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comparison wrapper.sh @ 6:2ddb9a21f635 draft

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Uploaded
author davidvanzessen
date Tue, 01 Nov 2016 10:48:38 -0400
parents 012a738edf5a
children ad9be244b104
comparison
equal deleted inserted replaced
5:012a738edf5a 6:2ddb9a21f635
11 functionality=$7 11 functionality=$7
12 unique=$8 12 unique=$8
13 naive_output_ca=$9 13 naive_output_ca=$9
14 naive_output_cg=${10} 14 naive_output_cg=${10}
15 naive_output_cm=${11} 15 naive_output_cm=${11}
16 filter_unique=${12} 16 naive_output_ce=${12}
17 class_filter=${13} 17 filter_unique=${13}
18 empty_region_filter=${14} 18 class_filter=${14}
19 fast=${15} 19 empty_region_filter=${15}
20 fast=${16}
20 mkdir $outdir 21 mkdir $outdir
21 22
22 tar -xzf $dir/style.tar.gz -C $outdir 23 tar -xzf $dir/style.tar.gz -C $outdir
23 24
24 echo "---------------- read parameters ----------------" 25 echo "---------------- read parameters ----------------"
369 then 370 then
370 echo "<img src='aa_histogram.png'/><br />" >> $output 371 echo "<img src='aa_histogram.png'/><br />" >> $output
371 echo "<img src='aa_histogram_IGA.png'/><br />" >> $output 372 echo "<img src='aa_histogram_IGA.png'/><br />" >> $output
372 echo "<img src='aa_histogram_IGG.png'/><br />" >> $output 373 echo "<img src='aa_histogram_IGG.png'/><br />" >> $output
373 echo "<img src='aa_histogram_IGM.png'/><br />" >> $output 374 echo "<img src='aa_histogram_IGM.png'/><br />" >> $output
375 echo "<img src='aa_histogram_IGE.png'/><br />" >> $output
374 fi 376 fi
375 377
376 echo "<embed src='baseline.pdf' width='700px' height='1000px'>" >> $output 378 echo "<embed src='baseline.pdf' width='700px' height='1000px'>" >> $output
377 echo "<embed src='baseline_IGA.pdf' width='700px' height='1000px'>" >> $output 379 echo "<embed src='baseline_IGA.pdf' width='700px' height='1000px'>" >> $output
378 echo "<embed src='baseline_IGG.pdf' width='700px' height='1000px'>" >> $output 380 echo "<embed src='baseline_IGG.pdf' width='700px' height='1000px'>" >> $output
379 echo "<embed src='baseline_IGM.pdf' width='700px' height='1000px'>" >> $output 381 echo "<embed src='baseline_IGM.pdf' width='700px' height='1000px'>" >> $output
382 echo "<embed src='baseline_IGE.pdf' width='700px' height='1000px'>" >> $output
380 383
381 echo "</div>" >> $output #antigen selection tab end 384 echo "</div>" >> $output #antigen selection tab end
382 385
383 echo "<div class='tabbertab' title='CSR'>" >> $output #CSR tab 386 echo "<div class='tabbertab' title='CSR'>" >> $output #CSR tab
384 387
430 bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGM.txz false false false $outdir/change_o/change-o-db-IGM.txt 433 bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGM.txz false false false $outdir/change_o/change-o-db-IGM.txt
431 bash $dir/change_o/define_clones.sh bygroup $outdir/change_o/change-o-db-IGM.txt gene first ham none min complete 3.0 $outdir/change_o/change-o-db-defined_clones-IGM.txt $outdir/change_o/change-o-defined_clones-summary-IGM.txt 434 bash $dir/change_o/define_clones.sh bygroup $outdir/change_o/change-o-db-IGM.txt gene first ham none min complete 3.0 $outdir/change_o/change-o-db-defined_clones-IGM.txt $outdir/change_o/change-o-defined_clones-summary-IGM.txt
432 else 435 else
433 echo "No IGM sequences" > "$outdir/change_o/change-o-db-defined_clones-IGM.txt" 436 echo "No IGM sequences" > "$outdir/change_o/change-o-db-defined_clones-IGM.txt"
434 echo "No IGM sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGM.txt" 437 echo "No IGM sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGM.txt"
438 fi
439
440 if [[ $(wc -l < $outdir/new_IMGT_IGE/1_Summary.txt) -gt "1" ]]; then
441 bash $dir/change_o/makedb.sh $outdir/new_IMGT_IGE.txz false false false $outdir/change_o/change-o-db-IGE.txt
442 bash $dir/change_o/define_clones.sh bygroup $outdir/change_o/change-o-db-IGE.txt gene first ham none min complete 3.0 $outdir/change_o/change-o-db-defined_clones-IGE.txt $outdir/change_o/change-o-defined_clones-summary-IGE.txt
443 else
444 echo "No IGE sequences" > "$outdir/change_o/change-o-db-defined_clones-IGE.txt"
445 echo "No IGE sequences" > "$outdir/change_o/change-o-defined_clones-summary-IGE.txt"
435 fi 446 fi
436 447
437 PWD="$tmp" 448 PWD="$tmp"
438 449
439 echo "<div class='tabbertab' title='Clonality'>" >> $output #clonality tab 450 echo "<div class='tabbertab' title='Clonality'>" >> $output #clonality tab
462 473
463 echo "<div class='tabbertab' title='All'>" >> $output 474 echo "<div class='tabbertab' title='All'>" >> $output
464 clonality_table $outdir/change_o/change-o-defined_clones-summary.txt $output 475 clonality_table $outdir/change_o/change-o-defined_clones-summary.txt $output
465 echo "</div>" >> $output 476 echo "</div>" >> $output
466 477
467 echo "<div class='tabbertab' title='Ca'>" >> $output 478 echo "<div class='tabbertab' title='IGA'>" >> $output
468 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGA.txt $output 479 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGA.txt $output
469 echo "</div>" >> $output 480 echo "</div>" >> $output
470 481
471 echo "<div class='tabbertab' title='Cg'>" >> $output 482 echo "<div class='tabbertab' title='IGG'>" >> $output
472 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGG.txt $output 483 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGG.txt $output
473 echo "</div>" >> $output 484 echo "</div>" >> $output
474 485
475 echo "<div class='tabbertab' title='Cm'>" >> $output 486 echo "<div class='tabbertab' title='IGM'>" >> $output
487 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGM.txt $output
488 echo "</div>" >> $output
489
490 echo "<div class='tabbertab' title='IGE'>" >> $output
476 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGM.txt $output 491 clonality_table $outdir/change_o/change-o-defined_clones-summary-IGM.txt $output
477 echo "</div>" >> $output 492 echo "</div>" >> $output
478 493
479 echo "<div class='tabbertab' title='Overview'>" >> $output 494 echo "<div class='tabbertab' title='Overview'>" >> $output
480 cat "$outdir/sequence_overview/index.html" >> $output 495 cat "$outdir/sequence_overview/index.html" >> $output
518 echo "<tr><td>The data for the 'IGG1' transition plot</td><td><a href='transition_IGG1_sum.txt' download='transition_IGG1_sum.txt' >Download</a></td></tr>" >> $output 533 echo "<tr><td>The data for the 'IGG1' transition plot</td><td><a href='transition_IGG1_sum.txt' download='transition_IGG1_sum.txt' >Download</a></td></tr>" >> $output
519 echo "<tr><td>The data for the 'IGG2' transition plot</td><td><a href='transition_IGG2_sum.txt' download='transition_IGG2_sum.txt' >Download</a></td></tr>" >> $output 534 echo "<tr><td>The data for the 'IGG2' transition plot</td><td><a href='transition_IGG2_sum.txt' download='transition_IGG2_sum.txt' >Download</a></td></tr>" >> $output
520 echo "<tr><td>The data for the 'IGG3' transition plot</td><td><a href='transition_IGG3_sum.txt' download='transition_IGG3_sum.txt' >Download</a></td></tr>" >> $output 535 echo "<tr><td>The data for the 'IGG3' transition plot</td><td><a href='transition_IGG3_sum.txt' download='transition_IGG3_sum.txt' >Download</a></td></tr>" >> $output
521 echo "<tr><td>The data for the 'IGG4' transition plot</td><td><a href='transition_IGG4_sum.txt' download='transition_IGG4_sum.txt' >Download</a></td></tr>" >> $output 536 echo "<tr><td>The data for the 'IGG4' transition plot</td><td><a href='transition_IGG4_sum.txt' download='transition_IGG4_sum.txt' >Download</a></td></tr>" >> $output
522 echo "<tr><td>The data for the 'IGM' transition plot</td><td><a href='transition_IGM_sum.txt' download='transition_IGM_sum.txt' >Download</a></td></tr>" >> $output 537 echo "<tr><td>The data for the 'IGM' transition plot</td><td><a href='transition_IGM_sum.txt' download='transition_IGM_sum.txt' >Download</a></td></tr>" >> $output
538 echo "<tr><td>The data for the 'IGE' transition plot</td><td><a href='transition_IGE_sum.txt' download='transition_IGE_sum.txt' >Download</a></td></tr>" >> $output
523 539
524 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Antigen Selection</td></tr>" >> $output 540 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Antigen Selection</td></tr>" >> $output
525 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 541 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
526 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 542 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
527 543
531 echo "<tr><td>Baseline IGA data</td><td><a href='baseline_IGA.txt' download='baseline_IGA.txt' >Download</a></td></tr>" >> $output 547 echo "<tr><td>Baseline IGA data</td><td><a href='baseline_IGA.txt' download='baseline_IGA.txt' >Download</a></td></tr>" >> $output
532 echo "<tr><td>Baseline IGG PDF</td><td><a href='baseline_IGG.pdf' download='baseline_IGG.pdf' >Download</a></td></tr>" >> $output 548 echo "<tr><td>Baseline IGG PDF</td><td><a href='baseline_IGG.pdf' download='baseline_IGG.pdf' >Download</a></td></tr>" >> $output
533 echo "<tr><td>Baseline IGG data</td><td><a href='baseline_IGG.txt' download='baseline_IGG.txt' >Download</a></td></tr>" >> $output 549 echo "<tr><td>Baseline IGG data</td><td><a href='baseline_IGG.txt' download='baseline_IGG.txt' >Download</a></td></tr>" >> $output
534 echo "<tr><td>Baseline IGM PDF</td><td><a href='baseline_IGM.pdf' download='baseline_IGM.pdf' >Download</a></td></tr>" >> $output 550 echo "<tr><td>Baseline IGM PDF</td><td><a href='baseline_IGM.pdf' download='baseline_IGM.pdf' >Download</a></td></tr>" >> $output
535 echo "<tr><td>Baseline IGM data</td><td><a href='baseline_IGM.txt' download='baseline_IGM.txt' >Download</a></td></tr>" >> $output 551 echo "<tr><td>Baseline IGM data</td><td><a href='baseline_IGM.txt' download='baseline_IGM.txt' >Download</a></td></tr>" >> $output
552 echo "<tr><td>Baseline IGE data</td><td><a href='baseline_IGE.txt' download='baseline_IGE.txt' >Download</a></td></tr>" >> $output
536 553
537 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>CSR</td></tr>" >> $output 554 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>CSR</td></tr>" >> $output
538 echo "<tr><td>The data for the CSR IGA pie plot</td><td><a href='IGA_pie.txt' download='IGA_pie.txt' >Download</a></td></tr>" >> $output 555 echo "<tr><td>The data for the CSR IGA pie plot</td><td><a href='IGA_pie.txt' download='IGA_pie.txt' >Download</a></td></tr>" >> $output
539 echo "<tr><td>The data for the CSR IGG pie plot</td><td><a href='IGG_pie.txt' download='IGG_pie.txt' >Download</a></td></tr>" >> $output 556 echo "<tr><td>The data for the CSR IGG pie plot</td><td><a href='IGG_pie.txt' download='IGG_pie.txt' >Download</a></td></tr>" >> $output
540 557
546 echo "<tr><td>The Change-O DB defined clones summary file of IGA</td><td><a href='change_o/change-o-defined_clones-summary-IGA.txt' download='change_o/change-o-defined_clones-summary-IGA.txt' >Download</a></td></tr>" >> $output 563 echo "<tr><td>The Change-O DB defined clones summary file of IGA</td><td><a href='change_o/change-o-defined_clones-summary-IGA.txt' download='change_o/change-o-defined_clones-summary-IGA.txt' >Download</a></td></tr>" >> $output
547 echo "<tr><td>The Change-O DB file with defined clones of IGG</td><td><a href='change_o/change-o-db-defined_clones-IGG.txt' download='change_o/change-o-db-defined_clones-IGG.txt' >Download</a></td></tr>" >> $output 564 echo "<tr><td>The Change-O DB file with defined clones of IGG</td><td><a href='change_o/change-o-db-defined_clones-IGG.txt' download='change_o/change-o-db-defined_clones-IGG.txt' >Download</a></td></tr>" >> $output
548 echo "<tr><td>The Change-O DB defined clones summary file of IGG</td><td><a href='change_o/change-o-defined_clones-summary-IGG.txt' download='change_o/change-o-defined_clones-summary-IGG.txt' >Download</a></td></tr>" >> $output 565 echo "<tr><td>The Change-O DB defined clones summary file of IGG</td><td><a href='change_o/change-o-defined_clones-summary-IGG.txt' download='change_o/change-o-defined_clones-summary-IGG.txt' >Download</a></td></tr>" >> $output
549 echo "<tr><td>The Change-O DB file with defined clones of IGM</td><td><a href='change_o/change-o-db-defined_clones-IGM.txt' download='change_o/change-o-db-defined_clones-IGM.txt' >Download</a></td></tr>" >> $output 566 echo "<tr><td>The Change-O DB file with defined clones of IGM</td><td><a href='change_o/change-o-db-defined_clones-IGM.txt' download='change_o/change-o-db-defined_clones-IGM.txt' >Download</a></td></tr>" >> $output
550 echo "<tr><td>The Change-O DB defined clones summary file of IGM</td><td><a href='change_o/change-o-defined_clones-summary-IGM.txt' download='change_o/change-o-defined_clones-summary-IGM.txt' >Download</a></td></tr>" >> $output 567 echo "<tr><td>The Change-O DB defined clones summary file of IGM</td><td><a href='change_o/change-o-defined_clones-summary-IGM.txt' download='change_o/change-o-defined_clones-summary-IGM.txt' >Download</a></td></tr>" >> $output
568 echo "<tr><td>The Change-O DB file with defined clones of IGE</td><td><a href='change_o/change-o-db-defined_clones-IGE.txt' download='change_o/change-o-db-defined_clones-IGE.txt' >Download</a></td></tr>" >> $output
569 echo "<tr><td>The Change-O DB defined clones summary file of IGE</td><td><a href='change_o/change-o-defined_clones-summary-IGE.txt' download='change_o/change-o-defined_clones-summary-IGE.txt' >Download</a></td></tr>" >> $output
551 570
552 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Filtered IMGT output files</td></tr>" >> $output 571 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Filtered IMGT output files</td></tr>" >> $output
553 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 572 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
554 echo "<tr><td>An IMGT archive with just the matched and filtered IGA sequences</td><td><a href='new_IMGT_IGA.txz' download='new_IMGT_IGA.txz' >Download</a></td></tr>" >> $output 573 echo "<tr><td>An IMGT archive with just the matched and filtered IGA sequences</td><td><a href='new_IMGT_IGA.txz' download='new_IMGT_IGA.txz' >Download</a></td></tr>" >> $output
555 echo "<tr><td>An IMGT archive with just the matched and filtered IGA1 sequences</td><td><a href='new_IMGT_IGA1.txz' download='new_IMGT_IGA1.txz' >Download</a></td></tr>" >> $output 574 echo "<tr><td>An IMGT archive with just the matched and filtered IGA1 sequences</td><td><a href='new_IMGT_IGA1.txz' download='new_IMGT_IGA1.txz' >Download</a></td></tr>" >> $output
558 echo "<tr><td>An IMGT archive with just the matched and filtered IGG1 sequences</td><td><a href='new_IMGT_IGG1.txz' download='new_IMGT_IGG1.txz' >Download</a></td></tr>" >> $output 577 echo "<tr><td>An IMGT archive with just the matched and filtered IGG1 sequences</td><td><a href='new_IMGT_IGG1.txz' download='new_IMGT_IGG1.txz' >Download</a></td></tr>" >> $output
559 echo "<tr><td>An IMGT archive with just the matched and filtered IGG2 sequences</td><td><a href='new_IMGT_IGG2.txz' download='new_IMGT_IGG2.txz' >Download</a></td></tr>" >> $output 578 echo "<tr><td>An IMGT archive with just the matched and filtered IGG2 sequences</td><td><a href='new_IMGT_IGG2.txz' download='new_IMGT_IGG2.txz' >Download</a></td></tr>" >> $output
560 echo "<tr><td>An IMGT archive with just the matched and filtered IGG3 sequences</td><td><a href='new_IMGT_IGG3.txz' download='new_IMGT_IGG3.txz' >Download</a></td></tr>" >> $output 579 echo "<tr><td>An IMGT archive with just the matched and filtered IGG3 sequences</td><td><a href='new_IMGT_IGG3.txz' download='new_IMGT_IGG3.txz' >Download</a></td></tr>" >> $output
561 echo "<tr><td>An IMGT archive with just the matched and filtered IGG4 sequences</td><td><a href='new_IMGT_IGG4.txz' download='new_IMGT_IGG4.txz' >Download</a></td></tr>" >> $output 580 echo "<tr><td>An IMGT archive with just the matched and filtered IGG4 sequences</td><td><a href='new_IMGT_IGG4.txz' download='new_IMGT_IGG4.txz' >Download</a></td></tr>" >> $output
562 echo "<tr><td>An IMGT archive with just the matched and filtered IGM sequences</td><td><a href='new_IMGT_IGM.txz' download='new_IMGT_IGM.txz' >Download</a></td></tr>" >> $output 581 echo "<tr><td>An IMGT archive with just the matched and filtered IGM sequences</td><td><a href='new_IMGT_IGM.txz' download='new_IMGT_IGM.txz' >Download</a></td></tr>" >> $output
582 echo "<tr><td>An IMGT archive with just the matched and filtered IGE sequences</td><td><a href='new_IMGT_IGE.txz' download='new_IMGT_IGM.txz' >Download</a></td></tr>" >> $output
563 583
564 echo "</table>" >> $output 584 echo "</table>" >> $output
565 585
566 echo "</div>" >> $output #downloads tab end 586 echo "</div>" >> $output #downloads tab end
567 587
607 if [[ $(wc -l < $outdir/new_IMGT_IGM/1_Summary.txt) -gt "1" ]]; then 627 if [[ $(wc -l < $outdir/new_IMGT_IGM/1_Summary.txt) -gt "1" ]]; then
608 cd $outdir/baseline/IGM 628 cd $outdir/baseline/IGM
609 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_IGM.txz "IGM" "$dir/baseline/IMGT-reference-seqs-IGHV-2015-11-05.fa" "$outdir/baseline_IGM.pdf" "Sequence.ID" "$outdir/baseline_IGM.txt" 629 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_IGM.txz "IGM" "$dir/baseline/IMGT-reference-seqs-IGHV-2015-11-05.fa" "$outdir/baseline_IGM.pdf" "Sequence.ID" "$outdir/baseline_IGM.txt"
610 else 630 else
611 echo "No IGM sequences" > "$outdir/baseline_IGM.txt" 631 echo "No IGM sequences" > "$outdir/baseline_IGM.txt"
632 fi
633
634 mkdir $outdir/baseline/IGE
635 if [[ $(wc -l < $outdir/new_IMGT_IGE/1_Summary.txt) -gt "1" ]]; then
636 cd $outdir/baseline/IGE
637 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_IGE.txz "IGE" "$dir/baseline/IMGT-reference-seqs-IGHV-2015-11-05.fa" "$outdir/baseline_IGE.pdf" "Sequence.ID" "$outdir/baseline_IGE.txt"
638 else
639 echo "No IGE sequences" > "$outdir/baseline_IGE.txt"
612 fi 640 fi
613 641
614 cd $tmp 642 cd $tmp
615 643
616 echo "Cleaning up *.RData files" 644 echo "Cleaning up *.RData files"
624 if [[ "$naive_output" == "yes" ]] 652 if [[ "$naive_output" == "yes" ]]
625 then 653 then
626 cp $outdir/new_IMGT_IGA.txz ${naive_output_ca} 654 cp $outdir/new_IMGT_IGA.txz ${naive_output_ca}
627 cp $outdir/new_IMGT_IGG.txz ${naive_output_cg} 655 cp $outdir/new_IMGT_IGG.txz ${naive_output_cg}
628 cp $outdir/new_IMGT_IGM.txz ${naive_output_cm} 656 cp $outdir/new_IMGT_IGM.txz ${naive_output_cm}
657 cp $outdir/new_IMGT_IGE.txz ${naive_output_ce}
629 fi 658 fi
630 659
631 echo "</table>" >> $outdir/base_overview.html 660 echo "</table>" >> $outdir/base_overview.html
632 661
633 mv $log $outdir/log.html 662 mv $log $outdir/log.html