Bio/Tools/Primer/Feature.pm

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