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Uploaded unafold.sh
author hogart
date Tue, 10 Mar 2015 05:44:28 -0400
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children bda10049b902
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0:e186a2d22ea0 1:51baa0ab6def
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383 <span class="author"><span>Sergei Ryazansky</span></span>
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422 </div><!-- /.actions -->
423 <div class="file-info">
424 77 lines (66 sloc)
425 <span class="file-info-divider"></span>
426 1.912 kb
427 </div>
428 </div>
429
430 <div class="blob-wrapper data type-shell">
431 <table class="highlight tab-size-8 js-file-line-container">
432 <tr>
433 <td id="L1" class="blob-num js-line-number" data-line-number="1"></td>
434 <td id="LC1" class="blob-code js-file-line"><span class="pl-c">#!/bin/bash</span></td>
435 </tr>
436 <tr>
437 <td id="L2" class="blob-num js-line-number" data-line-number="2"></td>
438 <td id="LC2" class="blob-code js-file-line"><span class="pl-s3">set</span> -e</td>
439 </tr>
440 <tr>
441 <td id="L3" class="blob-num js-line-number" data-line-number="3"></td>
442 <td id="LC3" class="blob-code js-file-line">
443 </td>
444 </tr>
445 <tr>
446 <td id="L4" class="blob-num js-line-number" data-line-number="4"></td>
447 <td id="LC4" class="blob-code js-file-line"><span class="pl-c">#arguments are -i input sequence file in fasta </span></td>
448 </tr>
449 <tr>
450 <td id="L5" class="blob-num js-line-number" data-line-number="5"></td>
451 <td id="LC5" class="blob-code js-file-line"><span class="pl-c"># -o output zip arhive </span></td>
452 </tr>
453 <tr>
454 <td id="L6" class="blob-num js-line-number" data-line-number="6"></td>
455 <td id="LC6" class="blob-code js-file-line"><span class="pl-c"># -t temp directory with results</span></td>
456 </tr>
457 <tr>
458 <td id="L7" class="blob-num js-line-number" data-line-number="7"></td>
459 <td id="LC7" class="blob-code js-file-line"><span class="pl-c"># -a DNA|RNA</span></td>
460 </tr>
461 <tr>
462 <td id="L8" class="blob-num js-line-number" data-line-number="8"></td>
463 <td id="LC8" class="blob-code js-file-line"><span class="pl-c"># -c tempreature (C)</span></td>
464 </tr>
465 <tr>
466 <td id="L9" class="blob-num js-line-number" data-line-number="9"></td>
467 <td id="LC9" class="blob-code js-file-line"><span class="pl-c"># -s [Na+] in M</span></td>
468 </tr>
469 <tr>
470 <td id="L10" class="blob-num js-line-number" data-line-number="10"></td>
471 <td id="LC10" class="blob-code js-file-line"><span class="pl-c"># -m [Mg++] in M</span></td>
472 </tr>
473 <tr>
474 <td id="L11" class="blob-num js-line-number" data-line-number="11"></td>
475 <td id="LC11" class="blob-code js-file-line"><span class="pl-c"># -b maxbp</span></td>
476 </tr>
477 <tr>
478 <td id="L12" class="blob-num js-line-number" data-line-number="12"></td>
479 <td id="LC12" class="blob-code js-file-line">
480 </td>
481 </tr>
482 <tr>
483 <td id="L13" class="blob-num js-line-number" data-line-number="13"></td>
484 <td id="LC13" class="blob-code js-file-line"><span class="pl-c">#-n, --NA=(RNA | DNA) (defaults to RNA)</span></td>
485 </tr>
486 <tr>
487 <td id="L14" class="blob-num js-line-number" data-line-number="14"></td>
488 <td id="LC14" class="blob-code js-file-line"><span class="pl-c">#-t, --temp=&lt;temperature&gt; (defaults to 37)</span></td>
489 </tr>
490 <tr>
491 <td id="L15" class="blob-num js-line-number" data-line-number="15"></td>
492 <td id="LC15" class="blob-code js-file-line"><span class="pl-c">#-N, --sodium=&lt;[Na+] in M&gt; (defaults to 1)</span></td>
493 </tr>
494 <tr>
495 <td id="L16" class="blob-num js-line-number" data-line-number="16"></td>
496 <td id="LC16" class="blob-code js-file-line"><span class="pl-c">#-M, --magnesium=&lt;[Mg++] in M&gt; (defaults to 0)</span></td>
497 </tr>
498 <tr>
499 <td id="L17" class="blob-num js-line-number" data-line-number="17"></td>
500 <td id="LC17" class="blob-code js-file-line"><span class="pl-c">#-p, --polymer</span></td>
501 </tr>
502 <tr>
503 <td id="L18" class="blob-num js-line-number" data-line-number="18"></td>
504 <td id="LC18" class="blob-code js-file-line"><span class="pl-c">#-C, --Ct=&lt;total strand concentration&gt;</span></td>
505 </tr>
506 <tr>
507 <td id="L19" class="blob-num js-line-number" data-line-number="19"></td>
508 <td id="LC19" class="blob-code js-file-line"><span class="pl-c">#-I, --noisolate</span></td>
509 </tr>
510 <tr>
511 <td id="L20" class="blob-num js-line-number" data-line-number="20"></td>
512 <td id="LC20" class="blob-code js-file-line"><span class="pl-c">#-m, --maxbp=&lt;maximum basepair distance&gt;</span></td>
513 </tr>
514 <tr>
515 <td id="L21" class="blob-num js-line-number" data-line-number="21"></td>
516 <td id="LC21" class="blob-code js-file-line"><span class="pl-c">#-c, --constraints=&lt;name of constraints file&gt; (defaults to prefix.aux)</span></td>
517 </tr>
518 <tr>
519 <td id="L22" class="blob-num js-line-number" data-line-number="22"></td>
520 <td id="LC22" class="blob-code js-file-line"><span class="pl-c">#-P, --percent=&lt;energy increment percent&gt; (defaults to 5)</span></td>
521 </tr>
522 <tr>
523 <td id="L23" class="blob-num js-line-number" data-line-number="23"></td>
524 <td id="LC23" class="blob-code js-file-line"><span class="pl-c">#-W, --window=&lt;window size&gt; (default set by sequence length)</span></td>
525 </tr>
526 <tr>
527 <td id="L24" class="blob-num js-line-number" data-line-number="24"></td>
528 <td id="LC24" class="blob-code js-file-line"><span class="pl-c">#-X, --max=&lt;maximum number of foldings&gt; (defaults to 100)</span></td>
529 </tr>
530 <tr>
531 <td id="L25" class="blob-num js-line-number" data-line-number="25"></td>
532 <td id="LC25" class="blob-code js-file-line"><span class="pl-c"># --ann=(none | p-num | ss-count) (defaults to none)</span></td>
533 </tr>
534 <tr>
535 <td id="L26" class="blob-num js-line-number" data-line-number="26"></td>
536 <td id="LC26" class="blob-code js-file-line"><span class="pl-c"># --mode=(auto | bases | lines) (defaults to auto)</span></td>
537 </tr>
538 <tr>
539 <td id="L27" class="blob-num js-line-number" data-line-number="27"></td>
540 <td id="LC27" class="blob-code js-file-line"><span class="pl-c"># --label=&lt;base numbering frequency&gt;</span></td>
541 </tr>
542 <tr>
543 <td id="L28" class="blob-num js-line-number" data-line-number="28"></td>
544 <td id="LC28" class="blob-code js-file-line"><span class="pl-c"># --rotate=&lt;structure rotation angle&gt;</span></td>
545 </tr>
546 <tr>
547 <td id="L29" class="blob-num js-line-number" data-line-number="29"></td>
548 <td id="LC29" class="blob-code js-file-line"><span class="pl-c"># --run-type=(text | html) (defaults to text)</span></td>
549 </tr>
550 <tr>
551 <td id="L30" class="blob-num js-line-number" data-line-number="30"></td>
552 <td id="LC30" class="blob-code js-file-line"><span class="pl-c"># --model=(EM | PF) (defaults to EM)</span></td>
553 </tr>
554 <tr>
555 <td id="L31" class="blob-num js-line-number" data-line-number="31"></td>
556 <td id="LC31" class="blob-code js-file-line"><span class="pl-c"># --circular</span></td>
557 </tr>
558 <tr>
559 <td id="L32" class="blob-num js-line-number" data-line-number="32"></td>
560 <td id="LC32" class="blob-code js-file-line"><span class="pl-c">#Obscure options:</span></td>
561 </tr>
562 <tr>
563 <td id="L33" class="blob-num js-line-number" data-line-number="33"></td>
564 <td id="LC33" class="blob-code js-file-line"><span class="pl-c"># --allpairs</span></td>
565 </tr>
566 <tr>
567 <td id="L34" class="blob-num js-line-number" data-line-number="34"></td>
568 <td id="LC34" class="blob-code js-file-line"><span class="pl-c"># --maxloop=&lt;maximum bulge/interior loop size&gt; (defaults to 30)</span></td>
569 </tr>
570 <tr>
571 <td id="L35" class="blob-num js-line-number" data-line-number="35"></td>
572 <td id="LC35" class="blob-code js-file-line"><span class="pl-c"># --nodangle</span></td>
573 </tr>
574 <tr>
575 <td id="L36" class="blob-num js-line-number" data-line-number="36"></td>
576 <td id="LC36" class="blob-code js-file-line"><span class="pl-c"># --simple</span></td>
577 </tr>
578 <tr>
579 <td id="L37" class="blob-num js-line-number" data-line-number="37"></td>
580 <td id="LC37" class="blob-code js-file-line"><span class="pl-c"># --prefilter=&lt;filter value&gt;</span></td>
581 </tr>
582 <tr>
583 <td id="L38" class="blob-num js-line-number" data-line-number="38"></td>
584 <td id="LC38" class="blob-code js-file-line">
585 </td>
586 </tr>
587 <tr>
588 <td id="L39" class="blob-num js-line-number" data-line-number="39"></td>
589 <td id="LC39" class="blob-code js-file-line">NA=RNA</td>
590 </tr>
591 <tr>
592 <td id="L40" class="blob-num js-line-number" data-line-number="40"></td>
593 <td id="LC40" class="blob-code js-file-line">TM=37</td>
594 </tr>
595 <tr>
596 <td id="L41" class="blob-num js-line-number" data-line-number="41"></td>
597 <td id="LC41" class="blob-code js-file-line">NAT=1</td>
598 </tr>
599 <tr>
600 <td id="L42" class="blob-num js-line-number" data-line-number="42"></td>
601 <td id="LC42" class="blob-code js-file-line">MG=0</td>
602 </tr>
603 <tr>
604 <td id="L43" class="blob-num js-line-number" data-line-number="43"></td>
605 <td id="LC43" class="blob-code js-file-line">
606 </td>
607 </tr>
608 <tr>
609 <td id="L44" class="blob-num js-line-number" data-line-number="44"></td>
610 <td id="LC44" class="blob-code js-file-line"><span class="pl-k">while</span> <span class="pl-s3">getopts</span> <span class="pl-s1"><span class="pl-pds">&quot;</span>:i:o:t:a:c:s:m:<span class="pl-pds">&quot;</span></span> OPTION<span class="pl-k">;</span></td>
611 </tr>
612 <tr>
613 <td id="L45" class="blob-num js-line-number" data-line-number="45"></td>
614 <td id="LC45" class="blob-code js-file-line"><span class="pl-k">do</span></td>
615 </tr>
616 <tr>
617 <td id="L46" class="blob-num js-line-number" data-line-number="46"></td>
618 <td id="LC46" class="blob-code js-file-line"> <span class="pl-k">case</span> <span class="pl-vo">$OPTION</span> in</td>
619 </tr>
620 <tr>
621 <td id="L47" class="blob-num js-line-number" data-line-number="47"></td>
622 <td id="LC47" class="blob-code js-file-line"> i) INPUT=<span class="pl-s1"><span class="pl-pds">&quot;</span><span class="pl-vo">$OPTARG</span><span class="pl-pds">&quot;</span></span>;;</td>
623 </tr>
624 <tr>
625 <td id="L48" class="blob-num js-line-number" data-line-number="48"></td>
626 <td id="LC48" class="blob-code js-file-line"> o) ZIP_ARHIVE=<span class="pl-s1"><span class="pl-pds">&quot;</span><span class="pl-vo">$OPTARG</span><span class="pl-pds">&quot;</span></span>;;</td>
627 </tr>
628 <tr>
629 <td id="L49" class="blob-num js-line-number" data-line-number="49"></td>
630 <td id="LC49" class="blob-code js-file-line"> t) TEMP_DIR=<span class="pl-s1"><span class="pl-pds">&quot;</span><span class="pl-vo">$OPTARG</span><span class="pl-pds">&quot;</span></span>;;</td>
631 </tr>
632 <tr>
633 <td id="L50" class="blob-num js-line-number" data-line-number="50"></td>
634 <td id="LC50" class="blob-code js-file-line"> a) NA=<span class="pl-s1"><span class="pl-pds">&quot;</span><span class="pl-vo">$OPTARG</span><span class="pl-pds">&quot;</span></span>;;</td>
635 </tr>
636 <tr>
637 <td id="L51" class="blob-num js-line-number" data-line-number="51"></td>
638 <td id="LC51" class="blob-code js-file-line"> c) TM=<span class="pl-s1"><span class="pl-pds">&quot;</span><span class="pl-vo">$OPTARG</span><span class="pl-pds">&quot;</span></span>;;</td>
639 </tr>
640 <tr>
641 <td id="L52" class="blob-num js-line-number" data-line-number="52"></td>
642 <td id="LC52" class="blob-code js-file-line"> s) NAT=<span class="pl-s1"><span class="pl-pds">&quot;</span><span class="pl-vo">$OPTARG</span><span class="pl-pds">&quot;</span></span>;;</td>
643 </tr>
644 <tr>
645 <td id="L53" class="blob-num js-line-number" data-line-number="53"></td>
646 <td id="LC53" class="blob-code js-file-line"> m) MG=<span class="pl-s1"><span class="pl-pds">&quot;</span><span class="pl-vo">$OPTARG</span><span class="pl-pds">&quot;</span></span>;;</td>
647 </tr>
648 <tr>
649 <td id="L54" class="blob-num js-line-number" data-line-number="54"></td>
650 <td id="LC54" class="blob-code js-file-line"> <span class="pl-k">esac</span></td>
651 </tr>
652 <tr>
653 <td id="L55" class="blob-num js-line-number" data-line-number="55"></td>
654 <td id="LC55" class="blob-code js-file-line"><span class="pl-k">done</span></td>
655 </tr>
656 <tr>
657 <td id="L56" class="blob-num js-line-number" data-line-number="56"></td>
658 <td id="LC56" class="blob-code js-file-line"> </td>
659 </tr>
660 <tr>
661 <td id="L57" class="blob-num js-line-number" data-line-number="57"></td>
662 <td id="LC57" class="blob-code js-file-line">mkdir -p <span class="pl-vo">${TEMP_DIR}</span>/unafold</td>
663 </tr>
664 <tr>
665 <td id="L58" class="blob-num js-line-number" data-line-number="58"></td>
666 <td id="LC58" class="blob-code js-file-line"><span class="pl-s3">cd</span> <span class="pl-vo">${TEMP_DIR}</span>/unafold</td>
667 </tr>
668 <tr>
669 <td id="L59" class="blob-num js-line-number" data-line-number="59"></td>
670 <td id="LC59" class="blob-code js-file-line">
671 </td>
672 </tr>
673 <tr>
674 <td id="L60" class="blob-num js-line-number" data-line-number="60"></td>
675 <td id="LC60" class="blob-code js-file-line">NA=<span class="pl-s1"><span class="pl-pds">$(</span><span class="pl-s3">echo</span> <span class="pl-vo">$NA</span> <span class="pl-k">|</span> tr <span class="pl-s1"><span class="pl-pds">&#39;</span>[:lower:]<span class="pl-pds">&#39;</span></span> <span class="pl-s1"><span class="pl-pds">&#39;</span>[:upper:]<span class="pl-pds">&#39;</span></span><span class="pl-pds">)</span></span></td>
676 </tr>
677 <tr>
678 <td id="L61" class="blob-num js-line-number" data-line-number="61"></td>
679 <td id="LC61" class="blob-code js-file-line">
680 </td>
681 </tr>
682 <tr>
683 <td id="L62" class="blob-num js-line-number" data-line-number="62"></td>
684 <td id="LC62" class="blob-code js-file-line"><span class="pl-c"># calucalation of RNA don&#39;t need the concentraion of salts</span></td>
685 </tr>
686 <tr>
687 <td id="L63" class="blob-num js-line-number" data-line-number="63"></td>
688 <td id="LC63" class="blob-code js-file-line"><span class="pl-k">if</span> [[ <span class="pl-vo">${NA}</span> <span class="pl-k">==</span> <span class="pl-s1"><span class="pl-pds">&#39;</span>DNA<span class="pl-pds">&#39;</span></span> ]]<span class="pl-k">;</span> <span class="pl-k">then</span></td>
689 </tr>
690 <tr>
691 <td id="L64" class="blob-num js-line-number" data-line-number="64"></td>
692 <td id="LC64" class="blob-code js-file-line"> UNAFold.pl -n <span class="pl-vo">${NA}</span> -t <span class="pl-vo">${TM}</span> -N <span class="pl-vo">${NAT}</span> -M <span class="pl-vo">${MG}</span> <span class="pl-vo">${INPUT}</span></td>
693 </tr>
694 <tr>
695 <td id="L65" class="blob-num js-line-number" data-line-number="65"></td>
696 <td id="LC65" class="blob-code js-file-line"><span class="pl-k">else</span></td>
697 </tr>
698 <tr>
699 <td id="L66" class="blob-num js-line-number" data-line-number="66"></td>
700 <td id="LC66" class="blob-code js-file-line"> UNAFold.pl -n <span class="pl-vo">${NA}</span> -t <span class="pl-vo">${TM}</span> <span class="pl-vo">${INPUT}</span></td>
701 </tr>
702 <tr>
703 <td id="L67" class="blob-num js-line-number" data-line-number="67"></td>
704 <td id="LC67" class="blob-code js-file-line"><span class="pl-k">fi</span></td>
705 </tr>
706 <tr>
707 <td id="L68" class="blob-num js-line-number" data-line-number="68"></td>
708 <td id="LC68" class="blob-code js-file-line">
709 </td>
710 </tr>
711 <tr>
712 <td id="L69" class="blob-num js-line-number" data-line-number="69"></td>
713 <td id="LC69" class="blob-code js-file-line"><span class="pl-s3">echo</span> <span class="pl-s1"><span class="pl-pds">&quot;</span><span class="pl-pds">&quot;</span></span></td>
714 </tr>
715 <tr>
716 <td id="L70" class="blob-num js-line-number" data-line-number="70"></td>
717 <td id="LC70" class="blob-code js-file-line"><span class="pl-s3">echo</span> <span class="pl-s1"><span class="pl-pds">&quot;</span>Parametres of UNAFold run:<span class="pl-pds">&quot;</span></span></td>
718 </tr>
719 <tr>
720 <td id="L71" class="blob-num js-line-number" data-line-number="71"></td>
721 <td id="LC71" class="blob-code js-file-line">cat <span class="pl-k">*</span>run</td>
722 </tr>
723 <tr>
724 <td id="L72" class="blob-num js-line-number" data-line-number="72"></td>
725 <td id="LC72" class="blob-code js-file-line">
726 </td>
727 </tr>
728 <tr>
729 <td id="L73" class="blob-num js-line-number" data-line-number="73"></td>
730 <td id="LC73" class="blob-code js-file-line"><span class="pl-s3">cd</span> ../</td>
731 </tr>
732 <tr>
733 <td id="L74" class="blob-num js-line-number" data-line-number="74"></td>
734 <td id="LC74" class="blob-code js-file-line">zip -r -q unafold.zip unafold</td>
735 </tr>
736 <tr>
737 <td id="L75" class="blob-num js-line-number" data-line-number="75"></td>
738 <td id="LC75" class="blob-code js-file-line">mv unafold.zip <span class="pl-vo">${ZIP_ARHIVE}</span></td>
739 </tr>
740 <tr>
741 <td id="L76" class="blob-num js-line-number" data-line-number="76"></td>
742 <td id="LC76" class="blob-code js-file-line">
743 </td>
744 </tr>
745 </table>
746
747 </div>
748
749 </div>
750
751 <a href="#jump-to-line" rel="facebox[.linejump]" data-hotkey="l" style="display:none">Jump to Line</a>
752 <div id="jump-to-line" style="display:none">
753 <form accept-charset="UTF-8" class="js-jump-to-line-form">
754 <input class="linejump-input js-jump-to-line-field" type="text" placeholder="Jump to line&hellip;" autofocus>
755 <button type="submit" class="button">Go</button>
756 </form>
757 </div>
758
759 </div>
760
761 </div><!-- /.repo-container -->
762 <div class="modal-backdrop"></div>
763 </div><!-- /.container -->
764 </div><!-- /.site -->
765
766
767 </div><!-- /.wrapper -->
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771 <ul class="site-footer-links right">
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790 </ul>
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793
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795 <div class="fullscreen-overlay js-fullscreen-overlay" id="fullscreen_overlay">
796 <div class="fullscreen-container js-suggester-container">
797 <div class="textarea-wrap">
798 <textarea name="fullscreen-contents" id="fullscreen-contents" class="fullscreen-contents js-fullscreen-contents" placeholder=""></textarea>
799 <div class="suggester-container">
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818
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823 </div>
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825
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