Bio::SeqFeature::Gene TranscriptI
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Summary
Bio::SeqFeature::Gene::TranscriptI - Interface for a feature representing a
transcript of exons, promoter(s), UTR, and a poly-adenylation site.
Package variables
No package variables defined.
Included modules
Carp
Inherit
Bio::SeqFeatureI
Synopsis
  #documentation needed
Description
A feature representing a transcript.
Methods
promotersDescriptionCode
exonsDescriptionCode
intronsDescriptionCode
poly_A_siteDescriptionCode
utrsDescriptionCode
mrnaDescriptionCode
cdsDescriptionCode
proteinDescriptionCode
parentDescriptionCode
Methods description
promoterscode    nextTop
 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 :
exonscodeprevnextTop
 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.
intronscodeprevnextTop
 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_sitecodeprevnextTop
 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 :
utrscodeprevnextTop
 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 :
mrnacodeprevnextTop
 Title   : mrna()
Usage : $mrna = $transcript->mrna();
Function: Get the mRNA of the transcript as a sequence object.
Returns : A Bio::PrimarySeqI implementing object. Args :
cdscodeprevnextTop
 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 :
proteincodeprevnextTop
 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 :
parentcodeprevnextTop
 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)
Methods code
promotersdescriptionprevnextTop
sub promoters {
    my ($self) = @_;
    $self->throw_not_implemented();
}
exonsdescriptionprevnextTop
sub exons {
    my ($self, $type) = @_;
    $self->throw_not_implemented();
}
intronsdescriptionprevnextTop
sub introns {
    my ($self) = @_;
    $self->throw_not_implemented();
}
poly_A_sitedescriptionprevnextTop
sub poly_A_site {
    my ($self) = @_;
    $self->throw_not_implemented();
}
utrsdescriptionprevnextTop
sub utrs {
    my ($self) = @_;
    $self->throw_not_implemented();
}
mrnadescriptionprevnextTop
sub mrna {
    my ($self) = @_;
    $self->throw_not_implemented();
}
cdsdescriptionprevnextTop
sub cds {
    my ($self) = @_;
    $self->throw_not_implemented();
}
proteindescriptionprevnextTop
sub protein {
    my ($self) = @_;
    $self->throw_not_implemented();
}
parentdescriptionprevnextTop
sub parent {
   my $self = shift;
   if( @_ ) {
       my $value = shift;
       # I really mean ! defined $value - 
# we will allow re-setting the parent to undef
if (! defined $value || $value->isa("Bio::SeqFeature::Gene::GeneStructureI")) { $self->{'_parent'} = $value; } else { $self->throw("$value must be a Bio::SeqFeature::Gene::GeneStructureI") } } return $self->{'_parent'}; } 1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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 Top
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 BugsTop
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://redmine.open-bio.org/projects/bioperl/
AUTHOR - Hilmar LappTop
Email hlapp@gmx.net
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _