bio::primerdesigner::remote(3pm) [debian man page]

Bio::PrimerDesigner::Remote(3pm)			User Contributed Perl Documentation			  Bio::PrimerDesigner::Remote(3pm)

NAME

       Bio::PrimerDesigner::Remote - A class for remote access to Bio::PrimerDesigner

SYNOPSIS

	 use Bio::PrimerDesigner::Remote;

DESCRIPTION

       Interface to the server-side binaries.  Passes the primer design paramaters to a remote CGI, which uses a server-side installation of
       Bio::PrimerDesigner to process the request.

METHODS

   CGI_request
       Passes arguments to the URL of the remote Bio::PrimerDesigner CGI and returns the raw output for further processing by local design
       classes.

   check
       Tests the URL to make sure the host is live and the CGI returns the expected results.

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, primer_designer.cgi.

perl v5.10.0							    2009-08-04					  Bio::PrimerDesigner::Remote(3pm)

PRIMER_DESIGNER(1p)					User Contributed Perl Documentation				       PRIMER_DESIGNER(1p)

NAME

       primer_designer.pl -- command-line interface Bio::PrimerDesigner

SYNOPSIS

	   ./primer_designer.pl [options] [dna_sequence or file]

	 Options:

	 -p|--program	Program (default "primer3")
	 -n|--number	Number of primer sets to return (default "5")
	 -b|--binary	Path to binary executable (default "/usr/local/bin")
	 -m|--method	"local" or "remote" (default "local")
	 -u|--url	URL of remote primer3/e-PCR system (default
			  "aceserver.biotech.ubc.ca/cgi-bin/primer_designer.cgi")
	 --list-aliases Print alias list to primer3 input options and exit
	 --list-params	Print a list of primer3/e-PCR input options and exit
	 -h|--help	Print help and exit

DESCRIPTION

       This script tests/demonstrates the Bio::PrimerDesigner interface to primer3 and e-PCR.  It can be used with a local installation of the
       unix binaries or remotely via an HTTP/CGI request.

AUTHOR

       Copyright (C) 2003-2009 Sheldon McKay <mckays@cshl.edu>, Ken Youens-Clark <kclark@cpan.org>.

SEE ALSO

       Bio::PrimerDesigner.

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.

perl v5.10.0							    2009-08-04						       PRIMER_DESIGNER(1p)