Bio::SeqFeature::Gene UTR
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Summary
Bio::SeqFeature::Gene::UTR - A feature representing an untranslated region
that is part of a transcriptional unit
Package variables
No package variables defined.
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
newDescriptionCode
primary_tagDescriptionCode
Methods description
newcode    nextTop
 Title   : new
Usage :
Function: We override the constructor here to set is_coding to false
unless explicitly overridden.
Example : Returns : Args :
primary_tagcodeprevnextTop
 Title   : primary_tag
Usage : $tag = $feat->primary_tag()
Function: Returns the primary tag for a feature,
eg 'utr5prime'. This method insures that 5prime/3prime information
is uniformly stored
Returns : a string
Args : none
Methods code
newdescriptionprevnextTop
sub new {
    my ($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;
}
primary_tagdescriptionprevnextTop
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(@_);
}

1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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/wiki/Mailing_lists - About the mailing lists
Support Top
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
Reporting BugsTop
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 the
web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - David BlockTop
Email dblock@gene.pbi.nrc.ca
CONTRIBUTORSTop
This is based on the Gene Structure scaffolding erected by Hilmar Lapp
(hlapp@gmx.net).
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _