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Bio-Tools-Primer3Redux-0.02
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/ Bio::Tools::Primer3Redux

NAME

Bio::Tools::Primer3Redux

SYNOPSIS

# parse primer3 output to get some data
# this is also called from Bio::Tools::Run::Primer3Redux
use Bio::Tools::Primer3Redux;

# read a primer3 output file
my $p3 = Bio::Tools::Primer3Redux->new(-file=>"data/primer3_output.txt");

# iterate through each result in the file
while (my $result = $p3->next_result) {
   # iterate through each primer pair
   while (my $pair = $p3->next_primer_pair) {
       # do stuff with primer pairs...
   }
}

DESCRIPTION

Bio::Tools::Primer3Redux 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 a reimplementation of the original Bio::Tools::Primer3 module by Rob Edwards, itself largely based on one written by Chad Matsalla (bioinformatics1@dieselwurks.com). Due to significant API changes between this and the previous Primer3 module, this has been redubbed Bio::Tools::Primer3Redux.

NAME

Bio::Tools::Primer3Redux - BioPerl-based tools for Primer3 (redone)

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:

http://bugzilla.open-bio.org/

AUTHOR -

Chris Fields

CONTRIBUTORS

Rob Edwards

redwards@utmem.edu

Brian Osborne bosborne at alum.mit.edu

Based heavily on work of Chad Matsalla

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 : 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   :
Status  : stable

next_result

Title    : next_result
Usage    : $obj->next_result
Function : Returns the next Bio::Tools::Primer3Redux::Result instance (if one)
Returns  : Bio::Tools::Primer3Redux::Result || undef
Args     : none
Status   : stable

start_document

Title    : start_document
Usage    : $obj->start_document
Function : initialize Primer3 output parsing
Returns  : none
Args     : none

end_document

Title    : end_document
Usage    : $obj->end_document
Function : clean up after parsing of Primer3 document is complete
Returns  : L<Bio::Tools::Primer3Redux::Result>
Args     : none

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.