Bio::SeqFeature::Gene GeneStructure
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Summary
Bio::SeqFeature::Gene::GeneStructure - A feature representing an arbitrarily complex structure of a gene
Package variables
No package variables defined.
Inherit
Bio::SeqFeature::Gene::GeneStructureI Bio::SeqFeature::Generic
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
BEGIN Code
new
No description
Code
transcriptsDescriptionCode
add_transcriptDescriptionCode
flush_transcriptsDescriptionCode
add_transcript_as_featuresDescriptionCode
promotersDescriptionCode
exonsDescriptionCode
intronsDescriptionCode
poly_A_sitesDescriptionCode
utrsDescriptionCode
sub_SeqFeatureDescriptionCode
flush_sub_SeqFeatureDescriptionCode
gene_cleanup
No description
Code
Methods description
transcriptscode    nextTop
 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 :
add_transcriptcodeprevnextTop
 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.
flush_transcriptscodeprevnextTop
 Title   : flush_transcripts()
Usage : $gene->flush_transcripts();
Function: Remove all transcripts from this gene structure.
Returns :
Args :
add_transcript_as_featurescodeprevnextTop
 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
promoterscodeprevnextTop
 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 :
exonscodeprevnextTop
 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.
intronscodeprevnextTop
 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 :
poly_A_sitescodeprevnextTop
 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 :
utrscodeprevnextTop
 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.
sub_SeqFeaturecodeprevnextTop
 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
flush_sub_SeqFeaturecodeprevnextTop
 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
BEGINTop
BEGIN {
    eval "use Scalar::Util qw(weaken);";
    if ($@) {
	$Bio::SeqFeature::Gene::GeneStructure::WeakRefs = 0;  
    } else { $Bio::SeqFeature::Gene::GeneStructure::WeakRefs = 1;
}
newdescriptionprevnextTop
sub new {
    my ($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 $self;
}
transcriptsdescriptionprevnextTop
sub transcripts {
    return @{shift->{'_transcripts'} || []};
}
add_transcriptdescriptionprevnextTop
sub add_transcript {
    my ($self, $fea) = @_;

    if(!$fea || ! $fea->isa('Bio::SeqFeature::Gene::TranscriptI') ) {
	$self->throw("$fea does not implement Bio::SeqFeature::Gene::TranscriptI");
    }
    unless( exists $self->{'_transcripts'}  ) {
	$self->{'_transcripts'} = [];
    }
    $self->_expand_region($fea);
    if( $Bio::SeqFeature::Gene::GeneStructure::WeakRefs ) {
	$fea->parent(weaken $self);
    } else {
	$fea->parent($self);
    }
    push(@{$self->{'_transcripts'}}, $fea);
}
flush_transcriptsdescriptionprevnextTop
sub flush_transcripts {
    my ($self) = @_;    
    if( defined $self->{'_transcripts'} ) {
	foreach my $t ( grep {defined} @{$self->{'_transcripts'} || []} ) {
	    $t->parent(undef); # remove bkwds pointers
$t = undef; } delete($self->{'_transcripts'}); }
}
add_transcript_as_featuresdescriptionprevnextTop
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);
}
promotersdescriptionprevnextTop
sub promoters {
    my ($self) = @_;
    my @transcripts = $self->transcripts();
    my @feas = ();

    foreach my $tr (@transcripts) {
	push(@feas, $tr->promoters());
    }
    return @feas;
}
exonsdescriptionprevnextTop
sub exons {
    my ($self, @args) = @_;
    my @transcripts = $self->transcripts();
    my @feas = ();

    foreach my $tr (@transcripts) {
	push(@feas, $tr->exons(@args));
    }
    return @feas;
}
intronsdescriptionprevnextTop
sub introns {
    my ($self) = @_;
    my @transcripts = $self->transcripts();
    my @feas = ();

    foreach my $tr (@transcripts) {
	push(@feas, $tr->introns());
    }
    return @feas;
}
poly_A_sitesdescriptionprevnextTop
sub poly_A_sites {
    my ($self) = @_;
    my @transcripts = $self->transcripts();
    my @feas = ();

    foreach my $tr (@transcripts) {
	push(@feas, $tr->poly_A_site());
    }
    return @feas;
}
utrsdescriptionprevnextTop
sub utrs {
    my ($self,@args) = @_;
    my @transcripts = $self->transcripts();
    my @feas = ();

    foreach my $tr (@transcripts) {
	push(@feas, $tr->utrs(@args));
    }
    return @feas;
}
sub_SeqFeaturedescriptionprevnextTop
sub sub_SeqFeature {
    my ($self) = @_;   
    my @feas = ();

    # get what the parent already has
@feas = $self->SUPER::sub_SeqFeature(); push(@feas, $self->transcripts()); return @feas;
}
flush_sub_SeqFeaturedescriptionprevnextTop
sub flush_sub_SeqFeature {
   my ($self,$fea_only) = @_;

   $self->SUPER::flush_sub_SeqFeature();
   if(! $fea_only) {
       $self->flush_transcripts();
   }
}
gene_cleanupdescriptionprevnextTop
sub gene_cleanup {
    my $self = shift;
    $self->flush_transcripts;
}

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
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _