NAME

       Bio::Tools::Primer3 - Create input for and work with the output from the program primer3

SYNOPSIS

        # parse primer3 output to get some data
        # this is also called from Bio::Tools::Run::Primer3
        use Bio::Tools::Primer3;

        # read a primer3 output file
        my $p3 = Bio::Tools::Primer3->new(-file=>"data/primer3_output.txt");

        # how many results were there?
        my $num = $p3->number_of_results;
        print "There were $num results\n";

        # get all the results
        my $all_results = $p3->all_results;
        print "ALL the results\n";
        foreach my $key (keys %{$all_results}) {
           print "$key\t${$all_results}{$key}\n";
        }

        # get specific results
        my $result1 = $p3->primer_results(1);
        print "The first primer is\n";
        foreach my $key (keys %{$result1}) {
           print "$key\t${$result1}{$key}\n";
        }

        # get the results as a Bio::Seq::PrimedSeq stream
        my $primer = $p3->next_primer;
        print "The left primer in the stream is ",
          $primer->get_primer('-left_primer')->seq->seq, "\n";

DESCRIPTION

       Bio::Tools::Primer3 creates the input files needed to design primers using primer3 and
       provides mechanisms to access data in the primer3 output files.

       This module provides a bioperl interface to the program primer3. See
       http://www-genome.wi.mit.edu/genome_software/other/primer3.html for details and to
       download the software.

       This module is based on one written by Chad Matsalla (bioinformatics1@dieselwurks.com)

       I have ripped some of his code, and added a lot of my own. I hope he is not mad at me!

       This is probably best run in one of the two following ways:

         i. To parse the output from Bio::Tools::Run::Primer3.
            You will most likely just use next_primer to get the results from
            Bio::Tools::Run::Primer3.
         ii. To parse the output of primer3 handed to it as a file name.

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send
       your comments and suggestions preferably to one of the Bioperl mailing lists.  Your
       participation is much appreciated.

         bioperl-l@bioperl.org                  - General discussion
         http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will
       be able look at the problem and quickly address it. Please include a thorough description
       of the problem with code and data examples if at all possible.

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

         https://redmine.open-bio.org/projects/bioperl/

AUTHOR -

         Rob Edwards

         redwards@utmem.edu

         Based heavily on work of

         Chad Matsalla

         bioinformatics1@dieselwurks.com

CONTRIBUTORS

         Brian Osborne bosborne at alum.mit.edu

APPENDIX

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

   new
         Title   : new()
         Usage   : my $primer3 = Bio::Tools::Primer3->new(-file=>$file);
         Function: Parse primer3 output
         Returns : Does not return anything. If called with a filename will
                   allow you to retrieve the results
         Args    : -file (optional) file of primer3 results to parse -verbose
                   (optional) set verbose output
         Notes   :

   number_of_results
         Title   : number_of_results()
         Usage   : my $count = $primer3->number_of_results();
         Function: Retrieve the number of primers returned from Primer3.
         Returns : A scalar
         Args    : None
         Notes   : This returns the count of the primers returned by Primer3
                    (aka how many of them there are).
                    This is one more than the maximum offset into the zero
                    based list of primers that is accessed by primer_results().

   all_results
         Title   : all_results()
         Usage   : my $results = $primer3->all_results();
                      or
                   my $results = $primer3->all_results('primer3 result name', 'other results');
         Function: Retrieve the results returned from Primer3.
         Returns : A reference to a hash
         Args    : Optional array of specific results to retrieve

   primer_results
         Title   : primer_results()
         Usage   : my $results = $primer3->primer_results(2); # results for third primer
         Function: Retrieve the results returned from Primer3 for specific primer pairs.
         Returns : A reference to a hash
         Args    : A number between 0 and the maximum number of primers to retrieve

   _readfile
         Title   : _readfile()
         Usage   : $self->_readfile();
         Function: An internal function that reads a file and sets up the results
         Returns : Nothing.
         Args    : None
         Notes   :

   next_primer
         Title   : next_primer()
         Usage   : while (my $primed_seq  = $primer3->next_primer()) {
         Function: Retrieve the primed sequence and a primer pair, one at a time
         Returns : Returns a Bio::Seq::PrimedSeq object, one at a time
         Args    : None
         Notes   : Use $primed_seq->annotated_seq to get an annotated sequence
                   object you can write out.

   primer_stream
         Title   : primer_stream()
         Usage   : while (my $primed_seq  = $primer3->primer_stream()) {
         Function: Retrieve the primer/sequences one at a time
         Returns : Returns a Bio::Seq::PrimedSeq object, one at a time
         Args    : None
         Notes   : Deprecated, just a link to next_primer

   _separate
         Title   : _separate()
         Usage   : $self->_separate();
         Function: An internal function that groups the results by number
                   (e.g. primer pair 1, etc)
         Returns : Nothing.
         Args    : None
         Notes   :

   _set_variable
         Title   : _set_variable()
         Usage   : $self->_set_variable('variable name', 'value');
         Function: An internal function that sets a variable
         Returns : Nothing.
         Args    : None
         Notes   : Used to set $self->{results} and $self->seqobject