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lib/Bio/Tools/Primer3Redux/Primer.pm  view on Meta::CPAN

# POD documentation - main docs before the code


# Let the code begin...

package Bio::Tools::Primer3Redux::Primer;
BEGIN {
  $Bio::Tools::Primer3Redux::Primer::AUTHORITY = 'cpan:CJFIELDS';
}
BEGIN {
  $Bio::Tools::Primer3Redux::Primer::VERSION = '0.09';
}

use strict;

# Object preamble - inherits from Bio::Root::Root

use base qw(Bio::SeqFeature::Generic);


sub oligo_type {
    shift->primary_tag(@_);
}


sub rank {
    my ($self, $rank) = @_;
    if (defined $rank) {
        $self->remove_tag('rank') if $self->has_tag('rank');
        $self->add_tag_value('rank', $rank);
    }
    $self->has_tag('rank') ? return ($self->get_tag_values('rank'))[0] : return;
}


sub validate_seq {
    my ($self) = shift;
    my $cached = $self->has_tag('sequence') ? ($self->get_tag_values('sequence'))[0] : '';
    my $seq = $self->seq->seq;
    if ($cached ne $seq) {
        $self->warn("Sequence [$seq] does not match predicted [$cached], check attached sequence");
        return 0;
    }
    return 1;
}


sub melting_temp {
    my ($self, $tm) = @_;
    if (defined $tm) {
        $self->remove_tag('tm') if $self->has_tag('tm');
        $self->add_tag_value('tm', $tm);
    }
    $self->has_tag('tm') ? return ($self->get_tag_values('tm'))[0] : return;
}


sub gc_content {
    my ($self, $gc) = @_;
    if (defined $gc) {
        $self->remove_tag('gc_percent') if $self->has_tag('gc_percent');
        $self->add_tag_value('gc_percent', $gc);
    }
    $self->has_tag('gc_percent') ? return ($self->get_tag_values('gc_percent'))[0] : return;
}


sub run_description {
    my ($self, $desc) = @_;
    if (defined $desc) {
        $self->remove_tag('explain') if $self->has_tag('explain');
        $self->add_tag_value('explain', $desc);
    }
    $self->has_tag('explain') ? return ($self->get_tag_values('explain'))[0] : return;
}

1;

__END__
=pod

=encoding utf-8

=head1 NAME

Bio::Tools::Primer3Redux::Primer

=head1 SYNOPSIS

 # get the Bio::Tools::Primer3Redux::Primer through Bio::Tools::Primer3Redux...

 # dies with an error if no sequence is attached, or if sequence region
 # does not match cached sequence from Primer3.  Useful if decorating an already
 # generated Bio::Seq with primers.

 $primer->validate_seq;

 my $seq = $primer->seq; # Bio::Seq object
 if ($primer->melting_temp < 55) {
    warn "Primer ".$primer->display_name." is below optimal temp";
 }

 # if primer3 EXPLAIN settings are used...
 print "Run parameters:".$primer->run_description."\n";

=head1 DESCRIPTION

This class is a simple subclass of Bio::SeqFeature::Generic that adds
convenience accessor methods for primer-specific data, such as Tm, GC content,
and other interesting bits of information returned from Primer3.  Beyond that,
the data can be persisted just as any Bio::SeqFeatureI; it doesn't add any
additional primary attributes that may not be persisted effectively.

=head1 NAME

Bio::Tools::Primer3Redux::Primer - Simple Decorator of a
Bio::SeqFeature::Generic with convenience methods for retrieving Tm, GC,
validating primer seq against attached sequence, etc.

=head1 FEEDBACK

=head2 Mailing Lists

User feedback is an integral part of the evolution of this and other

lib/Bio/Tools/Primer3Redux/Primer.pm  view on Meta::CPAN

Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
the web:

  http://bugzilla.open-bio.org/

=head1 AUTHOR - Chris Fields

  Email cjfields at bioperl dot org

Describe contact details here

=head1 CONTRIBUTORS

Additional contributors names and emails here

=head1 APPENDIX

The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _

=head2 oligo_type

 Title    : oligo_type
 Usage    : $obj->oligo_type
 Function : get/set the oligo type
 Returns  : the oligo type (forward_primer, reverse_primer, internal_oligo)
 Args     : optional string
 Note     : simple alias for primary_tag

=head2 rank

 Title    : rank
 Usage    : $obj->rank
 Function : get/set the rank
 Returns  : rank
 Args     : optional string

=head2 validate_seq

 Title    : validate_seq
 Usage    : $obj->validate_seq
 Function : Checks the calculated primer sequence against the actual sequence
            being analysed.
 Returns  : True (1) if validated, False (0) and a warning otherwise
 Args     : none

=head2 melting_temp

 Title    : melting_temp
 Usage    : $obj->melting_temp
 Function : returns the Tm calculated for the primer via Primer3
 Returns  : float
 Args     : optional Tm (possibly calculated via other means)

=head2 gc_content

 Title    : gc
 Usage    : $obj->gc
 Function : returns the GC content calculated for the primer via Primer3
 Returns  : float (percent)
 Args     : optional GC content (possibly calculated via other means)

=head2 run_description

 Title    : run_description
 Usage    : $obj->run_description
 Function : returns the run description for this primer (via Primer3)
 Returns  : string
 Args     : optional description

=head1 AUTHOR

cjfields <cjfields@bioperl.org>

=head1 COPYRIGHT AND LICENSE

This software is copyright (c) 2011 by Chris Fields.

This is free software; you can redistribute it and/or modify it under
the same terms as the Perl 5 programming language system itself.

=cut