Ace::Sequence::Transcript - Simple "Gene" Object
# 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->exons; # get the introns @introns = $genes->introns # get the CDSs (NOT IMPLEMENTED YET!) @cds = $genes->cds;
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.
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.
Most methods are inherited from Ace::Sequence::Feature. The following methods are also supported:
@exons = $gene->exons;
Return a list of Ace::Sequence::Feature objects corresponding to annotated exons.
@introns = $gene->introns;
Return a list of Ace::Sequence::Feature objects corresponding to annotated introns.
@cds = $gene->cds;
Return a list of Ace::Sequence::Feature objects corresponding to coding sequence. THIS IS NOT YET IMPLEMENTED.
$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.
Lincoln Stein <email@example.com> with extensive help from Jean Thierry-Mieg <firstname.lastname@example.org>
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.