Mercurial > repos > vipints > fml_gff3togtf

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GFFtools-GX	Tue Jun 10 19:57:56 2014 -0400
@@ -0,0 +1,906 @@
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+        <a href="/vipints/GFFtools-GX/commit/86358adfbbf002a88b60abbbba834c988c2b1803" class="message" data-pjax="true" title="text modified">text modified</a>
+
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+    <div class="commit-meta">
+      <button aria-label="Copy SHA" class="js-zeroclipboard zeroclipboard-link" data-clipboard-text="86358adfbbf002a88b60abbbba834c988c2b1803" data-copied-hint="copied!" type="button"><span class="octicon octicon-clippy"></span></button>
+      <a href="/vipints/GFFtools-GX/commit/86358adfbbf002a88b60abbbba834c988c2b1803" class="sha-block" data-pjax>latest commit <span class="sha">86358adfbb</span></a>
+
+      <div class="authorship">
+        <img alt="Vipin" class="gravatar js-avatar" data-user="1714549" height="20" src="https://avatars0.githubusercontent.com/u/1714549?s=140" width="20" />
+        <span class="author-name"><a href="/vipints" data-skip-pjax="true" rel="author">vipints</a></span>
+        authored <time class="updated" datetime="2014-06-10T19:46:10-04:00" is="relative-time">June 10, 2014</time>
+
+      </div>
+    </div>
+  </div>
+
+  <div class="file-wrap">
+    <table class="files" data-pjax>
+
+
+<tbody class=""
+  data-url="/vipints/GFFtools-GX/file-list/master"
+  data-deferred-content-error="Failed to load latest commit information.">
+    <tr>
+      <td class="icon">
+        <span class="octicon octicon-file-directory"></span>
+        <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" />
+      </td>
+      <td class="content">
+        <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>
+      </td>
+      <td class="message">
+        <span class="css-truncate css-truncate-target ">
+          <a href="/vipints/GFFtools-GX/commit/00dd26b8f36e14fe90fce6636998af1a5c80ca11" class="message" data-pjax="true" title="functional test added with files">functional test added with files</a>
+        </span>
+      </td>
+      <td class="age">
+        <span class="css-truncate css-truncate-target"><time datetime="2014-06-10T20:40:38Z" is="time-ago">June 10, 2014</time></span>
+      </td>
+    </tr>
+    <tr>
+      <td class="icon">
+        <span class="octicon octicon-file-text"></span>
+        <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" />
+      </td>
+      <td class="content">
+        <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>
+      </td>
+      <td class="message">
+        <span class="css-truncate css-truncate-target ">
+          <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>
+        </span>
+      </td>
+      <td class="age">
+        <span class="css-truncate css-truncate-target"><time datetime="2014-06-10T23:28:04Z" is="time-ago">June 10, 2014</time></span>
+      </td>
+    </tr>
+    <tr>
+      <td class="icon">
+        <span class="octicon octicon-file-text"></span>
+        <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" />
+      </td>
+      <td class="content">
+        <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>
+      </td>
+      <td class="message">
+        <span class="css-truncate css-truncate-target ">
+          <a href="/vipints/GFFtools-GX/commit/86358adfbbf002a88b60abbbba834c988c2b1803" class="message" data-pjax="true" title="text modified">text modified</a>
+        </span>
+      </td>
+      <td class="age">
+        <span class="css-truncate css-truncate-target"><time datetime="2014-06-10T23:46:10Z" is="time-ago">June 10, 2014</time></span>
+      </td>
+    </tr>
+    <tr>
+      <td class="icon">
+        <span class="octicon octicon-file-text"></span>
+        <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" />
+      </td>
+      <td class="content">
+        <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>
+      </td>
+      <td class="message">
+        <span class="css-truncate css-truncate-target ">
+          <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>
+        </span>
+      </td>
+      <td class="age">
+        <span class="css-truncate css-truncate-target"><time datetime="2014-06-09T19:12:02Z" is="time-ago">June 09, 2014</time></span>
+      </td>
+    </tr>
+    <tr>
+      <td class="icon">
+        <span class="octicon octicon-file-text"></span>
+        <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" />
+      </td>
+      <td class="content">
+        <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>
+      </td>
+      <td class="message">
+        <span class="css-truncate css-truncate-target ">
+          <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>
+        </span>
+      </td>
+      <td class="age">
+        <span class="css-truncate css-truncate-target"><time datetime="2014-06-03T22:02:31Z" is="time-ago">June 03, 2014</time></span>
+      </td>
+    </tr>
+    <tr>
+      <td class="icon">
+        <span class="octicon octicon-file-text"></span>
+        <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" />
+      </td>
+      <td class="content">
+        <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>
+      </td>
+      <td class="message">
+        <span class="css-truncate css-truncate-target ">
+          <a href="/vipints/GFFtools-GX/commit/d8d93d8aac537003e4f7fde1e6662b841bd06e44" class="message" data-pjax="true" title="desc text added">desc text added</a>
+        </span>
+      </td>
+      <td class="age">
+        <span class="css-truncate css-truncate-target"><time datetime="2014-06-09T19:20:21Z" is="time-ago">June 09, 2014</time></span>
+      </td>
+    </tr>
+    <tr>
+      <td class="icon">
+        <span class="octicon octicon-file-text"></span>
+        <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" />
+      </td>
+      <td class="content">
+        <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>
+      </td>
+      <td class="message">
+        <span class="css-truncate css-truncate-target ">
+          <a href="/vipints/GFFtools-GX/commit/00dd26b8f36e14fe90fce6636998af1a5c80ca11" class="message" data-pjax="true" title="functional test added with files">functional test added with files</a>
+        </span>
+      </td>
+      <td class="age">
+        <span class="css-truncate css-truncate-target"><time datetime="2014-06-10T20:40:38Z" is="time-ago">June 10, 2014</time></span>
+      </td>
+    </tr>
+    <tr>
+      <td class="icon">
+        <span class="octicon octicon-file-text"></span>
+        <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" />
+      </td>
+      <td class="content">
+        <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>
+      </td>
+      <td class="message">
+        <span class="css-truncate css-truncate-target ">
+          <a href="/vipints/GFFtools-GX/commit/5d913653e57fdd77e52822f161481ce91a86247a" class="message" data-pjax="true" title="license information updated">license information updated</a>
+        </span>
+      </td>
+      <td class="age">
+        <span class="css-truncate css-truncate-target"><time datetime="2014-06-10T23:33:25Z" is="time-ago">June 10, 2014</time></span>
+      </td>
+    </tr>
+    <tr>
+      <td class="icon">
+        <span class="octicon octicon-file-text"></span>
+        <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" />
+      </td>
+      <td class="content">
+        <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>
+      </td>
+      <td class="message">
+        <span class="css-truncate css-truncate-target ">
+          <a href="/vipints/GFFtools-GX/commit/f80dd4d3e12ca474a360c5a3340294dd3c1c998a" class="message" data-pjax="true" title="functional test done">functional test done</a>
+        </span>
+      </td>
+      <td class="age">
+        <span class="css-truncate css-truncate-target"><time datetime="2014-06-03T20:48:20Z" is="time-ago">June 03, 2014</time></span>
+      </td>
+    </tr>
+    <tr>
+      <td class="icon">
+        <span class="octicon octicon-file-text"></span>
+        <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" />
+      </td>
+      <td class="content">
+        <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>
+      </td>
+      <td class="message">
+        <span class="css-truncate css-truncate-target ">
+          <a href="/vipints/GFFtools-GX/commit/1654e766fb90d47f44a87338c91aecd23dfc761b" class="message" data-pjax="true" title="license information updated">license information updated</a>
+        </span>
+      </td>
+      <td class="age">
+        <span class="css-truncate css-truncate-target"><time datetime="2014-06-10T23:35:18Z" is="time-ago">June 10, 2014</time></span>
+      </td>
+    </tr>
+    <tr>
+      <td class="icon">
+        <span class="octicon octicon-file-text"></span>
+        <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" />
+      </td>
+      <td class="content">
+        <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>
+      </td>
+      <td class="message">
+        <span class="css-truncate css-truncate-target ">
+          <a href="/vipints/GFFtools-GX/commit/173145b45e3d6265517486cc06239e3a6dd21104" class="message" data-pjax="true" title="tool id changed">tool id changed</a>
+        </span>
+      </td>
+      <td class="age">
+        <span class="css-truncate css-truncate-target"><time datetime="2014-06-10T20:48:47Z" is="time-ago">June 10, 2014</time></span>
+      </td>
+    </tr>
+    <tr>
+      <td class="icon">
+        <span class="octicon octicon-file-text"></span>
+        <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" />
+      </td>
+      <td class="content">
+        <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>
+      </td>
+      <td class="message">
+        <span class="css-truncate css-truncate-target ">
+          <a href="/vipints/GFFtools-GX/commit/7b6f0278ee32204040542552b511df25491992b0" class="message" data-pjax="true" title="requirement field updated">requirement field updated</a>
+        </span>
+      </td>
+      <td class="age">
+        <span class="css-truncate css-truncate-target"><time datetime="2014-06-10T23:37:48Z" is="time-ago">June 10, 2014</time></span>
+      </td>
+    </tr>
+    <tr>
+      <td class="icon">
+        <span class="octicon octicon-file-text"></span>
+        <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" />
+      </td>
+      <td class="content">
+        <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>
+      </td>
+      <td class="message">
+        <span class="css-truncate css-truncate-target ">
+          <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>
+        </span>
+      </td>
+      <td class="age">
+        <span class="css-truncate css-truncate-target"><time datetime="2014-06-06T23:59:07Z" is="time-ago">June 06, 2014</time></span>
+      </td>
+    </tr>
+    <tr>
+      <td class="icon">
+        <span class="octicon octicon-file-text"></span>
+        <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" />
+      </td>
+      <td class="content">
+        <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>
+      </td>
+      <td class="message">
+        <span class="css-truncate css-truncate-target ">
+          <a href="/vipints/GFFtools-GX/commit/780bcbefa142032acae7058386de9ec4e4834754" class="message" data-pjax="true" title="doc text improved">doc text improved</a>
+        </span>
+      </td>
+      <td class="age">
+        <span class="css-truncate css-truncate-target"><time datetime="2014-06-08T18:04:11Z" is="time-ago">June 08, 2014</time></span>
+      </td>
+    </tr>
+    <tr>
+      <td class="icon">
+        <span class="octicon octicon-file-text"></span>
+        <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/images/spinners/octocat-spinner-32.gif" width="16" />
+      </td>
+      <td class="content">
+        <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>
+      </td>
+      <td class="message">
+        <span class="css-truncate css-truncate-target ">
+          <a href="/vipints/GFFtools-GX/commit/0b284f543f4c64c78f980537cd8ee2aae700182a" class="message" data-pjax="true" title="tool panel entries">tool panel entries</a>
+        </span>
+      </td>
+      <td class="age">
+        <span class="css-truncate css-truncate-target"><time datetime="2014-06-10T22:52:18Z" is="time-ago">June 10, 2014</time></span>
+      </td>
+    </tr>
+</tbody>
+
+    </table>
+  </div>
+
+
+  <div id="readme" class="clearfix announce instapaper_body ">
+    <span class="name">
+      <span class="octicon octicon-book"></span>
+      README
+    </span>
+
+    <div class="plain"><pre>A collection of tools for converting genome annotation between GTF (Gene Transfer Format),
+BED (Browser Extensible Data) and GFF (Generic Feature Format).
+
+INTRODUCTION
+
+Several genome annotation centers provide their data in GTF, BED, GFF3 etc. I have few programs
+they mainly deals with converting between GTF, BED and GFF3 formats. They are extensively tested
+with files from different centers like ENSEMBL, UCSC, JGI and NCBI AceView. Please follow the
+instructions below to clone these tools into your galaxy instance.
+
+CONTENTS
+
+Tool configuration files in *.xml format.
+
+    gtf_to_gff.xml
+    gff_to_gtf.xml
+    bed_to_gff.xml
+    gff_to_bed.xml
+    gbk_to_gff.xml
+
+Python based scripts.
+
+    gtf_to_gff.py: convert data from GTF to valid GFF3.
+    gff_to_gtf.py: convert data from GFF3 to GTF.
+    bed_to_gff.py: convert data from a 12 column UCSC wiggle BED format to GFF3.
+    gff_to_bed.py: convert gene transcript annotation from GFF3 to UCSC wiggle 12 column BED format.
+    gbk_to_gff.py: convert data from genbank format to GFF.
+    GFFParser.py: Parse GFF/GTF files.
+    helper.py: Utility functions.
+
+test-data: Test data set. (move to your galaxy_root_folder/test-data/)
+
+    You may need to move the test files into your test-data directory so galaxy can find them.
+    If you want to run the functional tests eg as:
+
+    exmaple:
+    sh run_functional_tests.sh -id fml_gtf2gff
+
+REQUIREMENTS
+
+    python
+
+COMMENTS/QUESTIONS
+
+I can be reached at vipin [at] cbio.mskcc.org
+
+LICENSE
+
+Copyright (C) 2009-2012 Friedrich Miescher Laboratory of the Max Planck Society
+              2013-2014 Memorial Sloan Kettering Cancer Center
+
+This program is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 3 of the License, or
+(at your option) any later version.
+
+COURTESY
+
+To the Galaxy Team.
+</pre></div>
+  </div>
+
+
+        </div>
+
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