NAME
Bio::PrimerDesigner::primer3 - An class for accessing primer3
SYNOPSIS
use Bio::PrimerDesigner::primer3;METHODS
Methods are called using the simplifed alias for each primer3 result or the raw primer3 BoulderIO key. Use the raw_output method to view the raw output.
binary_name
Defines the binary's name on the system.
check_params
Make sure we have required primer3 arguments.
design
Build the primer3 config file, run primer3, then parse the results. Expects to be passed a hash of primer3 input options. Returns an object that can be used to call result methods.
request
Figures out where the primer3 binary resides and accesses it with a list of parameters for designing primers.
check_results
Verify the validity of the design results.
list_aliases
Prints a list of shorthand aliases for the primer3 BoulderIO input format. The full input/ouput options and the aliases can be used interchangeably.
list_params
Returns a list of primer3 configuration options. primer3 will use reasonable default options for most parameters.
example
Runs a sample remote primer design job. Returns an Bio::PrimerDesigner::Result object.
_example_dna
Returns an example DNA sequence.
AUTHOR
Copyright (C) 2003-2008 Sheldon McKay <mckays@cshl.edu>, Ken Youens-Clark <kclark@cpan.org>.
LICENSE
This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; version 3 or any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
SEE ALSO
Bio::PrimerDesigner::epcr.