<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title>Ace::Sequence::Gene - Simple "Gene" Object</title> <link rev="made" href="mailto:root@localhost" /> </head> <body style="background-color: white"> <p><a name="__index__"></a></p> <!-- INDEX BEGIN --> <!-- <ul> <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> <li><a href="#see_also">SEE ALSO</a></li> <li><a href="#author">AUTHOR</a></li> </ul> --> <!-- INDEX END --> <p> </p> <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="item_exons"><code>exons()</code></a></strong><br /> </dt> <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="item_introns"><code>introns()</code></a></strong><br /> </dt> <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="item_cds"><code>cds()</code></a></strong><br /> </dt> <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="item_relative"><code>relative()</code></a></strong><br /> </dt> <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="#item_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/./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> </body> </html>