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.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support¶

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

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.

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:

  https://github.com/bioperl/bioperl-live/issues

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 : the removed features as a list
 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 
           transcript.
           Exon type is treated as a case-insensitive regular expression and 
           is optional. For consistency, use only the following types: 
           initial, internal, terminal.
 Returns : An array of Bio::SeqFeature::Gene::ExonI implementing objects.
 Args    : An optional string specifying the primary_tag of the feature.

exons_ordered¶

 Title   : exons_ordered
 Usage   : @exons = $gene->exons_ordered();
           @exons = $gene->exons_ordered("Internal");
 Function: Get an ordered list of all exon features or all exons of specified
           type of this transcript.
           Exon type is treated as a case-insensitive regular expression and 
           is optional. For consistency, use only the following types:
 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 : the deleted features as a list
 Args    : A string indicating the type of the exon (optional).

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 that 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::SeqFeature::Gene::Intron 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('utr3prime');
           @utr_sites = $transcript->utrs('utr5prime');
           @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: utr5prime utr3prime for UTR on the
           5' and 3' end of the CDS, respectively.
 Returns : An array of Bio::SeqFeature::Gene::UTR objects
           representing the UTR regions or sites.
 Args    : Optionally, either utr3prime, or utr5prime for the the type of UTR
           feature.

add_utr¶

 Title   : add_utr()
 Usage   : $transcript->add_utr($utrobj, 'utr3prime');
           $transcript->add_utr($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 'utr5prime' and 'utr3prime'
           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::UTR implementing object.

flush_utrs¶

 Title   : flush_utrs()
 Usage   : $transcript->flush_utrs();
           $transcript->flush_utrs('utr3prime');
 Function: Remove all or a specific type of UTR features/sites from this
           transcript.
           Cf. add_utr() for documentation about recognized types.
 Returns : a list of the removed features
 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 false.
           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    :

features¶

 Title   : features
 Usage   : my @features=$transcript->features;
 Function: returns all the features associated with this transcript
 Returns : a list of SeqFeatureI implementing objects
 Args    : none

features_ordered¶

 Title   : features_ordered
 Usage   : my @features=$transcript->features_ordered;
 Function: returns all the features associated with this transcript,
           in order by feature start, according to strand
 Returns : a list of SeqFeatureI implementing objects
 Args    : none