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.\" ========================================================================
.\"
.IX Title "Bio::SeqFeature::Gene::TranscriptI 3pm"
.TH Bio::SeqFeature::Gene::TranscriptI 3pm "2020-10-28" "perl v5.30.3" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
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.nh
.SH "NAME"
Bio::SeqFeature::Gene::TranscriptI \- Interface for a feature representing a
         transcript of exons, promoter(s), UTR, and a poly\-adenylation site.
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&  #documentation needed
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
A feature representing a transcript.
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  https://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "AUTHOR \- Hilmar Lapp"
.IX Header "AUTHOR - Hilmar Lapp"
Email hlapp@gmx.net
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
.SS "promoters"
.IX Subsection "promoters"
.Vb 3
\& 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    :
.Ve
.SS "exons"
.IX Subsection "exons"
.Vb 5
\& Title   : exons()
\& Usage   : @exons = $transcript\->exons();
\&           @inital = $transcript\->exons(\*(AqInitial\*(Aq);
\& 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.
.Ve
.SS "introns"
.IX Subsection "introns"
.Vb 6
\& 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    :
.Ve
.SS "poly_A_site"
.IX Subsection "poly_A_site"
.Vb 5
\& 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    :
.Ve
.SS "utrs"
.IX Subsection "utrs"
.Vb 3
\& 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    :
.Ve
.SS "mrna"
.IX Subsection "mrna"
.Vb 3
\& Title   : mrna()
\& Usage   : $mrna = $transcript\->mrna();
\& Function: Get the mRNA of the transcript as a sequence object.
\&
\& Returns : A Bio::PrimarySeqI implementing object.
\& Args    :
.Ve
.SS "cds"
.IX Subsection "cds"
.Vb 4
\& 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    :
.Ve
.SS "protein"
.IX Subsection "protein"
.Vb 3
\& 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    :
.Ve
.SS "parent"
.IX Subsection "parent"
.Vb 5
\& 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)
.Ve