NAME
FAST::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 FAST::Bio::SeqFeature::Gene::TranscriptI (interface) and FAST::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 FAST::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 FAST::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 FAST::Bio::SeqFeatureI objects and turn them into a
FAST::Bio::SeqFeature::Gene::Transcript object. Add that transcript to the gene.
Returns : nothing
Args : a list of FAST::Bio::SeqFeatureI compliant objectspromoters
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 FAST::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 FAST::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 FAST::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 FAST::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 FAST::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 FAST::Bio::SeqFeatureI. We override this here
to include the transcripts.
Returns : An array FAST::Bio::SeqFeatureI implementing objects.
Args : noneflush_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 FAST::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).