Raw content of Bio::Tools::Prediction::Exon # $Id: Exon.pm,v 1.10 2002/10/22 07:38:48 lapp Exp $ # # BioPerl module for Bio::Tools::Prediction::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::Tools::Prediction::Exon - A predicted exon feature =head1 SYNOPSIS See documentation of methods. =head1 DESCRIPTION A feature representing a predicted exon. This class actually inherits off Bio::SeqFeature::Gene::Exon and therefore has all that functionality (also implements Bio::SeqFeatureI), plus a few methods supporting predicted features, like various scores and a significance. Even though these were inspired by GenScan results, at least a subset should be generally useable for exon prediction results. =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::Tools::Prediction::Exon; use vars qw(@ISA); use strict; use Bio::SeqFeature::Gene::Exon; @ISA = qw(Bio::SeqFeature::Gene::Exon); sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($primary) = $self->_rearrange([qw(PRIMARY)],@args); return $self; } =head2 predicted_cds Title : predicted_cds Usage : $predicted_cds_dna = $exon->predicted_cds(); $exon->predicted_cds($predicted_cds_dna); Function: Get/Set the CDS (coding sequence) as predicted by a program. This method is independent of an attached_seq. There is no guarantee whatsoever that the returned CDS has anything to do (e.g., matches) with the sequence covered by the exons as annotated through this object. Example : Returns : A Bio::PrimarySeqI implementing object holding the DNA sequence defined as coding by a prediction of a program. Args : On set, a Bio::PrimarySeqI implementing object holding the DNA sequence defined as coding by a prediction of a program. =cut sub predicted_cds { my ($self, $cds) = @_; if(defined($cds)) { $self->{'_predicted_cds'} = $cds; } return $self->{'_predicted_cds'}; } =head2 predicted_protein Title : predicted_protein Usage : $predicted_protein_seq = $exon->predicted_protein(); $exon->predicted_protein($predicted_protein_seq); Function: Get/Set the protein translation as predicted by a program. This method is independent of an attached_seq. There is no guarantee whatsoever that the returned translation has anything to do with the sequence covered by the exons as annotated through this object, or the sequence returned by predicted_cds(), although it should usually be just the standard translation. Example : Returns : A Bio::PrimarySeqI implementing object holding the protein translation as predicted by a program. Args : On set, a Bio::PrimarySeqI implementing object holding the protein translation as predicted by a program. =cut sub predicted_protein { my ($self, $aa) = @_; if(defined($aa)) { $self->{'_predicted_aa'} = $aa; } return $self->{'_predicted_aa'}; } =head2 significance Title : significance Usage : $evalue = $obj->significance(); $obj->significance($evalue); Function: Returns : Args : =cut sub significance { my ($self, $value) = @_; return $self->_tag_value('signif', $value); } =head2 start_signal_score Title : start_signal_score Usage : $sc = $obj->start_signal_score(); $obj->start_signal_score($evalue); Function: Get/Set a score for the exon start signal (acceptor splice site or initiation signal). Returns : Args : =cut sub start_signal_score { my ($self, $value) = @_; return $self->_tag_value('AccScore', $value); } =head2 end_signal_score Title : end_signal_score Usage : $sc = $obj->end_signal_score(); $obj->end_signal_score($evalue); Function: Get/Set a score for the exon end signal (donor splice site or termination signal). Returns : Args : =cut sub end_signal_score { my ($self, $value) = @_; return $self->_tag_value('DonScore', $value); } =head2 coding_signal_score Title : coding_signal_score Usage : $sc = $obj->coding_signal_score(); $obj->coding_signal_score($evalue); Function: Get/Set a score for the exon coding signal (e.g., coding potential). Returns : Args : =cut sub coding_signal_score { my ($self, $value) = @_; return $self->_tag_value('CodScore', $value); } # # Everything else is just inherited from SeqFeature::Generic. # 1;