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<title>Ace::Sequence::Gene - Simple "Gene" Object</title>
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<li><a href="#name">NAME</a></li>
<li><a href="#synopsis">SYNOPSIS</a></li>
<li><a href="#description">DESCRIPTION</a></li>
<li><a href="#object_creation">OBJECT CREATION</a></li>
<li><a href="#object_methods">OBJECT METHODS</a></li>
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<p>
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<h1><a name="name">NAME</a></h1>
<p>Ace::Sequence::Gene - Simple "Gene" Object</p>
<p>
</p>
<hr />
<h1><a name="synopsis">SYNOPSIS</a></h1>
<pre>
# open database connection and get an Ace::Object sequence
use Ace::Sequence;</pre>
<pre>
# get a megabase from the middle of chromosome I
$seq = Ace::Sequence->new(-name => 'CHROMOSOME_I,
-db => $db,
-offset => 3_000_000,
-length => 1_000_000);</pre>
<pre>
# get all the genes
@genes = $seq->genes;</pre>
<pre>
# get the exons from the first one
@exons = $genes[0]->exons;</pre>
<pre>
# get the introns
@introns = $genes[0]->introns</pre>
<pre>
# get the CDSs (NOT IMPLEMENTED YET!)
@cds = $genes[0]->cds;</pre>
<p>
</p>
<hr />
<h1><a name="description">DESCRIPTION</a></h1>
<p>Ace::Sequence::Gene is a subclass of Ace::Sequence::Feature. It
inherits all the methods of Ace::Sequence::Feature, but adds the
ability to retrieve the annotated introns and exons of the gene.</p>
<p>
</p>
<hr />
<h1><a name="object_creation">OBJECT CREATION</a></h1>
<p>You will not ordinarily create an <em>Ace::Sequence::Gene</em> object
directly. Instead, objects will be created in response to a <code>genes()</code>
call to an <em>Ace::Sequence</em> object.</p>
<p>
</p>
<hr />
<h1><a name="object_methods">OBJECT METHODS</a></h1>
<p>Most methods are inherited from <em>Ace::Sequence::Feature</em>. The
following methods are also supported:</p>
<dl>
<dt><strong><a name="exons" class="item"><code>exons()</code></a></strong>
<dd>
<pre>
@exons = $gene->exons;</pre>
</dd>
<dd>
<p>Return a list of Ace::Sequence::Feature objects corresponding to
annotated exons.</p>
</dd>
<dt><strong><a name="introns" class="item"><code>introns()</code></a></strong>
<dd>
<pre>
@introns = $gene->introns;</pre>
</dd>
<dd>
<p>Return a list of Ace::Sequence::Feature objects corresponding to
annotated introns.</p>
</dd>
<dt><strong><a name="cds" class="item"><code>cds()</code></a></strong>
<dd>
<pre>
@cds = $gene->cds;</pre>
</dd>
<dd>
<p>Return a list of Ace::Sequence::Feature objects corresponding to
coding sequence. THIS IS NOT YET IMPLEMENTED.</p>
</dd>
<dt><strong><a name="relative" class="item"><code>relative()</code></a></strong>
<dd>
<pre>
$relative = $gene->relative;
$gene->relative(1);</pre>
</dd>
<dd>
<p>This turns on and off relative coordinates. By default, the exons and
intron features will be returned in the coordinate system used by the
gene. If <a href="#relative"><code>relative()</code></a> is set to a true value, then coordinates will be
expressed as relative to the start of the gene. The first exon will
(usually) be 1.</p>
</dd>
</dl>
<p>
</p>
<hr />
<h1><a name="see_also">SEE ALSO</a></h1>
<p><a href="/AcePerl/docs/./Ace.html">the Ace manpage</a>, <a href="/AcePerl/docs/./Ace/Object.html">the Ace::Object manpage</a>, <a href="/AcePerl/docs/./Ace/Sequence.html">the Ace::Sequence manpage</a>,<a href="/AcePerl/docs/./Ace/Sequence/Homol.html">the Ace::Sequence::Homol manpage</a>,
<a href="/AcePerl/docs/./Ace/Sequence/Feature.html">the Ace::Sequence::Feature manpage</a>, <a href="/AcePerl/docs/./Ace/Sequence/FeatureList.html">the Ace::Sequence::FeatureList manpage</a>, <em>GFF</em></p>
<p>
</p>
<hr />
<h1><a name="author">AUTHOR</a></h1>
<p>Lincoln Stein <<a href="mailto:lstein@cshl.org">lstein@cshl.org</a>> with extensive help from Jean
Thierry-Mieg <<a href="mailto:mieg@kaa.crbm.cnrs-mop.fr">mieg@kaa.crbm.cnrs-mop.fr</a>></p>
<p>Copyright (c) 1999, Lincoln D. Stein</p>
<p>This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself. See DISCLAIMER.txt for
disclaimers of warranty.</p>
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Mandriva
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2010.0
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i586
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media
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contrib-release
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by-pkgid
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c0b2316b5320756fc35b43f35335d7ce
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files
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