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.\" ========================================================================
.\"
.IX Title "Bio::SeqFeature::Gene::GeneStructure 3pm"
.TH Bio::SeqFeature::Gene::GeneStructure 3pm "2021-08-15" "perl v5.32.1" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
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.SH "NAME"
Bio::SeqFeature::Gene::GeneStructure \- A feature representing an arbitrarily complex structure of a gene
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&  # See documentation of methods.
.Ve
.SH "DESCRIPTION"
.IX Header "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.
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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 the
 web:
.PP
.Vb 1
\&  https://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "AUTHOR \- Hilmar Lapp"
.IX Header "AUTHOR - Hilmar Lapp"
Email hlapp\-at\-gmx.net
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
.SS "transcripts"
.IX Subsection "transcripts"
.Vb 4
\& 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    :
.Ve
.SS "add_transcript"
.IX Subsection "add_transcript"
.Vb 5
\& 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.
.Ve
.SS "flush_transcripts"
.IX Subsection "flush_transcripts"
.Vb 5
\& Title   : flush_transcripts()
\& Usage   : $gene\->flush_transcripts();
\& Function: Remove all transcripts from this gene structure.
\& Returns : 
\& Args    :
.Ve
.SS "add_transcript_as_features"
.IX Subsection "add_transcript_as_features"
.Vb 6
\& 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
.Ve
.SS "promoters"
.IX Subsection "promoters"
.Vb 3
\& 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    :
.Ve
.SS "exons"
.IX Subsection "exons"
.Vb 5
\& Title   : exons()
\& Usage   : @exons = $gene\->exons();
\&           @inital_exons = $gene\->exons(\*(AqInitial\*(Aq);
\& 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 \*(Aqcoding\*(Aq, 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.
.Ve
.SS "introns"
.IX Subsection "introns"
.Vb 3
\& 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    :
.Ve
.SS "poly_A_sites"
.IX Subsection "poly_A_sites"
.Vb 3
\& 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    :
.Ve
.SS "utrs"
.IX Subsection "utrs"
.Vb 6
\& Title   : utrs()
\& Usage   : @utr_sites = $gene\->utrs(\*(Aq3prime\*(Aq);
\&           @utr_sites = $gene\->utrs(\*(Aq5prime\*(Aq);
\&           @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\*(Aq and 3\*(Aq 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.
.Ve
.SS "sub_SeqFeature"
.IX Subsection "sub_SeqFeature"
.Vb 3
\& 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
.Ve
.SS "flush_sub_SeqFeature"
.IX Subsection "flush_sub_SeqFeature"
.Vb 4
\& 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).
.Ve