Raw content of Bio::SeqFeature::Gene::GeneStructure # $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;