The London Perl and Raku Workshop takes place on 26th Oct 2024. If your company depends on Perl, please consider sponsoring and/or attending.
 / 
Bio-Tools-Primer3Redux-0.01
River stage zero No dependents
1 ++
/ Bio::Tools::Run::Primer3Redux

NAME

Bio::Tools::Run::Primer3Redux

SYNOPSIS

  # design some primers.
  # the output will be put into temp.out
  use Bio::Tools::Run::Primer3Redux;
  use Bio::SeqIO;

  my $seqio = Bio::SeqIO->new(-file=>'data/dna1.fa');
  my $seq = $seqio->next_seq;

  my $primer3 = Bio::Tools::Run::Primer3Redux->new(-outfile => "temp.out",
                                            -path => "/usr/bin/primer3_core");

  # or after the fact you can change the program_name
  $primer3->program_name('my_superfast_primer3');

  unless ($primer3->executable) {
    print STDERR "primer3 can not be found. Is it installed?\n";
    exit(-1)
  }

  # 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::Primer3::result object with the results
  $results = $primer3->run($seq);

  # see the Bio::Tools::Primer3Redux POD for
  # things that you can get from this. For example:

  print "There were ", $results->num_primer_pairs, " primer pairs\n";

DESCRIPTION

Bio::Tools::Run::Primer3Redux creates the input files needed to design primers using primer3 and provides mechanisms to access data in the primer3 output files.

This module a refactoring of the original BioPerl primer3 tools, themselves a refactoring of the original Primer3 module written by Rob Edwards. See http://primer3.sourceforge.net for details and to download the software. This module should work for primer3 release 1 and above but is not guaranteed to work with earlier versions.

NAME

Bio::Tools::Run::Primer3Redux - Create input for and work with the output from the program primer3

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://bugzilla.open-bio.org/

AUTHOR

Chris Fields cjfields-at-bioperl-dot-org

Refactored from the original Primer3 parser by Rob Edwards, which in turn was based heavily on work of Chad Matsalla.

bioinformatics1@dieselwurks.com

CONTRIBUTORS

Rob Edwards redwards@utmem.edu Chad Matsalla bioinformatics1@dieselwurks.com Shawn Hoon shawnh-at-stanford.edu Jason Stajich jason-at-bioperl.org Brian Osborne osborne1-at-optonline.net Chris Fields cjfields-at-bioperl-dot-org

SEE ALSO

Bio::Tools::Primer3

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    : -outfile : file name send output results to
           -path    : path to primer3 executable
           -p3_settings_file :(optional) path to the settings file. Supported only by primer3 version 2 or above.
           -verbose :(optional) boolean value to set verbose output.

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    :

version

 Title   : version
 Usage   : $v = $prog->version();
 Function: Determine the version number of the program
 Example :
 Returns : float or undef
 Args    : none

set_parameters()

 Title   : set_parameters()
 Usage   : $primer3->set_parameters(key=>value)
 Function: Sets parameters for the input file
 Returns : Returns the number of arguments added
 Args    : See the primer3 docs.
 Notes   : To set individual parameters use the associated method:
           $primer3->PRIMER_MAX_TM(40)

get_parameters

 Title    : get_parameters
 Usage    : $obj->get_parameters
 Function :
 Returns  :
 Args     :

reset_parameters()

 Title   : reset_parameters()
 Usage   : $primer3->reset_parameters()
 Function: Resets all parameters to be undef
 Returns : none
 Args    : none; to reset specific targets call the specific method for that
           target (i.e. $primer3->PRIMER_MAX_TM(undef))

p3_settings_file()

 Title  : p3settingsfile()
 Usage  : $primer3->p3settingsfile($file_path);
 Function   : Getter/Setter for the Primer3 settings file.
 Returns    : A string containing the path of the named settings file.
 Args   : $file_path A valid file path to the settings file.
 Note   : This argument only works in primer3 version 2 or above.

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.
           See the Bio::Tools::Primer3 documentation for those functions.
 Args    : Same as for add_targets() (these are just delegated to that
           method prior creating the input file on the fly)
 Note    :

AUTHOR

cjfields <cjfields@bioperl.org>

COPYRIGHT AND LICENSE

This software is copyright (c) 2011 by Chris Fields.

This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself.