NAME

       Bio::SeqFeature::Gene::TranscriptI - Interface for a feature representing a
                transcript of exons, promoter(s), UTR, and a poly-adenylation site.

SYNOPSIS

         #documentation needed

DESCRIPTION

       A feature representing a transcript.

FEEDBACK

   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

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 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    :

   exons
        Title   : exons()
        Usage   : @exons = $transcript->exons();
                  @inital = $transcript->exons('Initial');
        Function: Get the individual exons this transcript comprises of, or all exons
                  of a specified type.

                  Refer to the documentation of the class that produced this
                  transcript object for information about the possible types.

                  See Bio::SeqFeature::Gene::ExonI for properties of the
                  returned objects.

        Returns : An array of Bio::SeqFeature::Gene::ExonI implementing objects
        Args    : An optional string specifying the type of the exon.

   introns
        Title   : introns()
        Usage   : @introns = $transcript->introns();
        Function: Get all introns this transcript comprises of.
        Returns : An array of Bio::SeqFeatureI implementing objects representing the
                  introns.
        Args    :

   poly_A_site
        Title   : poly_A_site()
        Usage   : $polyAsite = $transcript->poly_A_site();
        Function: Get the poly-adenylation site of this transcript.
        Returns : A Bio::SeqFeatureI implementing object.
        Args    :

   utrs
        Title   : utrs()
        Usage   : @utr_sites = $transcript->utrs();
        Function: Get the UTR regions this transcript comprises of.

                  See Bio::SeqFeature::Gene::ExonI for properties of the
                  returned objects.

        Returns : An array of Bio::SeqFeature::Gene::ExonI implementing objects
        Args    :

   mrna
        Title   : mrna()
        Usage   : $mrna = $transcript->mrna();
        Function: Get the mRNA of the transcript as a sequence object.

        Returns : A Bio::PrimarySeqI implementing object.
        Args    :

   cds
        Title   : cds()
        Usage   : $cds = $transcript->cds();
        Function: Get the CDS (coding sequence) of the transcript as a sequence
                  object.

        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.

        Returns : A Bio::PrimarySeqI implementing object.
        Args    :

   parent
        Title   : parent
        Usage   : $obj->parent($newval)
        Function: get the parent gene of the transcript
        Returns : value of parent - a Bio::SeqFeature::Gene::GeneStructureI-compliant object
        Args    : a Bio::SeqFeature::Gene::GeneStructureI-compliant object (optional)