Bio::Tools::Prediction Gene
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
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Summary
Bio::Tools::Prediction::Gene - a predicted gene structure feature
Package variables
No package variables defined.
Inherit
Bio::SeqFeature::Gene::Transcript
Synopsis
  #See documentation of methods.
Description
A feature representing a predicted gene structure. This class actually
inherits off Bio::SeqFeature::Gene::Transcript and therefore has all that
functionality, plus a few methods supporting predicted sequence features,
like a predicted CDS and a predicted translation.
Exons held by an instance of this class will usually be instances of
Bio::Tools::Prediction::Exon, although they do not have to be. Refer to the
documentation of the class that produced the instance.
Normally, you will not want to create an instance of this class yourself.
Instead, classes representing the results of gene structure prediction
programs will do that.
Methods
new
No description
Code
predicted_cdsDescriptionCode
predicted_proteinDescriptionCode
Methods description
predicted_cdscode    nextTop
 Title   : predicted_cds
Usage : $predicted_cds_dna = $gene->predicted_cds();
$gene->predicted_cds($predicted_cds_dna);
Function: Get/Set the CDS (coding sequence) as predicted by a program.
This method is independent of an attached_seq. There is no guarantee whatsoever that the returned CDS has anything to do (e.g., matches) with the sequence covered by the exons as annotated through this object. Example : Returns : A Bio::PrimarySeqI implementing object holding the DNA sequence defined as coding by a prediction of a program. Args : On set, a Bio::PrimarySeqI implementing object holding the DNA sequence defined as coding by a prediction of a program.
predicted_proteincodeprevnextTop
 Title   : predicted_protein
Usage : $predicted_protein_seq = $gene->predicted_protein();
$gene->predicted_protein($predicted_protein_seq);
Function: Get/Set the protein translation as predicted by a program.
This method is independent of an attached_seq. There is no guarantee whatsoever that the returned translation has anything to do with the sequence covered by the exons as annotated through this object, or the sequence returned by predicted_cds(), although it should usually be just the standard translation. Example : Returns : A Bio::PrimarySeqI implementing object holding the protein translation as predicted by a program. Args : On set, a Bio::PrimarySeqI implementing object holding the protein translation as predicted by a program.
Methods code
newdescriptionprevnextTop
sub new {
    my($class,@args) = @_;
    
    my $self = $class->SUPER::new(@args);

    my ($primary,$ptag) = $self->_rearrange([qw(PRIMARY PRIMARY_TAG)],@args);
    $self->primary_tag('predicted_gene') unless $primary || $ptag;

    return $self;
}
predicted_cdsdescriptionprevnextTop
sub predicted_cds {
    my ($self, $cds) = @_;

    if(defined($cds)) {
	$self->{'_predicted_cds'} = $cds;
    }
    return $self->{'_predicted_cds'};
}
predicted_proteindescriptionprevnextTop
sub predicted_protein {
    my ($self, $aa) = @_;

    if(defined($aa)) {
	$self->{'_predicted_aa'} = $aa;
    }
    return $self->{'_predicted_aa'};
}

#
# Everything else is just inherited from SeqFeature::GeneStructure.
#
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 one
of the Bioperl mailing lists. 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
the bugs and their resolution. Bug reports can be submitted via the
web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Hilmar LappTop
Email hlapp-at-gmx.net or hilmar.lapp-at-pharma.novartis.com
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _