Bio::Tools::Primer3(3pm)				User Contributed Perl Documentation				  Bio::Tools::Primer3(3pm)

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
";

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

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

	# 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, "
";

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)
		   to read a primer3 output 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	 : $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	 : $primer3->all_results() to print all results or
		   $primer3->all_results('primer3 result name',
		   'other results') to return a specific result
	 Function: Retrieve the results returned from Primer3.
	 Returns : A reference to a hash
	 Args	 : Optional array of results to retrieve

   primer_results
	 Title	 : primer_results()
	 Usage	 : $primer3->primer_results(2) to print results for the third
		   choice primer (indexed on 0)
	 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 feature, 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 feature, 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

perl v5.14.2							    2012-03-02						  Bio::Tools::Primer3(3pm)