Raw content of Bio::SeqFeature::Gene::GeneStructure
<![CDATA[# $Id: GeneStructure.pm,v 1.14 2002/10/22 07:38:41 lapp Exp $
#
# BioPerl module for Bio::SeqFeature::Gene::GeneStructure
#
# Cared for by Hilmar Lapp <hlapp@gmx.net>
#
# Copyright Hilmar Lapp
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::SeqFeature::Gene::GeneStructure - A feature representing an arbitrarily
complex structure of a gene
=head1 SYNOPSIS
See documentation of methods.
=head1 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.
=head1 FEEDBACK
=head2 Mailing Lists
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://bio.perl.org/MailList.html - About the mailing lists
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution.
Bug reports can be submitted via email or the web:
bioperl-bugs@bio.perl.org
http://bugzilla.bioperl.org/
=head1 AUTHOR - Hilmar Lapp
Email hlapp@gmx.net
Describe contact details here
=head1 APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::SeqFeature::Gene::GeneStructure;
use vars qw(@ISA);
use strict;
use Bio::SeqFeature::Generic;
use Bio::SeqFeature::Gene::GeneStructureI;
@ISA = qw(Bio::SeqFeature::Generic Bio::SeqFeature::Gene::GeneStructureI);
sub new {
my ($caller, @args) = @_;
my $self = $caller->SUPER::new(@args);
my ($primary) =
$self->_rearrange([qw(PRIMARY
)],@args);
$primary = 'genestructure' unless $primary;
$self->primary_tag($primary);
$self->strand(0) if(! defined($self->strand()));
return $self;
}
=head2 transcripts
Title : transcripts
Usage : @transcripts = $gene->transcripts();
Function: Get the transcripts of this gene structure. Many gene structures
will have only one transcript.
Returns : An array of Bio::SeqFeature::Gene::TranscriptI implementing objects.
Args :
=cut
sub transcripts {
my ($self) = @_;
return () unless exists($self->{'_transcripts'});
return @{$self->{'_transcripts'}};
}
=head2 add_transcript
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.
=cut
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);
}
=head2 flush_transcripts
Title : flush_transcripts()
Usage : $gene->flush_transcripts();
Function: Remove all transcripts from this gene structure.
Returns :
Args :
=cut
sub flush_transcripts {
my ($self) = @_;
if(exists($self->{'_transcripts'})) {
delete($self->{'_transcripts'});
}
}
=head2 add_transcript_as_features
Title : add_transcript_as_features
Usage : $gene->add_transcript_as_features(@featurelist);
Function: take a list of Bio::SeqFeatureI objects and turn them into a
Bio::SeqFeature::Gene::Transcript object. Add that transcript to the gene.
Returns : nothing
Args : a list of Bio::SeqFeatureI compliant objects
=cut
sub add_transcript_as_features{
my ($self,@features) = @_;
my $transcript=Bio::SeqFeature::Gene::Transcript->new;
foreach my $fea (@features) {
if ($fea->primary_tag =~ /utr/i) { #UTR / utr/ 3' utr / utr5 etc.
$transcript->add_utr($fea);
} elsif ($fea->primary_tag =~ /promot/i) { #allow for spelling differences
$transcript->add_promoter($fea);
} elsif ($fea->primary_tag =~ /poly.*A/i) { #polyA, POLY_A, etc.
$transcript->poly_A_site($fea);
} else { #assume the rest are exons
$transcript->add_exon($fea);
}
}
$self->add_transcript($transcript);
}
=head2 promoters
Title : promoters
Usage : @prom_sites = $gene->promoters();
Function: Get the promoter features of this gene structure.
This method basically merges the promoters returned by transcripts.
Note that OO-modeling of regulatory elements is not stable yet.
This means that this method might change or even disappear in a
future release. Be aware of this if you use it.
Returns : An array of Bio::SeqFeatureI implementing objects.
Args :
=cut
sub promoters {
my ($self) = @_;
my @transcripts = $self->transcripts();
my @feas = ();
foreach my $tr (@transcripts) {
push(@feas, $tr->promoters());
}
return @feas;
}
=head2 exons
Title : exons()
Usage : @exons = $gene->exons();
@inital_exons = $gene->exons('Initial');
Function: Get all exon features or all exons of a specified type of this gene
structure.
Exon type is treated as a case-insensitive regular expression and
optional. For consistency, use only the following types:
initial, internal, terminal, utr, utr5prime, and utr3prime.
A special and virtual type is 'coding', which refers to all types
except utr.
This method basically merges the exons returned by transcripts.
Returns : An array of Bio::SeqFeature::Gene::ExonI implementing objects.
Args : An optional string specifying the type of exon.
=cut
sub exons {
my ($self, @args) = @_;
my @transcripts = $self->transcripts();
my @feas = ();
foreach my $tr (@transcripts) {
push(@feas, $tr->exons(@args));
}
return @feas;
}
=head2 introns
Title : introns()
Usage : @introns = $gene->introns();
Function: Get all introns of this gene structure.
Note that this class currently generates these features on-the-fly,
that is, it simply treats all regions between exons as introns.
It assumes that the exons in the transcripts do not overlap.
This method basically merges the introns returned by transcripts.
Returns : An array of Bio::SeqFeatureI implementing objects.
Args :
=cut
sub introns {
my ($self) = @_;
my @transcripts = $self->transcripts();
my @feas = ();
foreach my $tr (@transcripts) {
push(@feas, $tr->introns());
}
return @feas;
}
=head2 poly_A_sites
Title : poly_A_sites()
Usage : @polyAsites = $gene->poly_A_sites();
Function: Get the poly-adenylation sites of this gene structure.
This method basically merges the poly-adenylation sites returned by
transcripts.
Returns : An array of Bio::SeqFeatureI implementing objects.
Args :
=cut
sub poly_A_sites {
my ($self) = @_;
my @transcripts = $self->transcripts();
my @feas = ();
foreach my $tr (@transcripts) {
push(@feas, $tr->poly_A_site());
}
return @feas;
}
=head2 utrs
Title : utrs()
Usage : @utr_sites = $gene->utrs('3prime');
@utr_sites = $gene->utrs('5prime');
@utr_sites = $gene->utrs();
Function: Get the features representing untranslated regions (UTR) of this
gene structure.
You may provide an argument specifying the type of UTR. Currently
the following types are recognized: 5prime 3prime for UTR on the
5' and 3' end of the CDS, respectively.
This method basically merges the UTRs returned by transcripts.
Returns : An array of Bio::SeqFeature::Gene::ExonI implementing objects
representing the UTR regions or sites.
Args : Optionally, either 3prime, or 5prime for the the type of UTR
feature.
=cut
sub utrs {
my ($self,@args) = @_;
my @transcripts = $self->transcripts();
my @feas = ();
foreach my $tr (@transcripts) {
push(@feas, $tr->utrs(@args));
}
return @feas;
}
=head2 sub_SeqFeature
Title : sub_SeqFeature
Usage : @feats = $gene->sub_SeqFeature();
Function: Returns an array of all subfeatures.
This method is defined in Bio::SeqFeatureI. We override this here
to include the transcripts.
Returns : An array Bio::SeqFeatureI implementing objects.
Args : none
=cut
sub sub_SeqFeature {
my ($self) = @_;
my @feas = ();
# get what the parent already has
@feas = $self->SUPER::sub_SeqFeature();
push(@feas, $self->transcripts());
return @feas;
}
=head2 flush_sub_SeqFeature
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).
=cut
sub flush_sub_SeqFeature {
my ($self,$fea_only) = @_;
$self->SUPER::flush_sub_SeqFeature();
if(! $fea_only) {
$self->flush_transcripts();
}
}
1;
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