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Uploaded version 2.1.0
author vipints
date Thu, 23 Apr 2015 17:43:11 -0400
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              <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>
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              <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>
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            <span class="css-truncate css-truncate-target"><time datetime="2015-04-19T21:50:45Z" is="time-ago">Apr 19, 2015</time></span>
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              <a href="/vipints/GFFtools-GX/commit/04ccdc96c4bf8d6b8420a05c9afa8c8540345e32" class="message" data-pjax="true" title="updated the toolpanel list">updated the toolpanel list</a>
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              <a href="/vipints/GFFtools-GX/commit/c75c2be2f54ca59449e999346de2427584789ec9" class="message" data-pjax="true" title="biopython required">biopython required</a>
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    </h3>

    <article class="markdown-body entry-content" itemprop="mainContentOfPage"><h1>
<a id="user-content-gfftools-gx-" class="anchor" href="#gfftools-gx-" aria-hidden="true"><span class="octicon octicon-link"></span></a>GFFtools-GX </h1>

<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>

<h5>
<a id="user-content-introduction" class="anchor" href="#introduction" aria-hidden="true"><span class="octicon octicon-link"></span></a>INTRODUCTION</h5>

<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>

<h5>
<a id="user-content-contents" class="anchor" href="#contents" aria-hidden="true"><span class="octicon octicon-link"></span></a>CONTENTS</h5>

<p>Included utilities are: </p>

<pre><code>BED-to-GFF: convert data from a 12 column UCSC wiggle BED format to GFF
GBK-to-GFF: convert data from genbank format to GFF
GFF-to-BED: convert data from GFF to 12 column BED format
GFF-to-GTF: convert data from GFF to GTF 
GTF-to-GFF: convert data from GTF to valid GFF
</code></pre>

<p>test-data: Test data set. (move to your galaxy-root-folder/test-data/)</p>

<pre><code>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
</code></pre>

<h5>
<a id="user-content-requirements" class="anchor" href="#requirements" aria-hidden="true"><span class="octicon octicon-link"></span></a>REQUIREMENTS</h5>

<pre><code>python2.6 or 2.7 and biopython  

Galaxy should be able to automatically install biopython via Galaxy toolshed.
</code></pre>

<h5>
<a id="user-content-commentsquestions" class="anchor" href="#commentsquestions" aria-hidden="true"><span class="octicon octicon-link"></span></a>COMMENTS/QUESTIONS</h5>

<p>I can be reached at vipin [at] cbio.mskcc.org </p>

<h5>
<a id="user-content-license" class="anchor" href="#license" aria-hidden="true"><span class="octicon octicon-link"></span></a>LICENSE</h5>

<p>Copyright (c) 2009-2012, Friedrich Miescher Laboratory of the Max Planck Society</p>

<pre><code>          2013-2015, Memorial Sloan Kettering Cancer Center
          Vipin T Sreedharan &lt;vipin@cbio.mskcc.org&gt;  
</code></pre>

<p>All rights reserved.</p>

<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>

<pre><code>Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:

    * Redistributions of source code must retain the above copyright notice,
      this list of conditions and the following disclaimer.

    * Redistributions in binary form must reproduce the above copyright notice,
      this list of conditions and the following disclaimer in the documentation
      and/or other materials provided with the distribution.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
</code></pre>

<h5>
<a id="user-content-courtesy" class="anchor" href="#courtesy" aria-hidden="true"><span class="octicon octicon-link"></span></a>COURTESY</h5>

<p>To the Galaxy Team.</p>
</article>
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