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.\" ========================================================================
.\"
.IX Title "Bio::PrimerDesigner::primer3 3pm"
.TH Bio::PrimerDesigner::primer3 3pm "2020-11-16" "perl v5.32.0" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
Bio::PrimerDesigner::primer3 \- An class for accessing primer3
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&  use Bio::PrimerDesigner::primer3;
.Ve
.SH "METHODS"
.IX Header "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.
.SS "binary_name"
.IX Subsection "binary_name"
Defines the binary's name on the system.
.SS "check_params"
.IX Subsection "check_params"
Make sure we have required primer3 arguments.
.SS "design"
.IX Subsection "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.
.SS "request"
.IX Subsection "request"
Figures out where the primer3 binary resides and accesses it with a
list of parameters for designing primers.
.SS "check_results"
.IX Subsection "check_results"
Verify the validity of the design results.
.SS "list_aliases"
.IX Subsection "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.
.SS "list_params"
.IX Subsection "list_params"
Returns a list of primer3 configuration options.  primer3 will use
reasonable default options for most parameters.
.SS "example"
.IX Subsection "example"
Runs a sample remote primer design job.  Returns an
Bio::PrimerDesigner::Result object.
.SS "_example_dna"
.IX Subsection "_example_dna"
Returns an example \s-1DNA\s0 sequence.
.SH "AUTHOR"
.IX Header "AUTHOR"
Copyright (C) 2003\-2009 Sheldon McKay <mckays@cshl.edu>,
Ken Youens-Clark <kclark@cpan.org>.
.SH "LICENSE"
.IX Header "LICENSE"
This program is free software; you can redistribute it and/or modify
it under the terms of the \s-1GNU\s0 General Public License as published by
the Free Software Foundation; version 3 or any later version.
.PP
This program is distributed in the hope that it will be useful, but
\&\s-1WITHOUT ANY WARRANTY\s0; without even the implied warranty of
\&\s-1MERCHANTABILITY\s0 or \s-1FITNESS FOR A PARTICULAR PURPOSE.\s0  See the \s-1GNU\s0
General Public License for more details.
.PP
You should have received a copy of the \s-1GNU\s0 General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, \s-1MA 02110\-1301
USA.\s0
.SH "SEE ALSO"
.IX Header "SEE ALSO"
Bio::PrimerDesigner::epcr.