Bio/SeqFeature/Gene/UTR.pm

   1 #
   2 # BioPerl module for Bio::SeqFeature::Gene::UTR
   3 #
   4 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   5 #
   6 # Cared for by David Block <dblock@gene.pbi.nrc.ca>
   7 #
   8 # Copyright David Block
   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::SeqFeature::Gene::UTR - A feature representing an untranslated region
  17           that is part of a transcriptional unit
  18
  19 =head1 SYNOPSIS
  20
  21 See documentation of methods
  22
  23 =head1 DESCRIPTION
  24
  25 A UTR is a Bio::SeqFeature::Gene::ExonI compliant object that is
  26 non-coding, and can be either 5' or 3' in a transcript.
  27
  28 =head1 FEEDBACK
  29
  30 =head2 Mailing Lists
  31
  32 User feedback is an integral part of the evolution of this and other
  33 Bioperl modules. Send your comments and suggestions preferably to
  34 the Bioperl mailing list.  Your participation is much appreciated.
  35
  36   bioperl-l@bioperl.org                  - General discussion
  37   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  38
  39 =head2 Support
  40
  41 Please direct usage questions or support issues to the mailing list:
  42
  43 I<bioperl-l@bioperl.org>
  44
  45 rather than to the module maintainer directly. Many experienced and
  46 reponsive experts will be able look at the problem and quickly
  47 address it. Please include a thorough description of the problem
  48 with code and data examples if at all possible.
  49
  50 =head2 Reporting Bugs
  51
  52 Report bugs to the Bioperl bug tracking system to help us keep track
  53 of the bugs and their resolution. Bug reports can be submitted via the
  54 web:
  55
  56   https://github.com/bioperl/bioperl-live/issues
  57
  58 =head1 AUTHOR - David Block
  59
  60 Email dblock@gene.pbi.nrc.ca
  61
  62 =head1 CONTRIBUTORS
  63
  64 This is based on the Gene Structure scaffolding erected by Hilmar Lapp
  65 (hlapp@gmx.net).
  66
  67 =head1 APPENDIX
  68
  69 The rest of the documentation details each of the object methods.
  70 Internal methods are usually preceded with a _
  71
  72 =cut
  73
  74
  75 # Let the code begin...
  76
  77
  78 package Bio::SeqFeature::Gene::UTR;
  79 use strict;
  80
  81 # Object preamble - inherits from Bio::Root::Root
  82
  83
  84 use base qw(Bio::SeqFeature::Gene::Exon);
  85
  86 =head2 new
  87
  88  Title   : new
  89  Usage   :
  90  Function: We override the constructor here to set is_coding to false
  91            unless explicitly overridden.
  92
  93  Example :
  94  Returns :
  95  Args    :
  96
  97
  98 =cut
  99
 100 sub new{
 101     my ($caller, @args) = @_;
 102
 103     if(! grep { lc($_) eq '-is_coding'; } @args) {
 104         push(@args, '-is_coding', 0);
 105     }
 106     my $self = $caller->SUPER::new(@args);
 107
 108     my ($primary, $prim) =
 109         $self->_rearrange([qw(PRIMARY PRIMARY_TAG)],@args);
 110
 111     $self->primary_tag('utr') unless $primary || $prim;
 112
 113     return $self;
 114 }
 115
 116 =head2 primary_tag
 117
 118  Title   : primary_tag
 119  Usage   : $tag = $feat->primary_tag()
 120  Function: Returns the primary tag for a feature,
 121            eg 'utr5prime'.  This method insures that 5prime/3prime information
 122            is uniformly stored
 123  Returns : a string
 124  Args    : none
 125
 126 =cut
 127
 128 sub primary_tag{
 129     my $self = shift;
 130     if(@_ && defined($_[0])) {
 131         my $val = shift;
 132         if ($val =~ /(3|5)/ ) {
 133             $val = "utr$1prime";
 134         } else {
 135             $self->warn("Primary tag should indicate if this is 3 or 5'. ".
 136                         "Preferred text is 'utr3prime' or 'utr5prime'.");
 137         }
 138         unshift(@_,$val);
 139     }
 140     return $self->SUPER::primary_tag(@_);
 141 }
 142
 143 1;