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   : 

cpanm Bio::Seq

perl -MCPAN -e shell
install Bio::Seq