FAST::Bio::SeqFeature::Gene::GeneStructure - A feature representing an arbitrarily complex structure of a gene
# See documentation of methods.
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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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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 :
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.
Title : flush_transcripts() Usage : $gene->flush_transcripts(); Function: Remove all transcripts from this gene structure. Returns : Args :
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 objects
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 :
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.
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 :
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 :
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.
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 : none
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).
To install FAST, copy and paste the appropriate command in to your terminal.
cpanm
cpanm FAST
CPAN shell
perl -MCPAN -e shell install FAST
For more information on module installation, please visit the detailed CPAN module installation guide.