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|
#!/usr/bin/perl
# $Id: primer_designer.cgi 6 2008-11-06 21:34:01Z kyclark $
use strict;
use warnings;
use CGI ':standard';
use CGI::Carp 'fatalsToBrowser';
use Bio::PrimerDesigner;
use Readonly;
Readonly my %BINARY => (
primer3 => \&primer3,
ePCR => \&ePCR,
);
print header;
check(param('check'));
#
# Get remote config info and re-hashify it.
#
my $input = param('config') or die "No config info provided";
my @config = split '#', $input;
my %config = ();
for (@config) {
my ($key, $value) = split '=', $_;
$config{$key} = $value;
}
#
# Get binary name.
#
my $binary = $config{'program'} or die "No program defined";
my $method = $BINARY{ $binary } or die "Invalid binary '$binary'";
delete $config{'program'};
$method->( %config );
# -------------------------------------------------------------------
sub primer3 {
my %config = @_ or die "no primer3 input";
my $primer3 = Bio::PrimerDesigner->new or die Bio::PrimerDesigner->error;
my $result = $primer3->design( %config )
or die $primer3->error;
print $result->raw_output;
}
# -------------------------------------------------------------------
sub ePCR {
my %config = @_;
my $local_epcr = Bio::PrimerDesigner->new( program => 'epcr')
or die Bio::PrimerDesigner->error;
my $result = $local_epcr->run( %config )
or die $local_epcr->error;
print $result->raw_output;
}
exit 0;
# -------------------------------------------------------------------
#
# Pass the request and parameters to the local Bio::PrimerDesigner.
#
$binary eq 'primer3' ? primer3( %config ) : ePCR( %config );
# -------------------------------------------------------------------
sub check{
=head2 check
Verifies that this CGI is active and supports the requested binary.
=cut
my $program = shift;
if ($program) {
print "$program OK\n" if $program =~ /e-PCR|primer3/;
exit;
}
}
=pod
=head1 NAME
primer_designer.cgi -- server-side wrapper for the primer3 and e-PCR binaries
=head1 SYNOPSIS
#
# Design request is made client-side.
#
use Bio::PrimerDesigner;
my $local_obj = Bio::PrimerDesigner (
method => 'remote',
program => 'primer3',
) or die Bio::PrimerDesigner->error;
#
# Get the program input options.
# (See Bio::PrimerDesigner docs for input options.)
#
my %options = %hash_of_input_options;
#
# make request and retrieve results of server-side processing
#
my $result = design( %options );
=head1 AUTHORS
Copyright (C) 2003-2009 Sheldon McKay E<lt>mckays@cshl.eduE<gt>,
Ken Youens-Clark E<lt>kclark@cpan.orgE<gt>.
=head1 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.
=head1 SEE ALSO
Bio::PrimerDesigner, Bio::PrimerDesigner::primer3, Bio::PrimerDesigner::e-PCR.
=cut
|
