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