Sheldon McKay > Bio-PrimerDesigner-0.07 > Bio::PrimerDesigner::primer3

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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.

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