Summary

Bio::SeqFeature::Gene::UTR - A feature representing an untranslated region
that is part of a transcriptional unit

Package variables

Included modules

Inherit

Bio::SeqFeature::Gene::Exon

Synopsis

See documentation of methods

Description

A UTR is a Bio::SeqFeature::Gene::ExonI compliant object that is
non-coding, and can be either 5' or 3' in a transcript.

Methods

Methods description

 Title   : new
 Usage   :
 Function: We override the constructor here to set is_coding to false
           unless explicitly overridden.

 Example :
 Returns : 
 Args    :

 Title   : primary_tag
 Usage   : $tag = $feat->primary_tag()
 Function: Returns the primary tag for a feature,
           eg 'utr5prime'.  This method insures that 5prime/3prime information
           is uniformly stored
 Returns : a string 
 Args    : none

Methods code

sub new {

    my ($caller, @args) = @_;

    if(! grep { lc($_) eq '-is_coding'; } @args) {
	push(@args, '-is_coding', 0);
    }
    my $self = $caller->SUPER::new(@args);

    my ($primary, $prim) = 
	$self->_rearrange([qw(PRIMARY PRIMARY_TAG)],@args);

    $self->primary_tag('utr') unless $primary || $prim;

    return $self;

}

sub primary_tag {

    my $self = shift;
    if(@_ && defined($_[0])) {
	my $val = shift;
	if ($val =~ /(3|5)/ ) { 
	    $val = "utr$1prime";
	} else { 
	    $self->warn("Primary tag should indicate if this is 3 or 5'. ".
			"Preferred text is 'utr3prime' or 'utr5prime'.");
	}
	unshift(@_,$val);
    }
    return $self->SUPER::primary_tag(@_);

}

General documentation

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.

  bioperl-l@bioperl.org              - General discussion
  http://bioperl.org/MailList.shtml  - About the mailing lists

Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
email or the web:

  bioperl-bugs@bioperl.org
  http://bugzilla.bioperl.org/

Email dblock@gene.pbi.nrc.ca

This is based on the Gene Structure scaffolding erected by Hilmar Lapp
(hlapp@gmx.net).

The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _