Bio/Tools/Primer/Feature.pm

   1 # $Id$
   2 #
   3 # BioPerl module for Bio::Tools::Primer::Feature
   4 #
   5 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   6 #
   7 # Cared for by Ewan Birney <birney@ebi.ac.uk>
   8 #
   9 # Copyright Ewan Birney
  10 #
  11 # You may distribute this module under the same terms as perl itself
  12
  13 # POD documentation - main docs before the code
  14
  15 =head1 NAME
  16
  17 Bio::Tools::Primer::Feature - position of a single primer
  18
  19 =head1 SYNOPSIS
  20
  21     use Bio::Tools::Primer::Feature;
  22
  23     my $pf = Bio::Tools::Primer::Feature->new( -start => $start, -end => $end, -strand => $strand);
  24     $pf->attach_seq($seq);
  25
  26     # is a SeqFeatureI
  27
  28     print "primer starts at ",$pf->start," with sequence ",$pf->seq->seq(),"\n";
  29
  30     # helper functions
  31
  32     print "GC percentage ",$pf->gc(),"\n";
  33     print "has inversion of size 4 at ",$pf->inversion(4),"\n";
  34
  35
  36
  37 =head1 DESCRIPTION
  38
  39 Primer Features represents one primer in a primer pair. This object is
  40 mainly for designing primers, and probably principly used in the
  41 primer design system
  42
  43 =head1 FEEDBACK
  44
  45 =head2 Mailing Lists
  46
  47 User feedback is an integral part of the evolution of this and other
  48 Bioperl modules. Send your comments and suggestions preferably to
  49 the Bioperl mailing list.  Your participation is much appreciated.
  50
  51   bioperl-l@bioperl.org                  - General discussion
  52   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  53
  54 =head2 Support
  55
  56 Please direct usage questions or support issues to the mailing list:
  57
  58 L<bioperl-l@bioperl.org>
  59
  60 rather than to the module maintainer directly. Many experienced and
  61 reponsive experts will be able look at the problem and quickly
  62 address it. Please include a thorough description of the problem
  63 with code and data examples if at all possible.
  64
  65 =head2 Reporting Bugs
  66
  67 Report bugs to the Bioperl bug tracking system to help us keep track
  68 of the bugs and their resolution. Bug reports can be submitted via the
  69 web:
  70
  71   http://bugzilla.open-bio.org/
  72
  73 =head1 AUTHOR - Ewan Birney
  74
  75 Email birney-at-ebi.ac.uk
  76
  77 =head1 APPENDIX
  78
  79 The rest of the documentation details each of the object methods.
  80 Internal methods are usually preceded with a _
  81
  82 =cut
  83
  84
  85 # Let the code begin...
  86
  87
  88
  89 package Bio::Tools::Primer::Feature;
  90
  91 use base qw(Bio::SeqFeature::Generic);
  92
  93
  94
  95 sub new {
  96     my ( $caller, @args) = @_;
  97     my ($self) = $caller->SUPER::new(@args);
  98
  99     # done - we hope
 100     return $self;
 101 }
 102
 103 sub gc_percent {
 104     my $self = shift;
 105
 106     my $seq = $self->seq();
 107
 108     if( !defined $seq ) {
 109         $self->throw("Primer feature has no attached sequence, can't calculate GC");
 110     }
 111
 112     my $str = $seq->seq();
 113
 114     my $count = $str =~ tr/GCgc/GCgc/;
 115
 116     return $count*100.0 / $seq->length;
 117 }
 118
 119 sub inversion {
 120     my $self = shift;
 121     my $size = shift;
 122
 123     if( !defined $size ) {
 124         $self->throw("Must have size paramter in inversion");
 125     }
 126
 127     my $seq = $self->seq();
 128
 129     if( !defined $seq ) {
 130         $self->throw("Primer feature has no attached sequence, can't calculate inversion");
 131     }
 132
 133     my $len = $seq->length - $size;
 134
 135     my $str = $seq->seq();
 136
 137     foreach my $i ( 0 .. $len ) {
 138         my $revstr = substr($str,$i,$size);
 139         my $orig = $revstr;
 140         $revstr = reverse $revstr;
 141         $revstr = s/[^ATGCNatgcn]/N/g;
 142
 143         $revstr =~ tr/ATGCNatgcn/TACGNtacgn/;
 144
 145         if( $str =~ /$revstr/ ) {
 146             return $orig;
 147         }
 148     }
 149
 150     return;
 151 }
 152
 153 1;