Raw content of Bio::SeqFeature::Gene::Exon # $Id: Exon.pm,v 1.8 2002/10/22 07:38:41 lapp Exp $ # # BioPerl module for Bio::SeqFeature::Gene::Exon # # 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 ", $exon->cds()->translate()->seq(), "\n"; =head1 DESCRIPTION This module implements a feature representing an exon by implementing the Bio::SeqFeature::Gene::ExonI interface. Apart from that, this class also implements Bio::SeqFeatureI by inheriting off Bio::SeqFeature::Generic. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bio.perl.org/MailList.html - About the mailing lists =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web: bioperl-bugs@bio.perl.org http://bugzilla.bioperl.org/ =head1 AUTHOR - Hilmar Lapp Email hlapp@gmx.net Describe contact details here =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::SeqFeature::Gene::Exon; use vars qw(@ISA); use strict; use Bio::SeqFeature::Generic; use Bio::SeqFeature::Gene::ExonI; @ISA = qw(Bio::SeqFeature::Generic Bio::SeqFeature::Gene::ExonI); # # A list of allowed exon types. See primary_tag(). # my @valid_exon_types = ('initial', 'internal', 'terminal'); sub new { my ($caller, @args) = @_; my $self = $caller->SUPER::new(@args); my ($primary) = $self->_rearrange([qw(PRIMARY)],@args); $primary = 'exon' unless $primary; $self->primary_tag($primary); # this will also set is_coding() $self->strand(0) if(! defined($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 undef 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;