/ 
bioperl-1.4
/ Bio::Tools::Primer3

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's 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'll 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://www.bioperl.org/MailList.html             - About the mailing lists

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 email
or the web:

  bioperl-bugs@bio.perl.org
  http://bugzilla.bioperl.org/

AUTHOR -

Rob Edwards

redwards@utmem.edu

Based heavily on work of 

Chad Matsalla

bioinformatics1@dieselwurks.com

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 : Doesn't 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   : Returns the maximum number of primers returned from Primer3.

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   :

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. I should just delete this, but my test scripts will all break.
          This will be removed before it goes really live, and is just a link to next_primer

next_primer()

Title   : next_primer()
Usage   : while (my $primed_seq  = $primer3->next_primer()) {
Function: Retrieve the primer/sequences 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.

_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   : Mainly used by Bio::Tools::Run::Primer3 to set $self->{results} and $self->seqobject

_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   :