Bio::Tools::Prediction
Exon
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Summary
Bio::Tools::Prediction::Exon - A predicted exon feature
Package variables
No package variables defined.
Included modules
Inherit
Synopsis
See documentation of methods.
Description
A feature representing a predicted exon. This class actually inherits
off Bio::SeqFeature::Gene::Exon and therefore has all that
functionality (also implements Bio::SeqFeatureI), plus a few methods
supporting predicted features, like various scores and a
significance. Even though these were inspired by GenScan results, at
least a subset should be generally useable for exon prediction
results.
Methods
Methods description
Title : coding_signal_score
Usage : $sc = $obj->coding_signal_score();
$obj->coding_signal_score($evalue);
Function: Get/Set a score for the exon coding signal (e.g., coding potential).
Returns :
Args : |
Title : end_signal_score
Usage : $sc = $obj->end_signal_score();
$obj->end_signal_score($evalue);
Function: Get/Set a score for the exon end signal (donor splice site
or termination signal).
Returns :
Args : |
Title : predicted_cds
Usage : $predicted_cds_dna = $exon->predicted_cds();
$exon->predicted_cds($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 = $exon->predicted_protein();
$exon->predicted_protein($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. |
Title : significance
Usage : $evalue = $obj->significance();
$obj->significance($evalue);
Function:
Returns :
Args : |
Title : start_signal_score
Usage : $sc = $obj->start_signal_score();
$obj->start_signal_score($evalue);
Function: Get/Set a score for the exon start signal (acceptor splice site
or initiation signal).
Returns :
Args : |
Methods code
sub coding_signal_score
{ my ($self, $value) = @_;
return $self->_tag_value('CodScore', $value);
}
1;} | sub end_signal_score
{ my ($self, $value) = @_;
return $self->_tag_value('DonScore', $value);} | sub new
{ my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my ($primary) = $self->_rearrange([qw(PRIMARY)],@args);
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 $self->{'_predicted_aa'};} | sub significance
{ my ($self, $value) = @_;
return $self->_tag_value('signif', $value);} | sub start_signal_score
{ my ($self, $value) = @_;
return $self->_tag_value('AccScore', $value);} | General documentation
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _