Mercurial > repos > davidvanzessen > mutation_analysis

comparison wrapper.sh @ 127:afb0937ec0dc draft default tip

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Uploaded
author davidvanzessen
date Tue, 13 Sep 2016 08:55:05 -0400
parents ffd5462da9d1
children
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126:ffd5462da9d1 127:afb0937ec0dc
370 370
371 tmp="$PWD" 371 tmp="$PWD"
372 372
373 cd $outdir/change_o 373 cd $outdir/change_o
374 374
375 bash $dir/change_o/makedb.sh $input false false false $outdir/change_o/change-o-db.txt 375 bash $dir/change_o/makedb.sh $outdir/new_IMGT.txz false false false $outdir/change_o/change-o-db.txt
376 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 376 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
377 377
378 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>&1 378 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
379 379
380 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" 380 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"
451 451
452 echo "<div class='tabbertab' title='Downloads'>" >> $output 452 echo "<div class='tabbertab' title='Downloads'>" >> $output
453 453
454 echo "<table class='pure-table pure-table-striped'>" >> $output 454 echo "<table class='pure-table pure-table-striped'>" >> $output
455 echo "<thead><tr><th>info</th><th>link</th></tr></thead>" >> $output 455 echo "<thead><tr><th>info</th><th>link</th></tr></thead>" >> $output
456 echo "<tr><td>The complete dataset</td><td><a href='merged.txt'>Download</a></td></tr>" >> $output 456 echo "<tr><td>The complete dataset</td><td><a href='merged.txt' download='merged.txt' >Download</a></td></tr>" >> $output
457 echo "<tr><td>The SHM Overview table as a dataset</td><td><a href='data_sum.txt'>Download</a></td></tr>" >> $output 457 echo "<tr><td>The filtered dataset</td><td><a href='filtered.txt' download='filtered.txt' >Download</a></td></tr>" >> $output
458 echo "<tr><td>The data used to generate the first SHM Overview plot</td><td><a href='plot1.txt'>Download</a></td></tr>" >> $output 458 echo "<tr><td>The SHM Overview table as a dataset</td><td><a href='data_sum.txt' download='data_sum.txt' >Download</a></td></tr>" >> $output
459 echo "<tr><td>The data used to generate the sexond SHM Overview plot</td><td><a href='plot2.txt'>Download</a></td></tr>" >> $output 459 echo "<tr><td>The data used to generate the first SHM Overview plot</td><td><a href='plot1.txt' download='plot1.txt' >Download</a></td></tr>" >> $output
460 echo "<tr><td>The data used to generate the third SHM Overview plot</td><td><a href='plot3.txt'>Download</a></td></tr>" >> $output 460 echo "<tr><td>The data used to generate the second SHM Overview plot</td><td><a href='plot2.txt' download='plot2.txt' >Download</a></td></tr>" >> $output
461 echo "<tr><td>The alignment info on the unmatched sequences</td><td><a href='unmatched.txt'>Download</a></td></tr>" >> $output 461 echo "<tr><td>The data used to generate the third SHM Overview plot</td><td><a href='plot3.txt' download='plot3.txt' >Download</a></td></tr>" >> $output
462 462 echo "<tr><td>The alignment info on the unmatched sequences</td><td><a href='unmatched.txt' download='unmatched.txt' >Download</a></td></tr>" >> $output
463 echo "<tr><td>Motif data per sequence ID</td><td><a href='motif_per_seq.txt'>Download</a></td></tr>" >> $output 463
464 echo "<tr><td>Mutation data per sequence ID</td><td><a href='mutation_by_id.txt'>Download</a></td></tr>" >> $output 464 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
465 echo "<tr><td>AA mutation data per sequence ID</td><td><a href='aa_id_mutations.txt'>Download</a></td></tr>" >> $output 465 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
466 echo "<tr><td>Absent AA location data per sequence ID</td><td><a href='absent_aa_id.txt'>Download</a></td></tr>" >> $output 466 echo "<tr><td>AA mutation data per sequence ID</td><td><a href='aa_id_mutations.txt' download='aa_id_mutations.txt' >Download</a></td></tr>" >> $output
467 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 467 echo "<tr><td>Absent AA location data per sequence ID</td><td><a href='absent_aa_id.txt' download='absent_aa_id.txt' >Download</a></td></tr>" >> $output
468 468 echo "<tr><td>CDR1+FR2+CDR2+FR3+CDR3 sequences that show up more than once</td><td><a href='sequence_overview/index.html'>View</a></td></tr>" >> $output
469 echo "<tr><td>Base count for every sequence</td><td><a href='base_overview.html'>Download</a></td></tr>" >> $output 469
470 470 echo "<tr><td>Base count for every sequence</td><td><a href='base_overview.html'>View</a></td></tr>" >> $output
471 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 471
472 echo "<tr><td>Baseline data</td><td><a href='baseline.txt'>Download</a></td></tr>" >> $output 472 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='baseline.pdf' >Download</a></td></tr>" >> $output
473 echo "<tr><td>Baseline ca PDF</td><td><a href='baseline_ca.pdf'>Download</a></td></tr>" >> $output 473 echo "<tr><td>Baseline data</td><td><a href='baseline.txt' download='baseline.txt' >Download</a></td></tr>" >> $output
474 echo "<tr><td>Baseline ca data</td><td><a href='baseline_ca.txt'>Download</a></td></tr>" >> $output 474 echo "<tr><td>Baseline ca PDF</td><td><a href='baseline_ca.pdf' download='baseline_ca.pdf' >Download</a></td></tr>" >> $output
475 echo "<tr><td>Baseline cg PDF</td><td><a href='baseline_cg.pdf'>Download</a></td></tr>" >> $output 475 echo "<tr><td>Baseline ca data</td><td><a href='baseline_ca.txt' download='baseline_ca.txt' >Download</a></td></tr>" >> $output
476 echo "<tr><td>Baseline cg data</td><td><a href='baseline_cg.txt'>Download</a></td></tr>" >> $output 476 echo "<tr><td>Baseline cg PDF</td><td><a href='baseline_cg.pdf' download='baseline_cg.pdf' >Download</a></td></tr>" >> $output
477 echo "<tr><td>Baseline cm PDF</td><td><a href='baseline_cm.pdf'>Download</a></td></tr>" >> $output 477 echo "<tr><td>Baseline cg data</td><td><a href='baseline_cg.txt' download='baseline_cg.txt' >Download</a></td></tr>" >> $output
478 echo "<tr><td>Baseline cm data</td><td><a href='baseline_cm.txt'>Download</a></td></tr>" >> $output 478 echo "<tr><td>Baseline cm PDF</td><td><a href='baseline_cm.pdf' download='baseline_cm.pdf' >Download</a></td></tr>" >> $output
479 479 echo "<tr><td>Baseline cm data</td><td><a href='baseline_cm.txt' download='baseline_cm.txt' >Download</a></td></tr>" >> $output
480 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 480
481 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 481 echo "<tr><td>An IMGT archive with just the matched and filtered sequences</td><td><a href='new_IMGT.txz' download='new_IMGT.txz' >Download</a></td></tr>" >> $output
482 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 482 echo "<tr><td>An IMGT archive with just the matched and filtered ca sequences</td><td><a href='new_IMGT_ca.txz' download='new_IMGT_ca.txz' >Download</a></td></tr>" >> $output
483 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 483 echo "<tr><td>An IMGT archive with just the matched and filtered ca1 sequences</td><td><a href='new_IMGT_ca1.txz' download='new_IMGT_ca1.txz' >Download</a></td></tr>" >> $output
484 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 484 echo "<tr><td>An IMGT archive with just the matched and filtered ca2 sequences</td><td><a href='new_IMGT_ca2.txz' download='new_IMGT_ca2.txz' >Download</a></td></tr>" >> $output
485 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 485 echo "<tr><td>An IMGT archive with just the matched and filtered cg sequences</td><td><a href='new_IMGT_cg.txz' download='new_IMGT_cg.txz' >Download</a></td></tr>" >> $output
486 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 486 echo "<tr><td>An IMGT archive with just the matched and filtered cg1 sequences</td><td><a href='new_IMGT_cg1.txz' download='new_IMGT_cg1.txz' >Download</a></td></tr>" >> $output
487 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 487 echo "<tr><td>An IMGT archive with just the matched and filtered cg2 sequences</td><td><a href='new_IMGT_cg2.txz' download='new_IMGT_cg2.txz' >Download</a></td></tr>" >> $output
488 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 488 echo "<tr><td>An IMGT archive with just the matched and filtered cg3 sequences</td><td><a href='new_IMGT_cg3.txz' download='new_IMGT_cg3.txz' >Download</a></td></tr>" >> $output
489 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 489 echo "<tr><td>An IMGT archive with just the matched and filtered cg4 sequences</td><td><a href='new_IMGT_cg4.txz' download='new_IMGT_cg4.txz' >Download</a></td></tr>" >> $output
490 490 echo "<tr><td>An IMGT archive with just the matched and filtered cm sequences</td><td><a href='new_IMGT_cm.txz' download='new_IMGT_cm.txz' >Download</a></td></tr>" >> $output
491 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 491
492 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 492 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='change_o/change-o-db-defined_clones.txt' >Download</a></td></tr>" >> $output
493 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 493 echo "<tr><td>The Change-O DB defined clones summary file</td><td><a href='change_o/change-o-defined_clones-summary.txt' download='change_o/change-o-defined_clones-summary.txt' >Download</a></td></tr>" >> $output
494 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 494 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='change_o/change-o-db-defined_clones-ca.txt' >Download</a></td></tr>" >> $output
495 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 495 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='change_o/change-o-defined_clones-summary-ca.txt' >Download</a></td></tr>" >> $output
496 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 496 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='change_o/change-o-db-defined_clones-cg.txt' >Download</a></td></tr>" >> $output
497 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 497 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='change_o/change-o-defined_clones-summary-cg.txt' >Download</a></td></tr>" >> $output
498 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 498 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='change_o/change-o-db-defined_clones-cm.txt' >Download</a></td></tr>" >> $output
499 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='change_o/change-o-defined_clones-summary-cm.txt' >Download</a></td></tr>" >> $output
499 500
500 echo "</table>" >> $output 501 echo "</table>" >> $output
501 502
502 echo "</div>" >> $output #downloads tab end 503 echo "</div>" >> $output #downloads tab end
503 504