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Bio::Tools::Run::PrimeUser)Contributed Perl DocumenBio::Tools::Run::Primer3(3)

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

SYNOPSIS
       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://frodo.wi.mit.edu/primer3/primer3_code.html for details and to
       download	the software. This module only works for primer3 release 1 but
       is not guaranteed to work with earlier versions.

	 # design some primers.
	 # the output will be put into temp.out
	 use Bio::Tools::Run::Primer3;
	 use Bio::SeqIO;

	 my $seqio = Bio::SeqIO->new(-file=>'data/dna1.fa');
	 my $seq = $seqio->next_seq;
	 my $primer3 = Bio::Tools::Run::Primer3->new(-seq => $seq,
						     -outfile => "temp.out",
						     -path => "/usr/bin/primer3_core");

	 # or after the	fact you can change the	program_name
	 $primer3->program_name('my_suprefast_primer3');

	 unless	($primer3->executable) {
	   print STDERR	"primer3 can not be found. Is it installed?\n";
	   exit(-1)
	 }

	 # what	are the	arguments, and what do they mean?
	 my $args = $primer3->arguments;

	 print "ARGUMENT\tMEANING\n";
	 foreach my $key (keys %{$args}) {print	"$key\t", $$args{$key},	"\n"}

	 # set the maximum and minimum Tm of the primer
	 $primer3->add_targets('PRIMER_MIN_TM'=>56, 'PRIMER_MAX_TM'=>90);

	 # design the primers. This runs primer3 and returns a
	 # Bio::Tools::Run::Primer3 object with	the results
	 $results = $primer3->run;

	 # see the Bio::Tools::Run::Primer3 pod	for
	 # things that you can get from	this. For example:

	 print "There were ", $results->number_of_results, " primers\n";

       Bio::Tools::Run::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!

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://www.bioperl.org/MailList.html		  - 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:

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

AUTHOR
       Rob Edwards

       redwards@utmem.edu

       Based heavily on	work of	Chad Matsalla

       bioinformatics1@dieselwurks.com

CONTRIBUTORS
       Shawn Hoon shawnh-at-stanford.edu Jason Stajich jason-at-bioperl.org
       Brian Osborne osborne1-at-optonline.net

SEE ALSO
       Bio::Tools::Primer3

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

   new()
	Title	: new()
	Usage	: my $primer3 =	Bio::Tools::Run::Primer3->new(-file=>$file) to read
		  a primer3 output file.
		  my $primer3 =	Bio::Tools::Run::Primer3->new(-seq=>sequence object)
		  design primers against sequence
	Function: Start	primer3	working	and adds a sequence. At	the moment it
		  will not clear out the old sequence, but I suppose it	should.
	Returns	: Does not return anything. If called with a filename will allow
		  you to retrieve the results
	Args	: -seq (optional) Bio::Seq object of sequence. This is required
		  to run primer3 but can be added later	with add_targets()
		       -outfile	file name to output results to (can also be added
		  with $primer3->outfile_name
		       -path path to primer3 executable, including program name, e.g.
		  "/usr/bin/primer3_core". This	can also be set	with program_name
		  and program_dir
		       -verbose	(optional) set verbose output
	Notes	:

   program_name
	Title	: program_name
	Usage	: $primer3->program_name()
	Function: holds	the program name
	Returns:  string
	Args	: None

   program_dir
	Title	: program_dir
	Usage	: $primer3->program_dir($dir)
	Function: returns the program directory, which may also	be obtained from ENV variable.
	Returns	:  string
	Args	:

   add_targets()
	Title	: add_targets()
	Usage	: $primer3->add_targets(key=>value)
	Function: Add any legal	value to the input command line.
	Returns	: Returns the number of	arguments added.
	Args	: Use $primer3->arguments to find a list of all	the values
		  that are allowed, or see the primer3 docs.
	Notes	: This will only do limited error checking at the moment,
		  but it should	work.

   run()
	Title	: run()
	Usage	: $primer3->run();
	Function: Run the primer3 program with the arguments that you have supplied.
	Returns	: A Bio::Tools::Primer3	object containing the results.
	Args	: None.
	Note	: See the Bio::Tools::Primer3 documentation for	those functions.

   arguments()
	Title	: arguments()
	Usage	: $hashref = $primer3->arguments();
	Function: Describes the	options	that you can set through Bio::Tools::Run::Primer3,
		  with a brief (one line) description of what they are and their
		  default values
	Returns	: A string (if an argument is supplied)	or a reference to a hash.
	Args	: If supplied with an argument will return a string of its
		  description.
		  If no	arguments are supplied,	will return all	the arguments as a
		  reference to a hash
	Notes	: Much of this is taken	from the primer3 README	file, and you should
		  read that file for a more detailed description.

   version
	Title	: version
	Usage	: $v = $prog->version();
	Function: Determine the	version	number of the program
	Example	:
	Returns	: float	or undef
	Args	: none

   _input_args()
	Title	: _input_args()
	Usage	: an internal method to	set the	input arguments	for Primer3
	Function: Define a hash	with keys for each of the input	arguments and values
		  as a short one line description
	Returns	: A reference to a hash.
	Args	: None.
	Notes	: Much of this is taken	from the primer3 README	file, and you should
		  read that file for a more detailed description.

perl v5.24.1			  2017-07-08	   Bio::Tools::Run::Primer3(3)

NAME | SYNOPSIS | FEEDBACK | AUTHOR | CONTRIBUTORS | SEE ALSO | APPENDIX

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