/ 
bioperl-1.2.2
/ Bio::SeqFeature::Gene::GeneStructure

NAME

Bio::SeqFeature::Gene::GeneStructure - A feature representing an arbitrarily complex structure of a gene

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.

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APPENDIX

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

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    :

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.

flush_transcripts

Title   : flush_transcripts()
Usage   : $gene->flush_transcripts();
Function: Remove all transcripts from this gene structure.
Returns : 
Args    :

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

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    :

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.

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    :

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    :

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.

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

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).