branch-1-6/Bio/Tools/Prediction/Exon.pm

   1 # $Id$
   2 #
   3 # BioPerl module for Bio::Tools::Prediction::Exon
   4 #
   5 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   6 #
   7 # Cared for by Hilmar Lapp <hlapp@gmx.net>
   8 #
   9 # Copyright Hilmar Lapp
  10 #
  11 # You may distribute this module under the same terms as perl itself
  12
  13 # POD documentation - main docs before the code
  14
  15 =head1 NAME
  16
  17 Bio::Tools::Prediction::Exon - A predicted exon feature
  18
  19 =head1 SYNOPSIS
  20
  21   # See documentation of methods.
  22
  23 =head1 DESCRIPTION
  24
  25 A feature representing a predicted exon. This class actually inherits
  26 off Bio::SeqFeature::Gene::Exon and therefore has all that
  27 functionality (also implements Bio::SeqFeatureI), plus a few methods
  28 supporting predicted features, like various scores and a
  29 significance. Even though these were inspired by GenScan results, at
  30 least a subset should be generally useable for exon prediction
  31 results.
  32
  33 =head1 FEEDBACK
  34
  35 =head2 Mailing Lists
  36
  37 User feedback is an integral part of the evolution of this
  38 and other Bioperl modules. Send your comments and suggestions preferably
  39  to one of the Bioperl mailing lists.
  40 Your participation is much appreciated.
  41
  42   bioperl-l@bioperl.org                  - General discussion
  43   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  44
  45 =head2 Support
  46
  47 Please direct usage questions or support issues to the mailing list:
  48
  49 I<bioperl-l@bioperl.org>
  50
  51 rather than to the module maintainer directly. Many experienced and
  52 reponsive experts will be able look at the problem and quickly
  53 address it. Please include a thorough description of the problem
  54 with code and data examples if at all possible.
  55
  56 =head2 Reporting Bugs
  57
  58 Report bugs to the Bioperl bug tracking system to help us keep track
  59 the bugs and their resolution.  Bug reports can be submitted via the
  60 web:
  61
  62   http://bugzilla.open-bio.org/
  63
  64 =head1 AUTHOR - Hilmar Lapp
  65
  66 Email hlapp-at-gmx.net
  67
  68 =head1 APPENDIX
  69
  70 The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
  71
  72 =cut
  73
  74
  75 # Let the code begin...
  76
  77
  78 package Bio::Tools::Prediction::Exon;
  79 use strict;
  80
  81
  82 use base qw(Bio::SeqFeature::Gene::Exon);
  83
  84 sub new {
  85     my($class,@args) = @_;
  86
  87     my $self = $class->SUPER::new(@args);
  88
  89     return $self;
  90 }
  91
  92
  93 =head2 predicted_cds
  94
  95  Title   : predicted_cds
  96  Usage   : $predicted_cds_dna = $exon->predicted_cds();
  97            $exon->predicted_cds($predicted_cds_dna);
  98  Function: Get/Set the CDS (coding sequence) as predicted by a program.
  99
 100            This method is independent of an attached_seq. There is no
 101            guarantee whatsoever that the returned CDS has anything to do
 102            (e.g., matches) with the sequence covered by the exons as annotated
 103            through this object.
 104
 105  Example :
 106  Returns : A Bio::PrimarySeqI implementing object holding the DNA sequence
 107            defined as coding by a prediction of a program.
 108  Args    : On set, a Bio::PrimarySeqI implementing object holding the DNA
 109            sequence defined as coding by a prediction of a program.
 110
 111 =cut
 112
 113 sub predicted_cds {
 114     my ($self, $cds) = @_;
 115
 116     if(defined($cds)) {
 117         $self->{'_predicted_cds'} = $cds;
 118     }
 119     return $self->{'_predicted_cds'};
 120 }
 121
 122 =head2 predicted_protein
 123
 124  Title   : predicted_protein
 125  Usage   : $predicted_protein_seq = $exon->predicted_protein();
 126            $exon->predicted_protein($predicted_protein_seq);
 127  Function: Get/Set the protein translation as predicted by a program.
 128
 129            This method is independent of an attached_seq. There is no
 130            guarantee whatsoever that the returned translation has anything to
 131            do with the sequence covered by the exons as annotated
 132            through this object, or the sequence returned by predicted_cds(),
 133            although it should usually be just the standard translation.
 134
 135  Example :
 136  Returns : A Bio::PrimarySeqI implementing object holding the protein
 137            translation as predicted by a program.
 138  Args    : On set, a Bio::PrimarySeqI implementing object holding the protein
 139            translation as predicted by a program.
 140
 141 =cut
 142
 143 sub predicted_protein {
 144     my ($self, $aa) = @_;
 145
 146     if(defined($aa)) {
 147         $self->{'_predicted_aa'} = $aa;
 148     }
 149     return $self->{'_predicted_aa'};
 150 }
 151
 152 =head2 significance
 153
 154  Title   : significance
 155  Usage   : $evalue = $obj->significance();
 156            $obj->significance($evalue);
 157  Function:
 158  Returns :
 159  Args    :
 160
 161
 162 =cut
 163
 164 sub significance {
 165     return shift->_tag_value('signif', @_);
 166 }
 167
 168 =head2 start_signal_score
 169
 170  Title   : start_signal_score
 171  Usage   : $sc = $obj->start_signal_score();
 172            $obj->start_signal_score($evalue);
 173  Function: Get/Set a score for the exon start signal (acceptor splice site
 174            or initiation signal).
 175  Returns :
 176  Args    :
 177
 178
 179 =cut
 180
 181 sub start_signal_score {
 182     return shift->_tag_value('AccScore', @_);
 183 }
 184
 185 =head2 end_signal_score
 186
 187  Title   : end_signal_score
 188  Usage   : $sc = $obj->end_signal_score();
 189            $obj->end_signal_score($evalue);
 190  Function: Get/Set a score for the exon end signal (donor splice site
 191            or termination signal).
 192  Returns :
 193  Args    :
 194
 195
 196 =cut
 197
 198 sub end_signal_score {
 199     return shift->_tag_value('DonScore', @_);
 200 }
 201
 202 =head2 coding_signal_score
 203
 204  Title   : coding_signal_score
 205  Usage   : $sc = $obj->coding_signal_score();
 206            $obj->coding_signal_score($evalue);
 207  Function: Get/Set a score for the exon coding signal (e.g., coding potential).
 208  Returns :
 209  Args    :
 210
 211
 212 =cut
 213
 214 sub coding_signal_score {
 215     return shift->_tag_value('CodScore', @_);
 216 }
 217
 218 #
 219 # Everything else is just inherited from SeqFeature::Generic.
 220 #
 221
 222 1;