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comparison GFFtools-GX @ 7:ee541c1852da

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Uploaded version 2.1.0
author vipints
date Thu, 23 Apr 2015 17:43:11 -0400
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466 <a href="/vipints/GFFtools-GX/commit/0ea921f8d7cc65bb044616b14dfdae59b54e2073" class="message" data-pjax="true" title="fixed">fixed</a>
467
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470 <button aria-label="Copy SHA" class="js-zeroclipboard zeroclipboard-link tooltipped tooltipped-s" data-clipboard-text="0ea921f8d7cc65bb044616b14dfdae59b54e2073" data-copied-hint="Copied!" type="button"><span class="octicon octicon-clippy"></span></button>
471 <a href="/vipints/GFFtools-GX/commit/0ea921f8d7cc65bb044616b14dfdae59b54e2073" class="sha-block" data-pjax>latest commit <span class="sha">0ea921f8d7</span></a>
472
473 <div class="authorship">
474 <img alt="@vipints" class="avatar" data-user="1714549" height="20" src="https://avatars0.githubusercontent.com/u/1714549?v=3&amp;s=40" width="20" />
475 <span class="author-name"><a href="/vipints" rel="author">vipints</a></span>
476 authored <time class="updated" datetime="2015-04-23T21:27:17Z" is="relative-time">Apr 23, 2015</time>
477
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480 </div>
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485
486 <table class="files" data-pjax>
487
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489 <tbody>
490 <tr class="warning include-fragment-error">
491 <td class="icon"><span class="octicon octicon-alert"></span></td>
492 <td class="content" colspan="3">Failed to load latest commit information.</td>
493 </tr>
494
495 <tr>
496 <td class="icon">
497 <span class="octicon octicon-file-directory"></span>
498 <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" />
499 </td>
500 <td class="content">
501 <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/tree/master/test-data" class="js-directory-link" id="24346e1b50066607059af36e3b684b24-99e7a2029aade02cb90a0e26ff6109547a6078ea" title="test-data">test-data</a></span>
502 </td>
503 <td class="message">
504 <span class="css-truncate css-truncate-target">
505 <a href="/vipints/GFFtools-GX/commit/46e670f9d93f3797740d21a100428fe195b6c83f" class="message" data-pjax="true" title="functional test perfomed after the change">functional test perfomed after the change</a>
506 </span>
507 </td>
508 <td class="age">
509 <span class="css-truncate css-truncate-target"><time datetime="2015-04-21T22:42:01Z" is="time-ago">Apr 21, 2015</time></span>
510 </td>
511 </tr>
512 <tr>
513 <td class="icon">
514 <span class="octicon octicon-file-text"></span>
515 <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" />
516 </td>
517 <td class="content">
518 <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/blob/master/.gitignore" class="js-directory-link" id="a084b794bc0759e7a6b77810e01874f2-0334fc9da4d9b7a262012ae6cae37002259af5b2" title=".gitignore">.gitignore</a></span>
519 </td>
520 <td class="message">
521 <span class="css-truncate css-truncate-target">
522 <a href="/vipints/GFFtools-GX/commit/c5b661defaf94700cf290651669846c8258e220d" class="message" data-pjax="true" title="ignored pyc and swap files">ignored pyc and swap files</a>
523 </span>
524 </td>
525 <td class="age">
526 <span class="css-truncate css-truncate-target"><time datetime="2014-07-18T22:28:50Z" is="time-ago">Jul 18, 2014</time></span>
527 </td>
528 </tr>
529 <tr>
530 <td class="icon">
531 <span class="octicon octicon-file-text"></span>
532 <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" />
533 </td>
534 <td class="content">
535 <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/blob/master/GFFParser.py" class="js-directory-link" id="4a9c2f3a2b51d00c039e9951aa5df3fd-505eece57e21af803c93cdb06d9d569c81d1d811" title="GFFParser.py">GFFParser.py</a></span>
536 </td>
537 <td class="message">
538 <span class="css-truncate css-truncate-target">
539 <a href="/vipints/GFFtools-GX/commit/cb38052d271326df1d0577bfe0f6a877458da8a6" class="message" data-pjax="true" title="added a new field to carryover the isoform level score from the GFF file- has to sync with main gfftools">added a new field to carryover the isoform level score from the GFF f…</a>
540 </span>
541 </td>
542 <td class="age">
543 <span class="css-truncate css-truncate-target"><time datetime="2015-04-19T21:50:45Z" is="time-ago">Apr 19, 2015</time></span>
544 </td>
545 </tr>
546 <tr>
547 <td class="icon">
548 <span class="octicon octicon-file-text"></span>
549 <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" />
550 </td>
551 <td class="content">
552 <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/blob/master/README.md" class="js-directory-link" id="04c6e90faac2675aa89e2176d2eec7d8-17e766c0f2926d94933cb7320afd6c1f5db293fb" title="README.md">README.md</a></span>
553 </td>
554 <td class="message">
555 <span class="css-truncate css-truncate-target">
556 <a href="/vipints/GFFtools-GX/commit/0ea921f8d7cc65bb044616b14dfdae59b54e2073" class="message" data-pjax="true" title="fixed">fixed</a>
557 </span>
558 </td>
559 <td class="age">
560 <span class="css-truncate css-truncate-target"><time datetime="2015-04-23T21:27:17Z" is="time-ago">Apr 23, 2015</time></span>
561 </td>
562 </tr>
563 <tr>
564 <td class="icon">
565 <span class="octicon octicon-file-text"></span>
566 <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" />
567 </td>
568 <td class="content">
569 <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/blob/master/bed_to_gff.py" class="js-directory-link" id="4fd14b034003e6ed6b3c1243f3f285ed-461ae7292d229b40fb98dec1d28a67aebfde7c96" title="bed_to_gff.py">bed_to_gff.py</a></span>
570 </td>
571 <td class="message">
572 <span class="css-truncate css-truncate-target">
573 <a href="/vipints/GFFtools-GX/commit/b882fc8c206c3203792da6c4c856005eb06934c4" class="message" data-pjax="true" title="removing print statement from the code">removing print statement from the code</a>
574 </span>
575 </td>
576 <td class="age">
577 <span class="css-truncate css-truncate-target"><time datetime="2015-04-14T23:41:11Z" is="time-ago">Apr 14, 2015</time></span>
578 </td>
579 </tr>
580 <tr>
581 <td class="icon">
582 <span class="octicon octicon-file-text"></span>
583 <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" />
584 </td>
585 <td class="content">
586 <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/blob/master/bed_to_gff.xml" class="js-directory-link" id="fd45df94f6d642a741c0c8d038949b37-2b5908455dd6730bd4bbd634f56316dfd70eca03" title="bed_to_gff.xml">bed_to_gff.xml</a></span>
587 </td>
588 <td class="message">
589 <span class="css-truncate css-truncate-target">
590 <a href="/vipints/GFFtools-GX/commit/34fdf81381a56ffc7e3a57736a49d516f20c120b" class="message" data-pjax="true" title="updated the gbk_to_gff wrapper and fixed typo">updated the gbk_to_gff wrapper and fixed typo</a>
591 </span>
592 </td>
593 <td class="age">
594 <span class="css-truncate css-truncate-target"><time datetime="2015-04-17T21:14:52Z" is="time-ago">Apr 17, 2015</time></span>
595 </td>
596 </tr>
597 <tr>
598 <td class="icon">
599 <span class="octicon octicon-file-text"></span>
600 <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" />
601 </td>
602 <td class="content">
603 <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/blob/master/gbk_to_gff.py" class="js-directory-link" id="8cedf4409efd74682d25ee79bb3574dc-6638d994bf8d1a8aaa231c70bf44b6021f9ccf1b" title="gbk_to_gff.py">gbk_to_gff.py</a></span>
604 </td>
605 <td class="message">
606 <span class="css-truncate css-truncate-target">
607 <a href="/vipints/GFFtools-GX/commit/84a145c7ee9efa171dbe1d64223e20ceb1930de6" class="message" data-pjax="true" title="gbk parsing and correctly assigning feature type">gbk parsing and correctly assigning feature type</a>
608 </span>
609 </td>
610 <td class="age">
611 <span class="css-truncate css-truncate-target"><time datetime="2015-04-17T21:04:25Z" is="time-ago">Apr 17, 2015</time></span>
612 </td>
613 </tr>
614 <tr>
615 <td class="icon">
616 <span class="octicon octicon-file-text"></span>
617 <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" />
618 </td>
619 <td class="content">
620 <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/blob/master/gbk_to_gff.xml" class="js-directory-link" id="5e708155a06e4244e26c978ed02c6fd2-c90e390761eb5390bda2e245b7eb7456d5e9c665" title="gbk_to_gff.xml">gbk_to_gff.xml</a></span>
621 </td>
622 <td class="message">
623 <span class="css-truncate css-truncate-target">
624 <a href="/vipints/GFFtools-GX/commit/34fdf81381a56ffc7e3a57736a49d516f20c120b" class="message" data-pjax="true" title="updated the gbk_to_gff wrapper and fixed typo">updated the gbk_to_gff wrapper and fixed typo</a>
625 </span>
626 </td>
627 <td class="age">
628 <span class="css-truncate css-truncate-target"><time datetime="2015-04-17T21:14:52Z" is="time-ago">Apr 17, 2015</time></span>
629 </td>
630 </tr>
631 <tr>
632 <td class="icon">
633 <span class="octicon octicon-file-text"></span>
634 <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" />
635 </td>
636 <td class="content">
637 <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/blob/master/gff_to_bed.py" class="js-directory-link" id="95b17a03c0948b20d1264fcd269b60fa-457e6d44dbc1f4531de174641f74f9e6ec689982" title="gff_to_bed.py">gff_to_bed.py</a></span>
638 </td>
639 <td class="message">
640 <span class="css-truncate css-truncate-target">
641 <a href="/vipints/GFFtools-GX/commit/f84e0d96db79436b685066c088bf1555a3bf29e1" class="message" data-pjax="true" title="changing the float behaviour to int">changing the float behaviour to int</a>
642 </span>
643 </td>
644 <td class="age">
645 <span class="css-truncate css-truncate-target"><time datetime="2015-04-22T16:25:13Z" is="time-ago">Apr 22, 2015</time></span>
646 </td>
647 </tr>
648 <tr>
649 <td class="icon">
650 <span class="octicon octicon-file-text"></span>
651 <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" />
652 </td>
653 <td class="content">
654 <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/blob/master/gff_to_bed.xml" class="js-directory-link" id="8c7d5ae4b79728262acfc56888f2444e-10754bece6a7a5a7c5dc9d533d92ddfa046e6b6b" title="gff_to_bed.xml">gff_to_bed.xml</a></span>
655 </td>
656 <td class="message">
657 <span class="css-truncate css-truncate-target">
658 <a href="/vipints/GFFtools-GX/commit/2c96e399526d372a61df5b4068bc91e08af49092" class="message" data-pjax="true" title="updated the wrapper version">updated the wrapper version</a>
659 </span>
660 </td>
661 <td class="age">
662 <span class="css-truncate css-truncate-target"><time datetime="2015-04-19T02:59:32Z" is="time-ago">Apr 18, 2015</time></span>
663 </td>
664 </tr>
665 <tr>
666 <td class="icon">
667 <span class="octicon octicon-file-text"></span>
668 <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" />
669 </td>
670 <td class="content">
671 <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/blob/master/gff_to_gtf.py" class="js-directory-link" id="88b7a441373dfec1e07cd28bb1eb8c3e-9ff53c56125edfa286255f489e61cda154a21693" title="gff_to_gtf.py">gff_to_gtf.py</a></span>
672 </td>
673 <td class="message">
674 <span class="css-truncate css-truncate-target">
675 <a href="/vipints/GFFtools-GX/commit/f76a6c972d5e4200f182bb25493a675ca3fe09ae" class="message" data-pjax="true" title="functional test performed and changed version to 0.6">functional test performed and changed version to 0.6</a>
676 </span>
677 </td>
678 <td class="age">
679 <span class="css-truncate css-truncate-target"><time datetime="2015-04-20T22:14:25Z" is="time-ago">Apr 20, 2015</time></span>
680 </td>
681 </tr>
682 <tr>
683 <td class="icon">
684 <span class="octicon octicon-file-text"></span>
685 <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" />
686 </td>
687 <td class="content">
688 <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/blob/master/gff_to_gtf.xml" class="js-directory-link" id="f4676750a1f71b9fbf35b537b0546842-a2b41ec7924d6609f219bdf8c0372af59ea747d2" title="gff_to_gtf.xml">gff_to_gtf.xml</a></span>
689 </td>
690 <td class="message">
691 <span class="css-truncate css-truncate-target">
692 <a href="/vipints/GFFtools-GX/commit/f76a6c972d5e4200f182bb25493a675ca3fe09ae" class="message" data-pjax="true" title="functional test performed and changed version to 0.6">functional test performed and changed version to 0.6</a>
693 </span>
694 </td>
695 <td class="age">
696 <span class="css-truncate css-truncate-target"><time datetime="2015-04-20T22:14:25Z" is="time-ago">Apr 20, 2015</time></span>
697 </td>
698 </tr>
699 <tr>
700 <td class="icon">
701 <span class="octicon octicon-file-text"></span>
702 <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" />
703 </td>
704 <td class="content">
705 <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/blob/master/gtf_to_gff.py" class="js-directory-link" id="6989ac39182645599caeb47b4e0e8ef6-6d786691f74f0c00db3da883f4e6e7e1d009d2c2" title="gtf_to_gff.py">gtf_to_gff.py</a></span>
706 </td>
707 <td class="message">
708 <span class="css-truncate css-truncate-target">
709 <a href="/vipints/GFFtools-GX/commit/1ee80e9b0a4b7a05094f42fd8836ec248af85d0e" class="message" data-pjax="true" title="updated the version 0.6 gtftogff">updated the version 0.6 gtftogff</a>
710 </span>
711 </td>
712 <td class="age">
713 <span class="css-truncate css-truncate-target"><time datetime="2015-04-20T23:08:52Z" is="time-ago">Apr 20, 2015</time></span>
714 </td>
715 </tr>
716 <tr>
717 <td class="icon">
718 <span class="octicon octicon-file-text"></span>
719 <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" />
720 </td>
721 <td class="content">
722 <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/blob/master/gtf_to_gff.xml" class="js-directory-link" id="a8bd25db400514c2556192045eacd820-dc2031de1c3daa1cf8644a5c62c9d4afce97ad39" title="gtf_to_gff.xml">gtf_to_gff.xml</a></span>
723 </td>
724 <td class="message">
725 <span class="css-truncate css-truncate-target">
726 <a href="/vipints/GFFtools-GX/commit/1ee80e9b0a4b7a05094f42fd8836ec248af85d0e" class="message" data-pjax="true" title="updated the version 0.6 gtftogff">updated the version 0.6 gtftogff</a>
727 </span>
728 </td>
729 <td class="age">
730 <span class="css-truncate css-truncate-target"><time datetime="2015-04-20T23:08:52Z" is="time-ago">Apr 20, 2015</time></span>
731 </td>
732 </tr>
733 <tr>
734 <td class="icon">
735 <span class="octicon octicon-file-text"></span>
736 <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" />
737 </td>
738 <td class="content">
739 <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/blob/master/helper.py" class="js-directory-link" id="702b6abf015bfdb4e41308ddd3b297a9-a711ed60defe1bd9ef579fada75e32da2313935c" title="helper.py">helper.py</a></span>
740 </td>
741 <td class="message">
742 <span class="css-truncate css-truncate-target">
743 <a href="/vipints/GFFtools-GX/commit/cb38052d271326df1d0577bfe0f6a877458da8a6" class="message" data-pjax="true" title="added a new field to carryover the isoform level score from the GFF file- has to sync with main gfftools">added a new field to carryover the isoform level score from the GFF f…</a>
744 </span>
745 </td>
746 <td class="age">
747 <span class="css-truncate css-truncate-target"><time datetime="2015-04-19T21:50:45Z" is="time-ago">Apr 19, 2015</time></span>
748 </td>
749 </tr>
750 <tr>
751 <td class="icon">
752 <span class="octicon octicon-file-text"></span>
753 <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" />
754 </td>
755 <td class="content">
756 <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/blob/master/tool_conf.xml.sample" class="js-directory-link" id="76a06ab03a6f35bfb6ff2be40e654b7e-e26478f762dbc5e03f339bc5598086009e4f8be0" title="tool_conf.xml.sample">tool_conf.xml.sample</a></span>
757 </td>
758 <td class="message">
759 <span class="css-truncate css-truncate-target">
760 <a href="/vipints/GFFtools-GX/commit/04ccdc96c4bf8d6b8420a05c9afa8c8540345e32" class="message" data-pjax="true" title="updated the toolpanel list">updated the toolpanel list</a>
761 </span>
762 </td>
763 <td class="age">
764 <span class="css-truncate css-truncate-target"><time datetime="2015-04-20T22:15:28Z" is="time-ago">Apr 20, 2015</time></span>
765 </td>
766 </tr>
767 <tr>
768 <td class="icon">
769 <span class="octicon octicon-file-text"></span>
770 <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" />
771 </td>
772 <td class="content">
773 <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/blob/master/tool_dependencies.xml" class="js-directory-link" id="1f1e2fcbf1ddc07a88bc59ca246c9a90-a0a1a7f1bb7e1a6a8b79f30629c8968f8b4c8d36" title="tool_dependencies.xml">tool_dependencies.xml</a></span>
774 </td>
775 <td class="message">
776 <span class="css-truncate css-truncate-target">
777 <a href="/vipints/GFFtools-GX/commit/c75c2be2f54ca59449e999346de2427584789ec9" class="message" data-pjax="true" title="biopython required">biopython required</a>
778 </span>
779 </td>
780 <td class="age">
781 <span class="css-truncate css-truncate-target"><time datetime="2015-04-21T22:54:33Z" is="time-ago">Apr 21, 2015</time></span>
782 </td>
783 </tr>
784 </tbody>
785 </table>
786
787 </div>
788
789
790 <div id="readme" class="boxed-group flush clearfix announce instapaper_body md">
791 <h3>
792 <span class="octicon octicon-book"></span>
793 README.md
794 </h3>
795
796 <article class="markdown-body entry-content" itemprop="mainContentOfPage"><h1>
797 <a id="user-content-gfftools-gx-" class="anchor" href="#gfftools-gx-" aria-hidden="true"><span class="octicon octicon-link"></span></a>GFFtools-GX </h1>
798
799 <p>A collection of tools for converting genome annotation between <a href="https://genome.ucsc.edu/FAQ/FAQformat.html#format4">GTF</a>, <a href="https://genome.ucsc.edu/FAQ/FAQformat.html#format1">BED</a>, <a href="http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html">GenBank</a> and <a href="https://genome.ucsc.edu/FAQ/FAQformat.html#format3">GFF</a>.</p>
800
801 <h5>
802 <a id="user-content-introduction" class="anchor" href="#introduction" aria-hidden="true"><span class="octicon octicon-link"></span></a>INTRODUCTION</h5>
803
804 <p>Several genome annotation centers provide their data in GTF, BED, GFF and GenBank format. I have few programs, they mainly deals with converting between GTF, BED GenBank and GFF formats. They are extensively tested with files from different centers like <a href="http://www.ensembl.org">ENSEMBL</a>, <a href="https://genome.ucsc.edu/">UCSC</a>, <a href="http://genome.jgi.doe.gov/">JGI</a> and <a href="http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/HelpJan.html">NCBI AceView</a>. These programs can be easily integrated into your galaxy instance.</p>
805
806 <h5>
807 <a id="user-content-contents" class="anchor" href="#contents" aria-hidden="true"><span class="octicon octicon-link"></span></a>CONTENTS</h5>
808
809 <p>Included utilities are: </p>
810
811 <pre><code>BED-to-GFF: convert data from a 12 column UCSC wiggle BED format to GFF
812 GBK-to-GFF: convert data from genbank format to GFF
813 GFF-to-BED: convert data from GFF to 12 column BED format
814 GFF-to-GTF: convert data from GFF to GTF
815 GTF-to-GFF: convert data from GTF to valid GFF
816 </code></pre>
817
818 <p>test-data: Test data set. (move to your galaxy-root-folder/test-data/)</p>
819
820 <pre><code>You may need to move the test files into your test-data directory so galaxy can find them.
821 If you want to run the functional tests eg as:
822
823 exmaple:
824 sh run_functional_tests.sh -id fml_gtf2gff
825 </code></pre>
826
827 <h5>
828 <a id="user-content-requirements" class="anchor" href="#requirements" aria-hidden="true"><span class="octicon octicon-link"></span></a>REQUIREMENTS</h5>
829
830 <pre><code>python2.6 or 2.7 and biopython
831
832 Galaxy should be able to automatically install biopython via Galaxy toolshed.
833 </code></pre>
834
835 <h5>
836 <a id="user-content-commentsquestions" class="anchor" href="#commentsquestions" aria-hidden="true"><span class="octicon octicon-link"></span></a>COMMENTS/QUESTIONS</h5>
837
838 <p>I can be reached at vipin [at] cbio.mskcc.org </p>
839
840 <h5>
841 <a id="user-content-license" class="anchor" href="#license" aria-hidden="true"><span class="octicon octicon-link"></span></a>LICENSE</h5>
842
843 <p>Copyright (c) 2009-2012, Friedrich Miescher Laboratory of the Max Planck Society</p>
844
845 <pre><code> 2013-2015, Memorial Sloan Kettering Cancer Center
846 Vipin T Sreedharan &lt;vipin@cbio.mskcc.org&gt;
847 </code></pre>
848
849 <p>All rights reserved.</p>
850
851 <p>Licensed under the BSD 2-Clause License: <a href="http://opensource.org/licenses/BSD-2-Clause">http://opensource.org/licenses/BSD-2-Clause</a></p>
852
853 <pre><code>Redistribution and use in source and binary forms, with or without
854 modification, are permitted provided that the following conditions are met:
855
856 * Redistributions of source code must retain the above copyright notice,
857 this list of conditions and the following disclaimer.
858
859 * Redistributions in binary form must reproduce the above copyright notice,
860 this list of conditions and the following disclaimer in the documentation
861 and/or other materials provided with the distribution.
862
863 THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
864 ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
865 WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
866 DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
867 FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
868 DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
869 SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
870 CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
871 OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
872 OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
873 </code></pre>
874
875 <h5>
876 <a id="user-content-courtesy" class="anchor" href="#courtesy" aria-hidden="true"><span class="octicon octicon-link"></span></a>COURTESY</h5>
877
878 <p>To the Galaxy Team.</p>
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