NAME

Bio::Das::Segment::Transcript - A transcript model

SYNOPSIS

  use Bio::Das;

  # contact a DAS server using the "elegans" data source
  my $das      = Bio::Das->new('http://www.wormbase.org/db/das' => 'elegans');

  # fetch a segment
  my $segment  = $das->segment(-ref=>'CHROMOSOME_I',-start=>10_000,-stop=>20_000);

  # get the transcripts
  my @transcript = $segment->features('transcript');

  # get the introns and exons from the first transcript
  my @introns = $transcript[0]->introns;
  my @exons   = $transcript[0]->exons;

  # get CDS - but this probably doesn't belong here
  my @cds     = $transcript[0]->cds;

DESCRIPTION

A Bio::Das::Segment::Transcript is a subclass of Bio::Das::Segment::Feature that is specialized for representing the union of introns and exons of a transcriptional unit. It inherits all the methods of its parent class, and adds methods for retrieving its component parts.

The feature type of a Bio::Das::Segment::Transcript is "transcript" and its method is "composite."

OBJECT CREATION

Bio::Das::Segment::Transcript objects are created by calling the features() method of a Bio::Das::Segment object created earlier. See the Bio::Das::Segment manpage for details.

OBJECT METHODS

All Bio::Das::Segment::Feature methods are available. In particular, the start() and stop() methods will return the start and end of the most proximal and distal exons.

In addition, this class adds or implements the following methods:

@introns = $feature->introns: The introns() method returns the introns of the transcript. Each intron is a Bio::Das::Segment::Feature object of type "intron".
@exons = $feature->exons: This method returns the exons.
@cds = $feature->cds: This method returns the CDS features associated with the transcript. Since this has more to do with translation than transcription, it is possible that this method will be deprecated in the future.
@segments = $feature->sub_seqFeature: This is an alias for exons(), and is compatible with the Bio::SeqFeatureI interface.

AUTHOR

Lincoln Stein <lstein@cshl.org>.