Bio/Tools/Prediction/Gene.pm

   1 #
   2 # BioPerl module for Bio::Tools::Prediction::Gene
   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::Gene - a predicted gene structure feature
  17
  18 =head1 SYNOPSIS
  19
  20   #See documentation of methods.
  21
  22 =head1 DESCRIPTION
  23
  24 A feature representing a predicted gene structure. This class actually
  25 inherits off Bio::SeqFeature::Gene::Transcript and therefore has all that
  26 functionality, plus a few methods supporting predicted sequence features,
  27 like a predicted CDS and a predicted translation.
  28
  29 Exons held by an instance of this class will usually be instances of
  30 Bio::Tools::Prediction::Exon, although they do not have to be. Refer to the
  31 documentation of the class that produced the instance.
  32
  33 Normally, you will not want to create an instance of this class yourself.
  34 Instead, classes representing the results of gene structure prediction
  35 programs will do that.
  36
  37 =head1 FEEDBACK
  38
  39 =head2 Mailing Lists
  40
  41 User feedback is an integral part of the evolution of this and other
  42 Bioperl modules. Send your comments and suggestions preferably to one
  43 of the Bioperl mailing lists.  Your participation is much appreciated.
  44
  45   bioperl-l@bioperl.org                  - General discussion
  46   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  47
  48 =head2 Support
  49
  50 Please direct usage questions or support issues to the mailing list:
  51
  52 I<bioperl-l@bioperl.org>
  53
  54 rather than to the module maintainer directly. Many experienced and
  55 reponsive experts will be able look at the problem and quickly
  56 address it. Please include a thorough description of the problem
  57 with code and data examples if at all possible.
  58
  59 =head2 Reporting Bugs
  60
  61 Report bugs to the Bioperl bug tracking system to help us keep track
  62 the bugs and their resolution.  Bug reports can be submitted via the
  63 web:
  64
  65   https://github.com/bioperl/bioperl-live/issues
  66
  67 =head1 AUTHOR - Hilmar Lapp
  68
  69 Email hlapp-at-gmx.net or hilmar.lapp-at-pharma.novartis.com
  70
  71 =head1 APPENDIX
  72
  73 The rest of the documentation details each of the object
  74 methods. Internal methods are usually preceded with a _
  75
  76 =cut
  77
  78
  79 # Let the code begin...
  80
  81
  82 package Bio::Tools::Prediction::Gene;
  83 use strict;
  84
  85
  86
  87 use base qw(Bio::SeqFeature::Gene::Transcript);
  88
  89 sub new {
  90     my($class,@args) = @_;
  91
  92     my $self = $class->SUPER::new(@args);
  93
  94     my ($primary,$ptag) = $self->_rearrange([qw(PRIMARY PRIMARY_TAG)],@args);
  95     $self->primary_tag('predicted_gene') unless $primary || $ptag;
  96
  97     return $self;
  98 }
  99
 100
 101 =head2 predicted_cds
 102
 103  Title   : predicted_cds
 104  Usage   : $predicted_cds_dna = $gene->predicted_cds();
 105            $gene->predicted_cds($predicted_cds_dna);
 106  Function: Get/Set the CDS (coding sequence) as predicted by a program.
 107
 108            This method is independent of an attached_seq. There is no
 109            guarantee whatsoever that the returned CDS has anything to do
 110            (e.g., matches) with the sequence covered by the exons as annotated
 111            through this object.
 112
 113  Example :
 114  Returns : A Bio::PrimarySeqI implementing object holding the DNA sequence
 115            defined as coding by a prediction of a program.
 116  Args    : On set, a Bio::PrimarySeqI implementing object holding the DNA
 117            sequence defined as coding by a prediction of a program.
 118
 119 =cut
 120
 121 sub predicted_cds {
 122     my ($self, $cds) = @_;
 123
 124     if(defined($cds)) {
 125         $self->{'_predicted_cds'} = $cds;
 126     }
 127     return $self->{'_predicted_cds'};
 128 }
 129
 130 =head2 predicted_protein
 131
 132  Title   : predicted_protein
 133  Usage   : $predicted_protein_seq = $gene->predicted_protein();
 134            $gene->predicted_protein($predicted_protein_seq);
 135  Function: Get/Set the protein translation as predicted by a program.
 136
 137            This method is independent of an attached_seq. There is no
 138            guarantee whatsoever that the returned translation has anything to
 139            do with the sequence covered by the exons as annotated
 140            through this object, or the sequence returned by predicted_cds(),
 141            although it should usually be just the standard translation.
 142
 143  Example :
 144  Returns : A Bio::PrimarySeqI implementing object holding the protein
 145            translation as predicted by a program.
 146  Args    : On set, a Bio::PrimarySeqI implementing object holding the protein
 147            translation as predicted by a program.
 148
 149 =cut
 150
 151 sub predicted_protein {
 152     my ($self, $aa) = @_;
 153
 154     if(defined($aa)) {
 155         $self->{'_predicted_aa'} = $aa;
 156     }
 157     return $self->{'_predicted_aa'};
 158 }
 159
 160 #
 161 # Everything else is just inherited from SeqFeature::GeneStructure.
 162 #
 163
 164 1;