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Bio::Tools::Primer3(3)User Contributed Perl DocumentatioBio::Tools::Primer3(3)

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://github.com/bioperl/bioperl-live/issues

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

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

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - | CONTRIBUTORS | APPENDIX

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