Mercurial > repos > davidvanzessen > shm_csr

comparison wrapper.sh @ 33:22fabe161cf3 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author davidvanzessen
date Thu, 15 Dec 2016 09:44:17 -0500
parents 4c5ba6b5d10d
children 96c1276ceefe
comparison
equal deleted inserted replaced
32:4c5ba6b5d10d 33:22fabe161cf3
408 then 408 then
409 echo "<img src='aa_histogram_IGE.png'/><br />" >> $output 409 echo "<img src='aa_histogram_IGE.png'/><br />" >> $output
410 fi 410 fi
411 411
412 412
413 if [ -e $outdir/baseline.pdf ] 413
414 then 414 if [[ "$fast" == "no" ]] ; then
415 echo "<embed src='baseline.pdf' width='700px' height='1000px'>" >> $output 415
416 fi 416 echo "---------------- baseline ----------------"
417 417 echo "---------------- baseline ----------------<br />" >> $log
418 if [ -e $outdir/baseline_IGA.pdf ] 418 tmp="$PWD"
419 then 419
420 echo "<embed src='baseline_IGA.pdf' width='700px' height='1000px'>" >> $output 420 mkdir $outdir/baseline
421 fi 421
422 422
423 if [ -e $outdir/baseline_IGG.pdf ] 423 mkdir $outdir/baseline/IGA_IGG_IGM
424 then 424 if [[ $(wc -l < $outdir/new_IMGT/1_Summary.txt) -gt "1" ]]; then
425 echo "<embed src='baseline_IGG.pdf' width='700px' height='1000px'>" >> $output 425 cd $outdir/baseline/IGA_IGG_IGM
426 fi 426 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT.txz "IGA_IGG_IGM" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline.pdf" "Sequence.ID" "$outdir/baseline.txt"
427 427 else
428 if [ -e $outdir/baseline_IGM.pdf ] 428 echo "No sequences" > "$outdir/baseline.txt"
429 then 429 fi
430 echo "<embed src='baseline_IGM.pdf' width='700px' height='1000px'>" >> $output 430
431 fi 431 mkdir $outdir/baseline/IGA
432 432 if [[ $(wc -l < $outdir/new_IMGT_IGA/1_Summary.txt) -gt "1" ]]; then
433 if [ -e $outdir/baseline_IGE.pdf ] 433 cd $outdir/baseline/IGA
434 then 434 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_IGA.txz "IGA" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGA.pdf" "Sequence.ID" "$outdir/baseline_IGA.txt"
435 echo "<embed src='baseline_IGE.pdf' width='700px' height='1000px'>" >> $output 435 else
436 echo "No IGA sequences" > "$outdir/baseline_IGA.txt"
437 fi
438
439 mkdir $outdir/baseline/IGG
440 if [[ $(wc -l < $outdir/new_IMGT_IGG/1_Summary.txt) -gt "1" ]]; then
441 cd $outdir/baseline/IGG
442 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_IGG.txz "cg" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGG.pdf" "Sequence.ID" "$outdir/baseline_IGG.txt"
443 else
444 echo "No IGG sequences" > "$outdir/baseline_IGG.txt"
445 fi
446
447 mkdir $outdir/baseline/IGM
448 if [[ $(wc -l < $outdir/new_IMGT_IGM/1_Summary.txt) -gt "1" ]]; then
449 cd $outdir/baseline/IGM
450 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/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGM.pdf" "Sequence.ID" "$outdir/baseline_IGM.txt"
451 else
452 echo "No IGM sequences" > "$outdir/baseline_IGM.txt"
453 fi
454
455 mkdir $outdir/baseline/IGE
456 if [[ $(wc -l < $outdir/new_IMGT_IGE/1_Summary.txt) -gt "1" ]]; then
457 cd $outdir/baseline/IGE
458 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/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGE.pdf" "Sequence.ID" "$outdir/baseline_IGE.txt"
459 else
460 echo "No IGE sequences" > "$outdir/baseline_IGE.txt"
461 fi
462
463 cd $tmp
464
465 echo "Cleaning up *.RData files"
466 find $outdir/baseline -name "*.RData" -type f -delete
467
468 if [ -e $outdir/baseline.pdf ]
469 then
470 echo "<embed src='baseline.pdf' width='700px' height='1000px'>" >> $output
471 fi
472
473 if [ -e $outdir/baseline_IGA.pdf ]
474 then
475 echo "<embed src='baseline_IGA.pdf' width='700px' height='1000px'>" >> $output
476 fi
477
478 if [ -e $outdir/baseline_IGG.pdf ]
479 then
480 echo "<embed src='baseline_IGG.pdf' width='700px' height='1000px'>" >> $output
481 fi
482
483 if [ -e $outdir/baseline_IGM.pdf ]
484 then
485 echo "<embed src='baseline_IGM.pdf' width='700px' height='1000px'>" >> $output
486 fi
487
488 if [ -e $outdir/baseline_IGE.pdf ]
489 then
490 echo "<embed src='baseline_IGE.pdf' width='700px' height='1000px'>" >> $output
491 fi
436 fi 492 fi
437 493
438 echo "</div>" >> $output #antigen selection tab end 494 echo "</div>" >> $output #antigen selection tab end
439 495
440 echo "<div class='tabbertab' title='CSR'>" >> $output #CSR tab 496 echo "<div class='tabbertab' title='CSR'>" >> $output #CSR tab
649 echo "</div>" >> $output #tabs end 705 echo "</div>" >> $output #tabs end
650 706
651 echo "</html>" >> $output 707 echo "</html>" >> $output
652 708
653 709
654 if [[ "$fast" == "no" ]] ; then
655
656 echo "---------------- baseline ----------------"
657 echo "---------------- baseline ----------------<br />" >> $log
658 tmp="$PWD"
659
660 mkdir $outdir/baseline
661
662
663 mkdir $outdir/baseline/IGA_IGG_IGM
664 if [[ $(wc -l < $outdir/new_IMGT/1_Summary.txt) -gt "1" ]]; then
665 cd $outdir/baseline/IGA_IGG_IGM
666 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT.txz "IGA_IGG_IGM" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline.pdf" "Sequence.ID" "$outdir/baseline.txt"
667 else
668 echo "No sequences" > "$outdir/baseline.txt"
669 fi
670
671 mkdir $outdir/baseline/IGA
672 if [[ $(wc -l < $outdir/new_IMGT_IGA/1_Summary.txt) -gt "1" ]]; then
673 cd $outdir/baseline/IGA
674 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_IGA.txz "IGA" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGA.pdf" "Sequence.ID" "$outdir/baseline_IGA.txt"
675 else
676 echo "No IGA sequences" > "$outdir/baseline_IGA.txt"
677 fi
678
679 mkdir $outdir/baseline/IGG
680 if [[ $(wc -l < $outdir/new_IMGT_IGG/1_Summary.txt) -gt "1" ]]; then
681 cd $outdir/baseline/IGG
682 bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_IGG.txz "cg" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGG.pdf" "Sequence.ID" "$outdir/baseline_IGG.txt"
683 else
684 echo "No IGG sequences" > "$outdir/baseline_IGG.txt"
685 fi
686
687 mkdir $outdir/baseline/IGM
688 if [[ $(wc -l < $outdir/new_IMGT_IGM/1_Summary.txt) -gt "1" ]]; then
689 cd $outdir/baseline/IGM
690 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/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGM.pdf" "Sequence.ID" "$outdir/baseline_IGM.txt"
691 else
692 echo "No IGM sequences" > "$outdir/baseline_IGM.txt"
693 fi
694
695 mkdir $outdir/baseline/IGE
696 if [[ $(wc -l < $outdir/new_IMGT_IGE/1_Summary.txt) -gt "1" ]]; then
697 cd $outdir/baseline/IGE
698 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/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGE.pdf" "Sequence.ID" "$outdir/baseline_IGE.txt"
699 else
700 echo "No IGE sequences" > "$outdir/baseline_IGE.txt"
701 fi
702
703 cd $tmp
704
705 echo "Cleaning up *.RData files"
706 find $outdir/baseline -name "*.RData" -type f -delete
707
708 fi
709
710 echo "---------------- naive_output.r ----------------" 710 echo "---------------- naive_output.r ----------------"
711 echo "---------------- naive_output.r ----------------<br />" >> $log 711 echo "---------------- naive_output.r ----------------<br />" >> $log
712 712
713 if [[ "$naive_output" == "yes" ]] 713 if [[ "$naive_output" == "yes" ]]
714 then 714 then