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

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.