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#
# BioPerl module for Bio::SeqFeature::Gene::Exon
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Hilmar Lapp <hlapp@gmx.net>
#
# Copyright Hilmar Lapp
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::SeqFeature::Gene::Exon - a feature representing an exon
=head1 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";
=head1 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 =E<gt> 0 to the constructor or call
$exon-E<gt>is_coding(0) otherwise.
Apart from that, this class also implements Bio::SeqFeatureI by
inheriting off Bio::SeqFeature::Generic.
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this
and other Bioperl modules. Send your comments and suggestions preferably
to one of the Bioperl mailing lists.
Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via the
web:
https://github.com/bioperl/bioperl-live/issues
=head1 AUTHOR - Hilmar Lapp
Email hlapp@gmx.net
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::SeqFeature::Gene::Exon;
use strict;
use base qw(Bio::SeqFeature::Generic Bio::SeqFeature::Gene::ExonI);
#
# A list of allowed exon types. See primary_tag().
#
my @valid_exon_types = ('initial', 'internal', 'terminal');
sub new {
my ($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 $self;
}
=head2 is_coding
Title : is_coding
Usage : if($exon->is_coding()) {
# do something
}
if($is_utr) {
$exon->is_coding(0);
}
Function: Get/set whether or not the exon codes for amino acid.
Returns : TRUE if the object represents a feature translated into protein,
and FALSE otherwise.
Args : A boolean value on set.
=cut
sub is_coding {
my ($self,$val) = @_;
if(defined($val)) {
$self->{'_iscoding'} = $val;
}
return $self->{'_iscoding'};
}
=head2 primary_tag
Title : primary_tag
Usage : $tag = $feat->primary_tag()
$feat->primary_tag('exon')
Function: Get/set the primary tag for the exon feature.
This method is overridden here in order to allow only for
tag values following a certain convention. For consistency reasons,
the tag value must either contain the string 'exon' or the string
'utr' (both case-insensitive). In the case of 'exon', a string
describing the type of exon may be appended or prefixed. Presently,
the following types are allowed: initial, internal, and terminal
(all case-insensitive).
If the supplied tag value matches 'utr' (case-insensitive),
is_coding() will automatically be set to FALSE, and to TRUE
otherwise.
Returns : A string.
Args : A string on set.
=cut
# sub primary_tag {
# my ($self,$value) = @_;
# if(defined($value)) {
# if((lc($value) =~ /utr/i) || (lc($value) eq "exon") ||
# ((lc($value) =~ /exon/i) &&
# (grep { $value =~ /$_/i; } @valid_exon_types))) {
# $self->is_coding($value =~ /utr/i ? 0 : 1);
# } else {
# $self->throw("primary tag $value is invalid for object of class ".
# ref($self));
# }
# }
# return $self->SUPER::primary_tag($value);
# }
=head2 location
Title : location
Usage : my $location = $exon->location()
Function: Returns a location object suitable for identifying the location
of the exon on the sequence or parent feature.
This method is overridden here to restrict allowed location types
to non-compound locations.
Returns : Bio::LocationI object
Args : none
=cut
sub location {
my ($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);
}
=head2 cds
Title : cds()
Usage : $cds = $exon->cds();
Function: Get the coding sequence of the exon as a sequence object.
The sequence of the returned object is prefixed by Ns (lower case)
if the frame of the exon is defined and different from zero. The
result is that the first base starts a codon (frame 0).
This implementation returns undef if the particular exon is
not translated to protein, i.e., is_coding() returns FALSE. Undef
will also be returned if no sequence is attached to this exon
feature.
Returns : A Bio::PrimarySeqI implementing object.
Args :
=cut
sub cds {
my ($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;
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