Bio/Tools/Prediction/Exon.pm

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