Bio::Tools::Prediction
Gene
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Summary
Bio::Tools::Prediction::Gene - a predicted gene structure feature
Package variables
No package variables defined.
Included modules
Inherit
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
Methods description
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. |
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
sub new
{ my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my ($primary) = $self->_rearrange([qw(PRIMARY)],@args);
$primary = 'predicted_gene' unless $primary;
$self->primary_tag($primary);
return $self;} | sub predicted_cds
{ my ($self, $cds) = @_;
if(defined($cds)) {
$self->{'_predicted_cds'} = $cds;
}
return $self->{'_predicted_cds'};} | sub predicted_protein
{ my ($self, $aa) = @_;
if(defined($aa)) {
$self->{'_predicted_aa'} = $aa;
}
return $self->{'_predicted_aa'};
}
1;} | General documentation
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _