lib/Bio/SeqFeature/Amplicon.pm

   1 #
   2 # BioPerl module for Bio::SeqFeature::Amplicon
   3 #
   4 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   5 #
   6 # Copyright Florent Angly
   7 #
   8 # You may distribute this module under the same terms as perl itself
   9
  10
  11 =head1 NAME
  12
  13 Bio::SeqFeature::Amplicon - Amplicon feature
  14
  15 =head1 SYNOPSIS
  16
  17   # Amplicon with explicit sequence
  18   use Bio::SeqFeature::Amplicon;
  19   my $amplicon = Bio::SeqFeature::Amplicon->new(
  20       -seq        => $seq_object,
  21       -fwd_primer => $primer_object_1,
  22       -rev_primer => $primer_object_2,
  23   );
  24
  25   # Amplicon with implicit sequence
  26   use Bio::Seq;
  27   my $template = Bio::Seq->new( -seq => 'AAAAACCCCCGGGGGTTTTT' );
  28   $amplicon = Bio::SeqFeature::Amplicon->new(
  29       -start => 6,
  30       -end   => 15,
  31   );
  32   $template->add_SeqFeature($amplicon);
  33   print "Amplicon start   : ".$amplicon->start."\n";
  34   print "Amplicon end     : ".$amplicon->end."\n";
  35   print "Amplicon sequence: ".$amplicon->seq->seq."\n";
  36   # Amplicon sequence should be 'CCCCCGGGGG'
  37
  38 =head1 DESCRIPTION
  39
  40 Bio::SeqFeature::Amplicon extends L<Bio::SeqFeature::Subseq> to represent an
  41 amplicon sequence and optional primer sequences.
  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 one
  49 of the Bioperl mailing lists.  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 I<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 the bugs and their resolution.  Bug reports can be submitted via
  69 the web:
  70
  71   https://github.com/bioperl/bioperl-live/issues
  72
  73 =head1 AUTHOR
  74
  75 Florent Angly <florent.angly@gmail.com>
  76
  77 =head1 APPENDIX
  78
  79 The rest of the documentation details each of the object
  80 methods. Internal methods are usually preceded with a _
  81
  82 =cut
  83
  84
  85 package Bio::SeqFeature::Amplicon;
  86
  87 use strict;
  88
  89 use base qw(Bio::SeqFeature::SubSeq);
  90
  91 =head2 new
  92
  93  Title   : new()
  94  Usage   : my $amplicon = Bio::SeqFeature::Amplicon( -seq => $seq_object );
  95  Function: Instantiate a new Bio::SeqFeature::Amplicon object
  96  Args    : -seq        , the sequence object or sequence string of the amplicon (optional)
  97            -fwd_primer , a Bio::SeqFeature primer object with specified location on amplicon (optional)
  98            -rev_primer , a Bio::SeqFeature primer object with specified location on amplicon (optional)
  99  Returns : A Bio::SeqFeature::Amplicon object
 100
 101 =cut
 102
 103 sub new {
 104     my ($class, @args) = @_;
 105     my $self = $class->SUPER::new(@args);
 106     my ($fwd_primer, $rev_primer) =
 107         $self->_rearrange([qw(FWD_PRIMER REV_PRIMER)], @args);
 108     $fwd_primer && $self->fwd_primer($fwd_primer);
 109     $rev_primer && $self->rev_primer($rev_primer);
 110     return $self;
 111 }
 112
 113
 114 sub _primer {
 115     # Get or set a primer. Type is either 'fwd' or 'rev'.
 116     my ($self, $type, $primer) = @_;
 117     if (defined $primer) {
 118         if ( not(ref $primer) || not $primer->isa('Bio::SeqFeature::Primer') ) {
 119             $self->throw("Expected a primer object but got a '".ref($primer)."'\n");
 120         }
 121         if ( not defined $self->location ) {
 122             $self->throw("Location of $type primer on amplicon is not known. ".
 123                 "Use start(), end() or location() to set it.");
 124         }
 125         $primer->primary_tag($type.'_primer');
 126         $self->add_SeqFeature($primer);
 127     }
 128     return (grep { $_->primary_tag eq $type.'_primer' } $self->get_SeqFeatures)[0];
 129 }
 130
 131
 132 =head2 fwd_primer
 133
 134  Title   : fwd_primer
 135  Usage   : my $primer = $feat->fwd_primer();
 136  Function: Get or set the forward primer. When setting it, the primary tag
 137            'fwd_primer' is added to the primer and its start, stop and strand
 138            attributes are set if needed, assuming that the forward primer is
 139            at the beginning of the amplicon and the reverse primer at the end.
 140  Args    : A Bio::SeqFeature::Primer object (optional)
 141  Returns : A Bio::SeqFeature::Primer object
 142
 143 =cut
 144
 145 sub fwd_primer {
 146     my ($self, $primer) = @_;
 147     return $self->_primer('fwd', $primer);
 148 }
 149
 150
 151 =head2 rev_primer
 152
 153  Title   : rev_primer
 154  Usage   : my $primer = $feat->rev_primer();
 155  Function: Get or set the reverse primer. When setting it, the primary tag
 156           'rev_primer' is added to the primer.
 157  Args    : A Bio::SeqFeature::Primer object (optional)
 158  Returns : A Bio::SeqFeature::Primer object
 159
 160 =cut
 161
 162 sub rev_primer {
 163     my ($self, $primer) = @_;
 164     return $self->_primer('rev', $primer);
 165 }
 166
 167
 168 1;