Bio::SeqFeature::Gene Exon
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Summary
Bio::SeqFeature::Gene::Exon - a feature representing an exon
Package variables
Privates (from "my" definitions)
@valid_exon_types = ('initial', 'internal', 'terminal')
Inherit
Bio::SeqFeature::Gene::ExonI Bio::SeqFeature::Generic
Synopsis
    # obtain an exon instance $exon somehow
print "exon from ", $exon->start(), " to ", $exon->end(),
" on seq ", $exon->seq_id(), ", strand ", $exon->strand(),
", encodes the peptide sequence ",
$exon->cds()->translate()->seq(), "\n";
Description
This module implements a feature representing an exon by implementing
the Bio::SeqFeature::Gene::ExonI interface. By default an Exon is
coding. Supply -is_coding => 0 to the constructor or call
$exon->is_coding(0) otherwise.
Apart from that, this class also implements Bio::SeqFeatureI by
inheriting off Bio::SeqFeature::Generic.
Methods
new
No description
Code
is_codingDescriptionCode
locationDescriptionCode
cdsDescriptionCode
Methods description
is_codingcode    nextTop
 Title   : is_coding
Usage : if($exon->is_coding()) {
# do something
}
if($is_utr) {
$exon->is_coding(0);
}
Function: Get/set whether or not the exon codes for amino acid.
Returns : TRUE if the object represents a feature translated into protein,
and FALSE otherwise.
Args : A boolean value on set.
locationcodeprevnextTop
 Title   : location
Usage : my $location = $exon->location()
Function: Returns a location object suitable for identifying the location
of the exon on the sequence or parent feature.
This method is overridden here to restrict allowed location types to non-compound locations. Returns : Bio::LocationI object Args : none
cdscodeprevnextTop
 Title   : cds()
Usage : $cds = $exon->cds();
Function: Get the coding sequence of the exon as a sequence object.
The sequence of the returned object is prefixed by Ns (lower case) if the frame of the exon is defined and different from zero. The result is that the first base starts a codon (frame 0). This implementation returns undef if the particular exon is not translated to protein, i.e., is_coding() returns FALSE. Undef will also be returned if no sequence is attached to this exon feature. Returns : A Bio::PrimarySeqI implementing object. Args :
Methods code
newdescriptionprevnextTop
sub new {
    my ($caller, @args) = @_;
    my $self = $caller->SUPER::new(@args);

    my ($is_coding) =
	$self->_rearrange([qw(IS_CODING)],@args);
    $self->primary_tag('exon') unless $self->primary_tag();
    $self->is_coding(defined($is_coding) ? $is_coding : 1);
    $self->strand(0) if(! defined($self->strand()));
    return $self;
}
is_codingdescriptionprevnextTop
sub is_coding {
    my ($self,$val) = @_;

    if(defined($val)) {
	$self->{'_iscoding'} = $val;
    }
    return $self->{'_iscoding'};
}
locationdescriptionprevnextTop
sub location {
   my ($self,$value) = @_;  

   if(defined($value) && $value->isa('Bio::Location::SplitLocationI')) {
       $self->throw("split or compound location is not allowed ".
		    "for an object of type " . ref($self));
   }
   return $self->SUPER::location($value);
}
cdsdescriptionprevnextTop
sub cds {
    my ($self) = @_;

    # UTR is not translated
return if(! $self->is_coding()); my $seq = $self->seq(); if(defined($seq) && defined($self->frame()) && ($self->frame() != 0)) { my $prefix = "n" x $self->frame(); $seq->seq($prefix . $seq->seq()); } return $seq; } 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 _
primary_tagTop
 Title   : primary_tag
Usage : $tag = $feat->primary_tag()
$feat->primary_tag('exon')
Function: Get/set the primary tag for the exon feature.
This method is overridden here in order to allow only for tag values following a certain convention. For consistency reasons, the tag value must either contain the string 'exon' or the string 'utr' (both case-insensitive). In the case of 'exon', a string describing the type of exon may be appended or prefixed. Presently, the following types are allowed: initial, internal, and terminal (all case-insensitive). If the supplied tag value matches 'utr' (case-insensitive), is_coding() will automatically be set to FALSE, and to TRUE otherwise. Returns : A string. Args : A string on set.