Bio/Tools/Primer/Pair.pm

   1 # BioPerl module for Bio::Tools::Primer::Pair
   2 #
   3 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   4 #
   5 # Cared for by Ewan Birney <birney@ebi.ac.uk>
   6 #
   7 # Copyright Ewan Birney
   8 #
   9 # You may distribute this module under the same terms as perl itself
  10
  11 # POD documentation - main docs before the code
  12
  13 =head1 NAME
  14
  15 Bio::Tools::Primer::Pair - two primers on left and right side
  16
  17 =head1 SYNOPSIS
  18
  19     use Bio::Tools::Primer::Pair;
  20
  21     my $pair = Bio::Tools::Primer::Pair->new( -left => $leftp , -right => $rightp);
  22
  23     # helper functions
  24
  25     print "GC percentage different",$pf->gc_difference(),"\n";
  26     print "product length is ",$pf->product_length,"\n";
  27
  28
  29
  30 =head1 DESCRIPTION
  31
  32 Primer Pairs represents one primer in a primer pair. This object is mainly for
  33 designing primers, and probably principly used in the primer design system
  34
  35 =head1 FEEDBACK
  36
  37 =head2 Mailing Lists
  38
  39 User feedback is an integral part of the evolution of this and other
  40 Bioperl modules. Send your comments and suggestions preferably to
  41 the Bioperl mailing list.  Your participation is much appreciated.
  42
  43   bioperl-l@bioperl.org                  - General discussion
  44   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  45
  46 =head2 Support
  47
  48 Please direct usage questions or support issues to the mailing list:
  49
  50 I<bioperl-l@bioperl.org>
  51
  52 rather than to the module maintainer directly. Many experienced and
  53 reponsive experts will be able look at the problem and quickly
  54 address it. Please include a thorough description of the problem
  55 with code and data examples if at all possible.
  56
  57 =head2 Reporting Bugs
  58
  59 Report bugs to the Bioperl bug tracking system to help us keep track
  60 of the bugs and their resolution. Bug reports can be submitted via the
  61 web:
  62
  63   https://github.com/bioperl/bioperl-live/issues
  64
  65 =head1 AUTHOR - Ewan Birney
  66
  67 Email birney-at-ebi.ac.uk
  68
  69 =head1 APPENDIX
  70
  71 The rest of the documentation details each of the object methods.
  72 Internal methods are usually preceded with a _
  73
  74 =cut
  75
  76
  77 # Let the code begin...
  78
  79
  80
  81 package Bio::Tools::Primer::Pair;
  82
  83 use base qw(Bio::Root::Root);
  84
  85 sub new {
  86     my ( $caller, @args) = @_;
  87     my ($self) = $caller->SUPER::new(@args);
  88
  89     my ($left,$right) = $self->_rearrange([qw(LEFT RIGHT)],@args);
  90
  91     if( !defined $left || !defined $right ) {
  92         $self->throw("Pair must be initialised with left and right primers");
  93     }
  94
  95     $self->left($left);
  96     $self->right($right);
  97
  98     # done - we hope
  99     return $self;
 100 }
 101
 102 sub left {
 103     my $self = shift;
 104     my $left = shift;
 105
 106     if( defined $left ) {
 107         if( !ref $left || !$left->isa("Bio::Tools::Primer::Feature") ) {
 108             $self->throw("left primer must be a Bio::Tools::Primer::Feature, not $left");
 109         }
 110         $self->{'left'} = $left;
 111     }
 112
 113     return $self->{'left'};
 114 }
 115
 116
 117 sub right {
 118     my $self = shift;
 119     my $right = shift;
 120
 121     if( defined $right ) {
 122         if( !ref $right || !$right->isa("Bio::Tools::Primer::Feature") ) {
 123             $self->throw("right primer must be a Bio::Tools::Primer::Feature, not $right");
 124         }
 125         $self->{'right'} = $right;
 126     }
 127
 128     return $self->{'right'};
 129 }
 130
 131 sub gc_difference {
 132     my $self = shift;
 133
 134     return abs ( $self->left->gc_percent - $self->right->gc_percent );
 135 }
 136
 137 sub product_length {
 138     my $self = shift;
 139
 140     return $self->right->end - $self->left->start +1;
 141 }
 142
 143
 144 1;