Ace::Sequence::Transcript3pm

Usage

    # 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;

Overview

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.

Pod errors

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

Around line 168:

You forgot a '=back' before '=head1'