man Ace::Sequence::Transcript (3): 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.

AUTHOR

Lincoln Stein <[email protected]> with extensive help from Jean Thierry-Mieg <[email protected]>

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: