Bio::SeqFeature::Gene
GeneStructure
Summary
Bio::SeqFeature::Gene::GeneStructure - A feature representing an arbitrarily
complex structure of a gene
Package variables
No package variables defined.
Included modules
Inherit
Synopsis
# See documentation of methods.
Description
A feature representing a gene structure. As of now, a gene structure
really is only a collection of transcripts. See
Bio::SeqFeature::Gene::TranscriptI (interface) and
Bio::SeqFeature::Gene::Transcript (implementation) for the features of
such objects.
Methods
Methods description
Title : transcripts
Usage : @transcripts = $gene->transcripts();
Function: Get the transcripts of this gene structure. Many gene structures
will have only one transcript.
Returns : An array of Bio::SeqFeature::Gene::TranscriptI implementing objects.
Args : |
Title : add_transcript()
Usage : $gene->add_transcript($transcript);
Function: Add a transcript to this gene structure.
Returns :
Args : A Bio::SeqFeature::Gene::TranscriptI implementing object. |
Title : flush_transcripts()
Usage : $gene->flush_transcripts();
Function: Remove all transcripts from this gene structure.
Returns :
Args : |
Title : add_transcript_as_features
Usage : $gene->add_transcript_as_features(@featurelist);
Function: take a list of Bio::SeqFeatureI objects and turn them into a
Bio::SeqFeature::Gene::Transcript object. Add that transcript to the gene.
Returns : nothing
Args : a list of Bio::SeqFeatureI compliant objects |
Title : promoters
Usage : @prom_sites = $gene->promoters();
Function: Get the promoter features of this gene structure.
This method basically merges the promoters returned by transcripts.
Note that OO-modeling of regulatory elements is not stable yet.
This means that this method might change or even disappear in a
future release. Be aware of this if you use it.
Returns : An array of Bio::SeqFeatureI implementing objects.
Args : |
Title : exons()
Usage : @exons = $gene->exons();
@inital_exons = $gene->exons('Initial');
Function: Get all exon features or all exons of a specified type of this gene
structure.
Exon type is treated as a case-insensitive regular expression and
optional. For consistency, use only the following types:
initial, internal, terminal, utr, utr5prime, and utr3prime.
A special and virtual type is 'coding', which refers to all types
except utr.
This method basically merges the exons returned by transcripts.
Returns : An array of Bio::SeqFeature::Gene::ExonI implementing objects.
Args : An optional string specifying the type of exon. |
Title : introns()
Usage : @introns = $gene->introns();
Function: Get all introns of this gene structure.
Note that this class currently generates these features on-the-fly,
that is, it simply treats all regions between exons as introns.
It assumes that the exons in the transcripts do not overlap.
This method basically merges the introns returned by transcripts.
Returns : An array of Bio::SeqFeatureI implementing objects.
Args : |
Title : poly_A_sites()
Usage : @polyAsites = $gene->poly_A_sites();
Function: Get the poly-adenylation sites of this gene structure.
This method basically merges the poly-adenylation sites returned by
transcripts.
Returns : An array of Bio::SeqFeatureI implementing objects.
Args : |
Title : utrs()
Usage : @utr_sites = $gene->utrs('3prime');
@utr_sites = $gene->utrs('5prime');
@utr_sites = $gene->utrs();
Function: Get the features representing untranslated regions (UTR) of this
gene structure.
You may provide an argument specifying the type of UTR. Currently
the following types are recognized: 5prime 3prime for UTR on the
5' and 3' end of the CDS, respectively.
This method basically merges the UTRs returned by transcripts.
Returns : An array of Bio::SeqFeature::Gene::ExonI implementing objects
representing the UTR regions or sites.
Args : Optionally, either 3prime, or 5prime for the the type of UTR
feature. |
Title : sub_SeqFeature
Usage : @feats = $gene->sub_SeqFeature();
Function: Returns an array of all subfeatures.
This method is defined in Bio::SeqFeatureI. We override this here
to include the transcripts.
Returns : An array Bio::SeqFeatureI implementing objects.
Args : none |
Title : flush_sub_SeqFeature
Usage : $gene->flush_sub_SeqFeature();
$gene->flush_sub_SeqFeature(1);
Function: Removes all subfeatures.
This method is overridden from Bio::SeqFeature::Generic to flush
all additional subfeatures, i.e., transcripts, which is
almost certainly not what you want. To remove only features added
through $gene->add_sub_SeqFeature($feature) pass any
argument evaluating to TRUE.
Example :
Returns : none
Args : Optionally, an argument evaluating to TRUE will suppress flushing
of all gene structure-specific subfeatures (transcripts). |
Methods code
sub new
{ my ($caller, @args) = @_;
my $self = $caller->SUPER::new(@args);
$self->_register_for_cleanup(\&gene_cleanup);
my ($primary) =
$self->_rearrange([qw(PRIMARY
)],@args);
$primary = 'genestructure' unless $primary;
$self->primary_tag($primary);
$self->strand(0) if(! defined($self->strand()));
return $self;} | sub transcripts
{ return @{shift->{'_transcripts'} || []};} | sub add_transcript
{ my ($self, $fea) = @_;
if(!$fea || ! $fea->isa('Bio::SeqFeature::Gene::TranscriptI') ) {
$self->throw("$fea does not implement Bio::SeqFeature::Gene::TranscriptI");
}
if(! exists($self->{'_transcripts'})) {
$self->{'_transcripts'} = [];
}
$self->_expand_region($fea);
$fea->parent($self);
push(@{$self->{'_transcripts'}}, $fea);} | sub flush_transcripts
{ my ($self) = @_;
if(exists($self->{'_transcripts'})) {
foreach my $t ( grep {defined} @{$self->{'_transcripts'} || []} ) {
$t->parent(undef);
$t = undef;
}
delete($self->{'_transcripts'});
}} | sub add_transcript_as_features
{ my ($self,@features) = @_;
my $transcript=Bio::SeqFeature::Gene::Transcript->new;
foreach my $fea (@features) {
if ($fea->primary_tag =~ /utr/i) {
$transcript->add_utr($fea);
} elsif ($fea->primary_tag =~ /promot/i) {
$transcript->add_promoter($fea);
} elsif ($fea->primary_tag =~ /poly.*A/i) {
$transcript->poly_A_site($fea);
} else {
$transcript->add_exon($fea);
}
}
$self->add_transcript($transcript);} | sub promoters
{ my ($self) = @_;
my @transcripts = $self->transcripts();
my @feas = ();
foreach my $tr (@transcripts) {
push(@feas, $tr->promoters());
}
return @feas;} | sub exons
{ my ($self, @args) = @_;
my @transcripts = $self->transcripts();
my @feas = ();
foreach my $tr (@transcripts) {
push(@feas, $tr->exons(@args));
}
return @feas;} | sub introns
{ my ($self) = @_;
my @transcripts = $self->transcripts();
my @feas = ();
foreach my $tr (@transcripts) {
push(@feas, $tr->introns());
}
return @feas;} | sub poly_A_sites
{ my ($self) = @_;
my @transcripts = $self->transcripts();
my @feas = ();
foreach my $tr (@transcripts) {
push(@feas, $tr->poly_A_site());
}
return @feas;} | sub utrs
{ my ($self,@args) = @_;
my @transcripts = $self->transcripts();
my @feas = ();
foreach my $tr (@transcripts) {
push(@feas, $tr->utrs(@args));
}
return @feas;} | sub sub_SeqFeature
{ my ($self) = @_;
my @feas = ();
@feas = $self->SUPER::sub_SeqFeature();
push(@feas, $self->transcripts());
return @feas;} | sub flush_sub_SeqFeature
{ my ($self,$fea_only) = @_;
$self->SUPER::flush_sub_SeqFeature();
if(! $fea_only) {
$self->flush_transcripts();
}} | sub gene_cleanup
{ my $self = shift;
$self->flush_transcripts();} | General documentation
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _