Bio::Tools::Primer3Redux
# 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... } }
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.
Bio::Tools::Primer3Redux - BioPerl-based tools for Primer3 (redone)
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
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.
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/
Chris Fields
Rob Edwards redwards@utmem.edu Brian Osborne bosborne at alum.mit.edu Based heavily on work of Chad Matsalla
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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
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
Title : start_document Usage : $obj->start_document Function : initialize Primer3 output parsing Returns : none Args : none
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
cjfields <cjfields@bioperl.org>
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.
To install Bio::Tools::Primer3Redux, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Tools::Primer3Redux
CPAN shell
perl -MCPAN -e shell install Bio::Tools::Primer3Redux
For more information on module installation, please visit the detailed CPAN module installation guide.