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Ace/Sequence/Transcript.pm  view on Meta::CPAN

			      -offset => 3_000_000,
			      -length => 1_000_000);

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

    # 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;

=head1 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.

=head1  OBJECT CREATION

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

=head1 OBJECT METHODS

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

=over 4

=item exons()

  @exons = $gene->exons;

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

=item introns()

  @introns = $gene->introns;

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

=item cds()

  @cds = $gene->cds;

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

=item 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.

=head1 SEE ALSO

L<Ace>, L<Ace::Object>, L<Ace::Sequence>,L<Ace::Sequence::Homol>,
L<Ace::Sequence::Feature>, L<Ace::Sequence::FeatureList>, L<GFF>

=head1 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.

=cut