Bio::SeqFeature::Gene::Transcript(3)

NAME
Bio::SeqFeature::Gene::Transcript - A feature representing a transcript

SYNOPSIS
See documentation of methods.

DESCRIPTION
A feature representing a transcript.

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AUTHOR - Hilmar Lapp
Email hlapp@gmx.net

Describe contact details here

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

  promoters
 Title   : promoters()
 Usage   : @proms = $transcript->promoters();
 Function: Get the promoter features/sites of this transcript.
           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 representing the
           promoter regions or sites.
 Args    :

  add_promoter
 Title   : add_promoter()
 Usage   : $transcript->add_promoter($feature);
 Function: Add a promoter feature/site to this transcript.
           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 :
 Args    : A Bio::SeqFeatureI implementing object.

  flush_promoters
 Title   : flush_promoters()
 Usage   : $transcript->flush_promoters();
 Function: Remove all promoter features/sites from this transcript.
           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 :
 Args    : none

  exons
 Title   : exons()
 Usage   : @exons = $gene->exons();
           ($inital_exon) = $gene->exons('Initial');
 Function: Get all exon features or all exons of 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 (utr, utr5prime, utr3prime).
 Returns : An array of Bio::SeqFeature::Gene::ExonI implementing objects.
 Args    : An optional string specifying the primary_tag of the feature.

  add_exon
 Title   : add_exon()
 Usage   : $transcript->add_exon($exon,'initial');
 Function: Add a exon feature to this transcript.
           The second argument denotes the type of exon. Mixing exons with and
           without a type is likely to cause trouble in exons(). Either
           leave out the type for all exons or for none.
           Presently, the following types are known: initial, internal,
           terminal, utr, utr5prime, and utr3prime (all case-insensitive).
           UTR should better be added through utrs()/add_utr().
           If you wish to use other or additional types, you will almost
           certainly have to call exon_type_sortorder() in order to replace
           the default sort order, or mrna(), cds(), protein(), and exons()
           may yield unexpected results.
 Returns :
 Args    : A Bio::SeqFeature::Gene::ExonI implementing object.
           A string indicating the type of the exon (optional).

  flush_exons
 Title   : flush_exons()
 Usage   : $transcript->flush_exons();
           $transcript->flush_exons('terminal');
 Function: Remove all or a certain type of exon features from this transcript.
           See add_exon() for documentation about types.
           Calling without a type will not flush UTRs. Call flush_utrs() for
           this purpose.
 Returns :
 Args    : A string indicating the type of the exon (optional).

  exon_type_sortorder
 Title   : exon_type_sortorder
 Usage   : $transcript->exon_type_sortorder('type1','type2','type3');
           $tableref = $transcript->exon_type_sortorder();
           Bio::SeqFeature::Gene::Transcript->exon_type_sortorder('type1','type2','type3');
 Function: Install or retrieve the sort-order of exon types.
           Ordering exons by type is only of relevance for methods
           constructing a sequence corresponding to the transcript object
           (e.g., mrna(), cds(), etc). For instance, an initial exon would
           have to be put before an internal exon.
           The sort-order installed by default covers only the exon types
           documented in exons(). If you use a different set or additional
           types, you must call this method with the proper ordering before
           you can obtain meaningful results from methods that concatenate
           the sequence of exons. On installing a sort-order, pass all types
           you are using in ascending order.
           You can also retrieve the installed order. Do not modify the
           returned hash table (the method returns a reference) unless you know
           exactly what you are doing. Inspecting the keys of the table will
           tell you which types are currently known.
           This method can also be called as a class method. When called as
           class method it will operate on the default sort-order, which will
           be propagated to every object instantiated thereafter. When called
           as instance method it will operate only on the private copy of the
           object.
 Returns : A reference to a hash table representing the sort-order.
 Args    : On installing an order, an array of exon types in ascending order.

  introns
 Title   : introns()
 Usage   : @introns = $gene->introns();
 Function: Get all intron features this gene structure.
           Note that this implementation generates these features on-the-fly,
           that is, it simply treats all regions between exons as introns,
           assuming that exons do not overlap. A consequence is that a
           consistent correspondence between the elements in the returned
           array and the array exons() returns will exist only if the
           exons are properly sorted within their types (forward for plus-
           strand and reverse for minus-strand transcripts). To ensure
           correctness the elements in the array returned will always be
           sorted.
 Returns : An array of Bio::SeqFeatureI implementing objects representing the
           intron regions.
 Args    :

  poly_A_site
 Title   : poly_A_site()
 Usage   : $polyAsite = $transcript->poly_A_site();
 Function: Get/set the poly-adenylation feature/site of this transcript.
 Returns : A Bio::SeqFeatureI implementing object representing the
           poly-adenylation region.
 Args    : A Bio::SeqFeatureI implementing object on set, or FALSE to flush
           a previously set object.

  utrs
 Title   : utrs()
 Usage   : @utr_sites = $transcript->utrs('3prime');
           @utr_sites = $transcript->utrs('5prime');
           @utr_sites = $transcript->utrs();
 Function: Get the features representing untranslated regions (UTR) of this
           transcript.
           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.
 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.

  add_utr
 Title   : add_utr()
 Usage   : $transcript->add_utr($utrobj, '3prime');
           $transcript->add_utr($utrobj);
 Function: Add a UTR feature/site to this transcript.
           The second parameter is optional and denotes the type of the UTR
           feature. Presently recognized types include '5prime' and '3prime'
           for UTR on the 5' and 3' end of a gene, respectively.
           Calling this method is the same as calling
           add_exon($utrobj, 'utr'.$type). In this sense a UTR object is a
           special exon object, which is transcribed, not spliced out, but
           not translated.
           Note that the object supplied should return FALSE for is_coding().
           Otherwise cds() and friends will become confused.
 Returns :
 Args    : A Bio::SeqFeature::Gene::ExonI implementing object.

  flush_utrs
 Title   : flush_utrs()
 Usage   : $transcript->flush_utrs();
           $transcript->flush_utrs('3prime');
 Function: Remove all or a specific type of UTR features/sites from this
           transcript.
           Cf. add_utr() for documentation about recognized types.
 Returns :
 Args    : Optionally a string denoting the type of UTR feature.

  sub_SeqFeature
 Title   : sub_SeqFeature
 Usage   : @feats = $transcript->sub_SeqFeature();
 Function: Returns an array of all subfeatures.
           This method is defined in Bio::SeqFeatureI. We override this here
           to include the exon etc features.
 Returns : An array Bio::SeqFeatureI implementing objects.
 Args    : none

  flush_sub_SeqFeature
 Title   : flush_sub_SeqFeature
 Usage   : $transcript->flush_sub_SeqFeature();
           $transcript->flush_sub_SeqFeature(1);
 Function: Removes all subfeatures.
           This method is overridden from Bio::SeqFeature::Generic to flush
           all additional subfeatures like exons, promoters, etc., which is
           almost certainly not what you want. To remove only features added
           through $transcript->add_sub_SeqFeature($feature) pass any
           argument evaluating to TRUE.
 Example :
 Returns : none
 Args    : Optionally, an argument evaluating to TRUE will suppress flushing
           of all transcript-specific subfeatures (exons etc.).

  cds
 Title   : cds
 Usage   : $seq = $transcript->cds();
 Function: Returns the CDS (coding sequence) as defined by the exons of this
           transcript and the attached sequence.
           If no sequence is attached this method will return undef.
           Note that the implementation provided here returns a concatenation
           of all coding exons, thereby assuming that exons do not overlap.
           Note also that you cannot set the CDS via this method. Set a single
           CDS feature as a single exon, or derive your own class if you want
           to store a predicted CDS.
 Example :
 Returns : A Bio::PrimarySeqI implementing object.
 Args    :

  protein
 Title   : protein()
 Usage   : $protein = $transcript->protein();
 Function: Get the protein encoded by the transcript as a sequence object.
           The implementation provided here simply calls translate() on the
           object returned by cds().
 Returns : A Bio::PrimarySeqI implementing object.
 Args    :

  mrna
 Title   : mrna()
 Usage   : $mrna = $transcript->mrna();
 Function: Get the mRNA of the transcript as a sequence object.
           The difference to cds() is that the sequence object returned by
           this methods will also include UTR and the poly-adenylation site,
           but not promoter sequence (TBD).
           HL: do we really need this method?
 Returns : A Bio::PrimarySeqI implementing object.
 Args    :