Bio::SeqFeature::Gene::Transcript.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

NAME

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

SYNOPSIS

   # See documentation of methods.
 
 

DESCRIPTION

A feature representing a transcript.

FEEDBACK

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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:
   http://bugzilla.open-bio.org/
 
 

AUTHOR - Hilmar Lapp

Email hlapp@gmx.net

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 : 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