debian man page for ace::sequence::transcript

Ace::Sequence::Transcript(3pm)				User Contributed Perl Documentation			    Ace::Sequence::Transcript(3pm)

NAME
       Ace::Sequence::Transcript - 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 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;

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 transcripts()
       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.

POD ERRORS
       Hey! The above document had some coding errors, which are explained below:

       Around line 168:
	   You forgot a '=back' before '=head1'

perl v5.14.2							    2001-05-22					    Ace::Sequence::Transcript(3pm)