Bio::SeqFeature::Gene::UTR - A feature representing an untranslated region

BioPerl documentation Contained in the BioPerl distribution.

Index

Code Index:

NAME

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

SYNOPSIS

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See documentation of methods

DESCRIPTION

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

FEEDBACK

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Mailing Lists

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

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 Bugs

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 Block

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Email dblock@gene.pbi.nrc.ca

CONTRIBUTORS

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

APPENDIX

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

new

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

 Example :
 Returns : 
 Args    :

primary_tag

 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
BioPerl documentation Contained in the BioPerl distribution. 
#
# BioPerl module for Bio::SeqFeature::Gene::UTR
#
# Please direct questions and support issues to <bioperl-l@bioperl.org> 
#
# Cared for by David Block <dblock@gene.pbi.nrc.ca>
#
# Copyright David Block
#
# You may distribute this module under the same terms as perl itself

# POD documentation - main docs before the code



# Let the code begin...


package Bio::SeqFeature::Gene::UTR;
use strict;

# Object preamble - inherits from Bio::Root::Root


use base qw(Bio::SeqFeature::Gene::Exon);


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(@_);
}

1;