><td>An IMGT archive with just the matched and filtered ca1 sequences</td><td><a href='new_IMGT_ca1.txz'>Download</a></td></tr>" >> $output
394 echo "<tr><td>An IMGT archive with just the matched and filtered ca2 sequences</td><td><a href='new_IMGT_ca2.txz'>Download</a></td></tr>" >> $output 398 echo "<tr><td>An IMGT archive with just the matched and filtered ca2 sequences</td><td><a href='new_IMGT_ca2.txz'>Download</a></td></tr>" >> $output
395 echo "<tr><td>An IMGT archive with just the matched and filtered cg sequences</td><td><a href='new_IMGT_cg.txz'>Download</a></td></tr>" >> $output 399 echo "<tr><td>An IMGT archive with just the matched and filtered cg sequences</td><td><a href='new_IMGT_cg.txz'>Download</a></td></tr>" >> $output
396 echo "<tr><td>An IMGT archive with just the matched and filtered cg1 sequences</td><td><a href='new_IMGT_cg1.txz'>Download</a></td></tr>" >> $output 400 echo "<tr><td>An IMGT archive with just the matched and filtered cg1 sequences</td><td><a href='new_IMGT_cg1.txz'>Download</a></td></tr>" >> $output
397 echo "<tr><td>An IMGT archive with just the matched and filtered cg2 sequences</td><td><a href='new_IMGT_cg2.txz'>Download</a></td></tr>" >> $output 401 echo "<tr><td>An IMGT archive with just the matched and filtered cg2 sequences</td><td><a href='new_IMGT_cg2.txz'>Download</a></td></tr>" >> $output
398 echo "<tr><td>An IMGT archive with just the matched and filtered cg3 sequences</td><td><a href='new_IMGT_cg3.txz'>Download</a></td></tr>" >> $output 402 echo "<tr><td>An IMGT archive with just the matched and filtered cg3 sequences</td><td><a href='new_IMGT_cg3.txz'>Download</a></td></tr>" >> $output
399 echo "<tr><td>An IMGT archive with just the matched and filtered cg4 sequences</td><td><a href='new_IMGT_cg4.txz'>Download</a></td></tr>" >> $output 403 echo "<tr><td>An IMGT archive with just the matched and filtered cg4 sequences</td><td><a href='new_IMGT_cg4.txz'>Download</a></td></tr>" >> $output
400 echo "<tr><td>An IMGT archive with just the matched and filtered cm sequences</td><td><a href='new_IMGT_cm.txz'>Download</a></td></tr>" >> $output 404 echo "<tr><td>An IMGT archive with just the matched and filtered cm sequences</td><td><a href='new_IMGT_cm.txz'>Download</a></td></tr>" >> $output
401 echo "<tr><td>The Change-O DB file with defined clones</td><td><a href='change_o/change-o-db-defined_clones.txt'>Download</a></td></tr>" >> $output 405
406 echo "<tr><td>The Change-O DB file with defined clones and subclass annotation</td><td><a href='change_o/change-o-db-defined_clones.txt'>Download</a></td></tr>" >> $output
402 echo "<tr><td>The Change-O DB defined clones summary file</td><td><a href='change_o/change-o-defined_clones-summary.txt'>Download</a></td></tr>" >> $output 407 echo "<tr><td>The Change-O DB defined clones summary file</td><td><a href='change_o/change-o-defined_clones-summary.txt'>Download</a></td></tr>" >> $output
408 echo "<tr><td>The Change-O DB file with defined clones of ca</td><td><a href='change_o/change-o-db-defined_clones-ca.txt'>Download</a></td></tr>" >> $output
409 echo "<tr><td>The Change-O DB defined clones summary file of ca</td><td><a href='change_o/change-o-defined_clones-summary-ca.txt'>Download</a></td></tr>" >> $output
410 echo "<tr><td>The Change-O DB file with defined clones of cg</td><td><a href='change_o/change-o-db-defined_clones-cg.txt'>Download</a></td></tr>" >> $output
411 echo "<tr><td>The Change-O DB defined clones summary file of cg</td><td><a href='change_o/change-o-defined_clones-summary-cg.txt'>Download</a></td></tr>" >> $output
412 echo "<tr><td>The Change-O DB file with defined clones of cm</td><td><a href='change_o/change-o-db-defined_clones-cm.txt'>Download</a></td></tr>" >> $output
413 echo "<tr><td>The Change-O DB defined clones summary file of cm</td><td><a href='change_o/change-o-defined_clones-summary-cm.txt'>Download</a></td></tr>" >> $output
414
403 echo "</table>" >> $output 415 echo "</table>" >> $output
404 416
405 echo "</div>" >> $output #downloads tab end 417 echo "</div>" >> $output #downloads tab end
406 418
407 echo "</div>" >> $output #tabs end 419 echo "</div>" >> $output #tabs end
460 fi 472 fi
461 473
462 echo "</table>" >> $outdir/base_overview.html 474 echo "</table>" >> $outdir/base_overview.html
463 475
464 echo "---------------- change-o MakeDB ----------------" 476 echo "---------------- change-o MakeDB ----------------"
465 echo "---------------- change-o MakeDB ----------------<br />" >> $log
466 477
467 mkdir $outdir/change_o 478 mkdir $outdir/change_o
468 479
469 tmp="$PWD" 480 tmp="$PWD"
470 481
471 cd $outdir/change_o 482 cd $outdir/change_o
472 483
473 bash $dir/change_o/makedb.sh $input false false false $outdir/change_o/change-o-db.txt 484 bash $dir/change_o/makedb.sh $input false false false $outdir/change_o/change-o-db.txt
474
475 echo "---------------- change-o DefineClones ----------------"
476 echo "---------------- change-o DefineClones ----------------<br />" >> $log
477
478 bash $dir/change_o/define_clones.sh bygroup $outdir/change_o/change-o-db.txt gene first ham none min complete 3.0 $outdir/change_o/change-o-db-defined_clones.txt $outdir/change_o/change-o-defined_clones-summary.txt 485 bash $dir/change_o/define_clones.sh bygroup $outdir/change_o/change-o-db.txt gene first ham none min complete 3.0 $outdir/change_o/change-o-db-defined_clones.txt $outdir/change_o/change-o-defined_clones-summary.txt
486
487 Rscript $dir/merge.r $outdir/change_o/change-o-db-defined_clones.txt $outdir/merged.txt "all" "Sequence.ID,best_match" "SEQUENCE_ID" "Sequence.ID" $outdir/change_o/change-o-db-defined_clones.txt 2>&1
488
489 echo "Rscript $dir/merge.r $outdir/change_o/change-o-db-defined_clones.txt $outdir/$outdir/merged.txt 'all' 'Sequence.ID,best_match' 'Sequence.ID' 'Sequence.ID' '\t' $outdir/change_o/change-o-db-defined_clones.txt 2>&1"
490
491 if [[ $(wc -l < $outdir/new_IMGT_ca/1_Summary.txt) -gt "1" ]]; then
492 bash $dir/change_o/makedb.sh $outdir/new_IMGT_ca.txz false false false $outdir/change_o/change-o-db-ca.txt
493 bash $dir/change_o/define_clones.sh bygroup $outdir/change_o/change-o-db-ca.txt gene first ham none min complete 3.0 $outdir/change_o/change-o-db-defined_clones-ca.txt $outdir/change_o/change-o-defined_clones-summary-ca.txt
494 else
495 echo "No ca sequences" > "$outdir/change_o/change-o-db-defined_clones-ca.txt"
496 echo "No ca sequences" > "$outdir/change_o/change-o-defined_clones-summary-ca.txt"
497 fi
498
499 if [[ $(wc -l < $outdir/new_IMGT_cg/1_Summary.txt) -gt "1" ]]; then
500 bash $dir/change_o/makedb.sh $outdir/new_IMGT_cg.txz false false false $outdir/change_o/change-o-db-cg.txt
501 bash $dir/change_o/define_clones.sh bygroup $outdir/change_o/change-o-db-cg.txt gene first ham none min complete 3.0 $outdir/change_o/change-o-db-defined_clones-cg.txt $outdir/change_o/change-o-defined_clones-summary-cg.txt
502 else
503 echo "No cg sequences" > "$outdir/change_o/change-o-db-defined_clones-cg.txt"
504 echo "No cg sequences" > "$outdir/change_o/change-o-defined_clones-summary-cg.txt"
505 fi
506
507 if [[ $(wc -l < $outdir/new_IMGT_cm/1_Summary.txt) -gt "1" ]]; then
508 bash $dir/change_o/makedb.sh $outdir/new_IMGT_cm.txz false false false $outdir/change_o/change-o-db-cm.txt
509 bash $dir/change_o/define_clones.sh bygroup $outdir/change_o/change-o-db-cm.txt gene first ham none min complete 3.0 $outdir/change_o/change-o-db-defined_clones-cm.txt $outdir/change_o/change-o-defined_clones-summary-cm.txt
510 else
511 echo "No cm sequences" > "$outdir/change_o/change-o-db-defined_clones-cm.txt"
512 echo "No cm sequences" > "$outdir/change_o/change-o-defined_clones-summary-cm.txt"
513 fi
479 514
480 PWD="$tmp" 515 PWD="$tmp"
481 516
482 mv $log $outdir/log.html 517 mv $log $outdir/log.html
483 518