Bio::SeqFeature::Gene::Exon(3pm) User Contributed Perl Documentation Bio::SeqFeature::Gene::Exon(3pm)
NAME
Bio::SeqFeature::Gene::Exon - a feature representing an exon
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(), "
";
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 $exon->is_coding(0) otherwise.
Apart from that, this class also implements Bio::SeqFeatureI by inheriting off Bio::SeqFeature::Generic.
FEEDBACK
Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably
to one of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
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Support
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address
it. Please include a thorough description of the problem with code and data examples if at all possible.
Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the
web:
https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Hilmar Lapp
Email hlapp@gmx.net
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
is_coding
Title : is_coding
Usage : if($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.
primary_tag
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.
location
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
cds
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 :
perl v5.14.2 2012-03-02 Bio::SeqFeature::Gene::Exon(3pm)