oracular (3) Bio::PrimerDesigner::primer3.3pm.gz

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) 2003-2009 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.