Lincoln D. Stein > AcePerl > Ace::Sequence::Gene

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NAME ^

Ace::Sequence::Gene - Simple "Gene" Object

SYNOPSIS ^

    # open database connection and get an Ace::Object sequence
    use Ace::Sequence;

    # 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);

    # get all the genes
    @genes = $seq->genes;

    # get the exons from the first one
    @exons = $genes[0]->exons;

    # get the introns
    @introns = $genes[0]->introns

    # get the CDSs (NOT IMPLEMENTED YET!)
    @cds = $genes[0]->cds;

DESCRIPTION ^

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.

OBJECT CREATION ^

You will not ordinarily create an Ace::Sequence::Gene object directly. Instead, objects will be created in response to a genes() call to an Ace::Sequence object.

OBJECT METHODS ^

Most methods are inherited from Ace::Sequence::Feature. The following methods are also supported:

exons()
  @exons = $gene->exons;

Return a list of Ace::Sequence::Feature objects corresponding to annotated exons.

introns()
  @introns = $gene->introns;

Return a list of Ace::Sequence::Feature objects corresponding to annotated introns.

cds()
  @cds = $gene->cds;

Return a list of Ace::Sequence::Feature objects corresponding to coding sequence. THIS IS NOT YET IMPLEMENTED.

relative()
  $relative = $gene->relative;
  $gene->relative(1);

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 relative() 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.

SEE ALSO ^

Ace, Ace::Object, Ace::Sequence,Ace::Sequence::Homol, Ace::Sequence::Feature, Ace::Sequence::FeatureList, GFF

AUTHOR ^

Lincoln Stein <lstein@cshl.org> with extensive help from Jean Thierry-Mieg <mieg@kaa.crbm.cnrs-mop.fr>

Copyright (c) 1999, Lincoln D. Stein

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.

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