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 listsSupport
Please direct usage questions or support issues to the mailing list:
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
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 : Noneprogram_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 : noneset_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.