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comparison GFFtools-GX @ 1:c6cf723c2ed4

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Uploaded version 2.0.0 of gfftools to integrate local Galaxy instances.
author vipints
date Tue, 10 Jun 2014 19:57:56 -0400
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488 <a href="/vipints/GFFtools-GX/commit/86358adfbbf002a88b60abbbba834c988c2b1803" class="sha-block" data-pjax>latest commit <span class="sha">86358adfbb</span></a>
489
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491 <img alt="Vipin" class="gravatar js-avatar" data-user="1714549" height="20" src="https://avatars0.githubusercontent.com/u/1714549?s=140" width="20" />
492 <span class="author-name"><a href="/vipints" data-skip-pjax="true" rel="author">vipints</a></span>
493 authored <time class="updated" datetime="2014-06-10T19:46:10-04:00" is="relative-time">June 10, 2014</time>
494
495 </div>
496 </div>
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509 <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" />
510 </td>
511 <td class="content">
512 <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/tree/master/test-data" class="js-directory-link" id="24346e1b50066607059af36e3b684b24-8cea31e39d3636381f3f9c0e26ba10c7886e2977" title="test-data">test-data</a></span>
513 </td>
514 <td class="message">
515 <span class="css-truncate css-truncate-target ">
516 <a href="/vipints/GFFtools-GX/commit/00dd26b8f36e14fe90fce6636998af1a5c80ca11" class="message" data-pjax="true" title="functional test added with files">functional test added with files</a>
517 </span>
518 </td>
519 <td class="age">
520 <span class="css-truncate css-truncate-target"><time datetime="2014-06-10T20:40:38Z" is="time-ago">June 10, 2014</time></span>
521 </td>
522 </tr>
523 <tr>
524 <td class="icon">
525 <span class="octicon octicon-file-text"></span>
526 <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" />
527 </td>
528 <td class="content">
529 <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/blob/master/GFFParser.py" class="js-directory-link" id="4a9c2f3a2b51d00c039e9951aa5df3fd-3d795ad080f42cb17a58a6c6e762c337d33ef8b9" title="GFFParser.py">GFFParser.py</a></span>
530 </td>
531 <td class="message">
532 <span class="css-truncate css-truncate-target ">
533 <a href="/vipints/GFFtools-GX/commit/9aafbf99a85bc47686d6bbcebbaec85aa2521536" class="message" data-pjax="true" title="added doc text to the functions">added doc text to the functions</a>
534 </span>
535 </td>
536 <td class="age">
537 <span class="css-truncate css-truncate-target"><time datetime="2014-06-10T23:28:04Z" is="time-ago">June 10, 2014</time></span>
538 </td>
539 </tr>
540 <tr>
541 <td class="icon">
542 <span class="octicon octicon-file-text"></span>
543 <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" />
544 </td>
545 <td class="content">
546 <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/blob/master/README" class="js-directory-link" id="c47c7c7383225ab55ff591cb59c41e6b-2bcefcccef6585fed1e686fdcce8201514500050" title="README">README</a></span>
547 </td>
548 <td class="message">
549 <span class="css-truncate css-truncate-target ">
550 <a href="/vipints/GFFtools-GX/commit/86358adfbbf002a88b60abbbba834c988c2b1803" class="message" data-pjax="true" title="text modified">text modified</a>
551 </span>
552 </td>
553 <td class="age">
554 <span class="css-truncate css-truncate-target"><time datetime="2014-06-10T23:46:10Z" is="time-ago">June 10, 2014</time></span>
555 </td>
556 </tr>
557 <tr>
558 <td class="icon">
559 <span class="octicon octicon-file-text"></span>
560 <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" />
561 </td>
562 <td class="content">
563 <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/blob/master/bed_to_gff.py" class="js-directory-link" id="4fd14b034003e6ed6b3c1243f3f285ed-61383bb4effef34a00a95a3a8c2f4ed34d576f75" title="bed_to_gff.py">bed_to_gff.py</a></span>
564 </td>
565 <td class="message">
566 <span class="css-truncate css-truncate-target ">
567 <a href="/vipints/GFFtools-GX/commit/c4433430d6a77ab127584aca9fcf4b092b83381b" class="message" data-pjax="true" title="imporved the desc text in bed2gff">imporved the desc text in bed2gff</a>
568 </span>
569 </td>
570 <td class="age">
571 <span class="css-truncate css-truncate-target"><time datetime="2014-06-09T19:12:02Z" is="time-ago">June 09, 2014</time></span>
572 </td>
573 </tr>
574 <tr>
575 <td class="icon">
576 <span class="octicon octicon-file-text"></span>
577 <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" />
578 </td>
579 <td class="content">
580 <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/blob/master/bed_to_gff.xml" class="js-directory-link" id="fd45df94f6d642a741c0c8d038949b37-ee194b9f0108cf3a827cf92a4ebd3ca8aec2d5e0" title="bed_to_gff.xml">bed_to_gff.xml</a></span>
581 </td>
582 <td class="message">
583 <span class="css-truncate css-truncate-target ">
584 <a href="/vipints/GFFtools-GX/commit/25a73e190f096adbddfd638b40f14a2492895830" class="message" data-pjax="true" title="functional test done bed to gff conv">functional test done bed to gff conv</a>
585 </span>
586 </td>
587 <td class="age">
588 <span class="css-truncate css-truncate-target"><time datetime="2014-06-03T22:02:31Z" is="time-ago">June 03, 2014</time></span>
589 </td>
590 </tr>
591 <tr>
592 <td class="icon">
593 <span class="octicon octicon-file-text"></span>
594 <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" />
595 </td>
596 <td class="content">
597 <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/blob/master/gbk_to_gff.py" class="js-directory-link" id="8cedf4409efd74682d25ee79bb3574dc-c517f2ad12e8768f5b79863db992dd7e67d27d7d" title="gbk_to_gff.py">gbk_to_gff.py</a></span>
598 </td>
599 <td class="message">
600 <span class="css-truncate css-truncate-target ">
601 <a href="/vipints/GFFtools-GX/commit/d8d93d8aac537003e4f7fde1e6662b841bd06e44" class="message" data-pjax="true" title="desc text added">desc text added</a>
602 </span>
603 </td>
604 <td class="age">
605 <span class="css-truncate css-truncate-target"><time datetime="2014-06-09T19:20:21Z" is="time-ago">June 09, 2014</time></span>
606 </td>
607 </tr>
608 <tr>
609 <td class="icon">
610 <span class="octicon octicon-file-text"></span>
611 <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" />
612 </td>
613 <td class="content">
614 <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/blob/master/gbk_to_gff.xml" class="js-directory-link" id="5e708155a06e4244e26c978ed02c6fd2-1112eaa8921c4fc10d5948a999a5ce7175f64411" title="gbk_to_gff.xml">gbk_to_gff.xml</a></span>
615 </td>
616 <td class="message">
617 <span class="css-truncate css-truncate-target ">
618 <a href="/vipints/GFFtools-GX/commit/00dd26b8f36e14fe90fce6636998af1a5c80ca11" class="message" data-pjax="true" title="functional test added with files">functional test added with files</a>
619 </span>
620 </td>
621 <td class="age">
622 <span class="css-truncate css-truncate-target"><time datetime="2014-06-10T20:40:38Z" is="time-ago">June 10, 2014</time></span>
623 </td>
624 </tr>
625 <tr>
626 <td class="icon">
627 <span class="octicon octicon-file-text"></span>
628 <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" />
629 </td>
630 <td class="content">
631 <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/blob/master/gff_to_bed.py" class="js-directory-link" id="95b17a03c0948b20d1264fcd269b60fa-37e6f149ae4fe61d761212c00e9300d3e4ecf7bb" title="gff_to_bed.py">gff_to_bed.py</a></span>
632 </td>
633 <td class="message">
634 <span class="css-truncate css-truncate-target ">
635 <a href="/vipints/GFFtools-GX/commit/5d913653e57fdd77e52822f161481ce91a86247a" class="message" data-pjax="true" title="license information updated">license information updated</a>
636 </span>
637 </td>
638 <td class="age">
639 <span class="css-truncate css-truncate-target"><time datetime="2014-06-10T23:33:25Z" is="time-ago">June 10, 2014</time></span>
640 </td>
641 </tr>
642 <tr>
643 <td class="icon">
644 <span class="octicon octicon-file-text"></span>
645 <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" />
646 </td>
647 <td class="content">
648 <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/blob/master/gff_to_bed.xml" class="js-directory-link" id="8c7d5ae4b79728262acfc56888f2444e-f2932e276ede0949dc550dc46565cfd36c5c677a" title="gff_to_bed.xml">gff_to_bed.xml</a></span>
649 </td>
650 <td class="message">
651 <span class="css-truncate css-truncate-target ">
652 <a href="/vipints/GFFtools-GX/commit/f80dd4d3e12ca474a360c5a3340294dd3c1c998a" class="message" data-pjax="true" title="functional test done">functional test done</a>
653 </span>
654 </td>
655 <td class="age">
656 <span class="css-truncate css-truncate-target"><time datetime="2014-06-03T20:48:20Z" is="time-ago">June 03, 2014</time></span>
657 </td>
658 </tr>
659 <tr>
660 <td class="icon">
661 <span class="octicon octicon-file-text"></span>
662 <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" />
663 </td>
664 <td class="content">
665 <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/blob/master/gff_to_gtf.py" class="js-directory-link" id="88b7a441373dfec1e07cd28bb1eb8c3e-a864f8b163c7458da0012144ccd2aa3fbbd3eff9" title="gff_to_gtf.py">gff_to_gtf.py</a></span>
666 </td>
667 <td class="message">
668 <span class="css-truncate css-truncate-target ">
669 <a href="/vipints/GFFtools-GX/commit/1654e766fb90d47f44a87338c91aecd23dfc761b" class="message" data-pjax="true" title="license information updated">license information updated</a>
670 </span>
671 </td>
672 <td class="age">
673 <span class="css-truncate css-truncate-target"><time datetime="2014-06-10T23:35:18Z" is="time-ago">June 10, 2014</time></span>
674 </td>
675 </tr>
676 <tr>
677 <td class="icon">
678 <span class="octicon octicon-file-text"></span>
679 <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" />
680 </td>
681 <td class="content">
682 <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/blob/master/gff_to_gtf.xml" class="js-directory-link" id="f4676750a1f71b9fbf35b537b0546842-3d421e35bfca497c46026f49066f408104f08116" title="gff_to_gtf.xml">gff_to_gtf.xml</a></span>
683 </td>
684 <td class="message">
685 <span class="css-truncate css-truncate-target ">
686 <a href="/vipints/GFFtools-GX/commit/173145b45e3d6265517486cc06239e3a6dd21104" class="message" data-pjax="true" title="tool id changed">tool id changed</a>
687 </span>
688 </td>
689 <td class="age">
690 <span class="css-truncate css-truncate-target"><time datetime="2014-06-10T20:48:47Z" is="time-ago">June 10, 2014</time></span>
691 </td>
692 </tr>
693 <tr>
694 <td class="icon">
695 <span class="octicon octicon-file-text"></span>
696 <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" />
697 </td>
698 <td class="content">
699 <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/blob/master/gtf_to_gff.py" class="js-directory-link" id="6989ac39182645599caeb47b4e0e8ef6-38a340975f42f7845b9377275929364265bfb0f1" title="gtf_to_gff.py">gtf_to_gff.py</a></span>
700 </td>
701 <td class="message">
702 <span class="css-truncate css-truncate-target ">
703 <a href="/vipints/GFFtools-GX/commit/7b6f0278ee32204040542552b511df25491992b0" class="message" data-pjax="true" title="requirement field updated">requirement field updated</a>
704 </span>
705 </td>
706 <td class="age">
707 <span class="css-truncate css-truncate-target"><time datetime="2014-06-10T23:37:48Z" is="time-ago">June 10, 2014</time></span>
708 </td>
709 </tr>
710 <tr>
711 <td class="icon">
712 <span class="octicon octicon-file-text"></span>
713 <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" />
714 </td>
715 <td class="content">
716 <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/blob/master/gtf_to_gff.xml" class="js-directory-link" id="a8bd25db400514c2556192045eacd820-ec16bf58738e8a83c26484936b468b19069fa9f9" title="gtf_to_gff.xml">gtf_to_gff.xml</a></span>
717 </td>
718 <td class="message">
719 <span class="css-truncate css-truncate-target ">
720 <a href="/vipints/GFFtools-GX/commit/a637fd1e39ae8781052a2fcd8b381ffa16fcf2b8" class="message" data-pjax="true" title="base template wrapper for gtf to gff program">base template wrapper for gtf to gff program</a>
721 </span>
722 </td>
723 <td class="age">
724 <span class="css-truncate css-truncate-target"><time datetime="2014-06-06T23:59:07Z" is="time-ago">June 06, 2014</time></span>
725 </td>
726 </tr>
727 <tr>
728 <td class="icon">
729 <span class="octicon octicon-file-text"></span>
730 <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" />
731 </td>
732 <td class="content">
733 <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/blob/master/helper.py" class="js-directory-link" id="702b6abf015bfdb4e41308ddd3b297a9-7ccc8705a62e0a1068040b37b704d7dc511ef44f" title="helper.py">helper.py</a></span>
734 </td>
735 <td class="message">
736 <span class="css-truncate css-truncate-target ">
737 <a href="/vipints/GFFtools-GX/commit/780bcbefa142032acae7058386de9ec4e4834754" class="message" data-pjax="true" title="doc text improved">doc text improved</a>
738 </span>
739 </td>
740 <td class="age">
741 <span class="css-truncate css-truncate-target"><time datetime="2014-06-08T18:04:11Z" is="time-ago">June 08, 2014</time></span>
742 </td>
743 </tr>
744 <tr>
745 <td class="icon">
746 <span class="octicon octicon-file-text"></span>
747 <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" />
748 </td>
749 <td class="content">
750 <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>
751 </td>
752 <td class="message">
753 <span class="css-truncate css-truncate-target ">
754 <a href="/vipints/GFFtools-GX/commit/0b284f543f4c64c78f980537cd8ee2aae700182a" class="message" data-pjax="true" title="tool panel entries">tool panel entries</a>
755 </span>
756 </td>
757 <td class="age">
758 <span class="css-truncate css-truncate-target"><time datetime="2014-06-10T22:52:18Z" is="time-ago">June 10, 2014</time></span>
759 </td>
760 </tr>
761 </tbody>
762
763 </table>
764 </div>
765
766
767 <div id="readme" class="clearfix announce instapaper_body ">
768 <span class="name">
769 <span class="octicon octicon-book"></span>
770 README
771 </span>
772
773 <div class="plain"><pre>A collection of tools for converting genome annotation between GTF (Gene Transfer Format),
774 BED (Browser Extensible Data) and GFF (Generic Feature Format).
775
776 INTRODUCTION
777
778 Several genome annotation centers provide their data in GTF, BED, GFF3 etc. I have few programs
779 they mainly deals with converting between GTF, BED and GFF3 formats. They are extensively tested
780 with files from different centers like ENSEMBL, UCSC, JGI and NCBI AceView. Please follow the
781 instructions below to clone these tools into your galaxy instance.
782
783 CONTENTS
784
785 Tool configuration files in *.xml format.
786
787 gtf_to_gff.xml
788 gff_to_gtf.xml
789 bed_to_gff.xml
790 gff_to_bed.xml
791 gbk_to_gff.xml
792
793 Python based scripts.
794
795 gtf_to_gff.py: convert data from GTF to valid GFF3.
796 gff_to_gtf.py: convert data from GFF3 to GTF.
797 bed_to_gff.py: convert data from a 12 column UCSC wiggle BED format to GFF3.
798 gff_to_bed.py: convert gene transcript annotation from GFF3 to UCSC wiggle 12 column BED format.
799 gbk_to_gff.py: convert data from genbank format to GFF.
800 GFFParser.py: Parse GFF/GTF files.
801 helper.py: Utility functions.
802
803 test-data: Test data set. (move to your galaxy_root_folder/test-data/)
804
805 You may need to move the test files into your test-data directory so galaxy can find them.
806 If you want to run the functional tests eg as:
807
808 exmaple:
809 sh run_functional_tests.sh -id fml_gtf2gff
810
811 REQUIREMENTS
812
813 python
814
815 COMMENTS/QUESTIONS
816
817 I can be reached at vipin [at] cbio.mskcc.org
818
819 LICENSE
820
821 Copyright (C) 2009-2012 Friedrich Miescher Laboratory of the Max Planck Society
822 2013-2014 Memorial Sloan Kettering Cancer Center
823
824 This program is free software; you can redistribute it and/or modify
825 it under the terms of the GNU General Public License as published by
826 the Free Software Foundation; either version 3 of the License, or
827 (at your option) any later version.
828
829 COURTESY
830
831 To the Galaxy Team.
832 </pre></div>
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