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1 # $Id: UTR.pm,v 1.6 2002/10/22 07:45:20 lapp Exp $
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2 #
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3 # BioPerl module for Bio::SeqFeature::Gene::UTR
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4 #
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5 # Cared for by David Block <dblock@gene.pbi.nrc.ca>
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6 #
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7 # Copyright David Block
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8 #
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9 # You may distribute this module under the same terms as perl itself
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10
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11 # POD documentation - main docs before the code
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12
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13 =head1 NAME
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14
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15 Bio::SeqFeature::Gene::UTR - A feature representing an untranslated region
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16 that is part of a transcription unit
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17
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18 =head1 SYNOPSIS
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19
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20 See documentation of methods
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21
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22 =head1 DESCRIPTION
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23
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24 A UTR is a Bio::SeqFeature::Gene::ExonI compliant object that is
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25 non-coding, and can be either 5' or 3' in a transcript.
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26
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27 =head1 FEEDBACK
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28
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29 =head2 Mailing Lists
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30
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31 User feedback is an integral part of the evolution of this and other
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32 Bioperl modules. Send your comments and suggestions preferably to
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33 the Bioperl mailing list. Your participation is much appreciated.
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34
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35 bioperl-l@bioperl.org - General discussion
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36 http://bioperl.org/MailList.shtml - About the mailing lists
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37
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38 =head2 Reporting Bugs
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39
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40 Report bugs to the Bioperl bug tracking system to help us keep track
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41 of the bugs and their resolution. Bug reports can be submitted via
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42 email or the web:
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43
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44 bioperl-bugs@bioperl.org
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45 http://bugzilla.bioperl.org/
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46
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47 =head1 AUTHOR - David Block
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48
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49 Email dblock@gene.pbi.nrc.ca
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50
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51 =head1 CONTRIBUTORS
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52
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53 This is based on the Gene Structure scaffolding erected by Hilmar Lapp
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54 (hlapp@gmx.net).
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55
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56 =head1 APPENDIX
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57
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58 The rest of the documentation details each of the object methods.
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59 Internal methods are usually preceded with a _
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60
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61 =cut
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62
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63
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64 # Let the code begin...
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65
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66
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67 package Bio::SeqFeature::Gene::UTR;
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68 use vars qw(@ISA);
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69 use strict;
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70
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71 # Object preamble - inherits from Bio::Root::Root
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72
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73 use Bio::SeqFeature::Gene::NC_Feature;
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74
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75 @ISA = qw(Bio::SeqFeature::Gene::NC_Feature);
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76
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77 sub new {
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78 my($class,@args) = @_;
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79
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80 my $self = $class->SUPER::new(@args);
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81 return $self;
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82 }
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83
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84 =head2 primary_tag
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85
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86 Title : primary_tag
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87 Usage : $tag = $feat->primary_tag()
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88 Function: Returns the primary tag for a feature,
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89 eg 'utr5prime'. This method insures that 5prime/3prime information
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90 is uniformly stored
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91 Returns : a string
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92 Args : none
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93
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94 =cut
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95
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96 sub primary_tag{
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97 my ($self,$val) = @_;
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98 if( defined $val ) {
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99 if ($val =~ /(3|5)/ ) { $val = "utr$1prime" }
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100 else { $self->warn("tag should contain indication if this is 3 or 5 prime. Preferred text is 'utr3prime' or 'utr5prime'. Using user text of '$val'");}
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101 }
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102 $self->SUPER::primary_tag($val);
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103
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104 }
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105
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106 1;
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