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Bio::PrimerDesigner.3pm

NAME

Bio::PrimerDesigner - Design PCR Primers using primer3 and epcr

SYNOPSIS

   use Bio::PrimerDesigner;
 
   my $pd = Bio::PrimerDesigner->new;
 
   #
   # Define the DNA sequence, etc.
   #
   my $dna   = "CGTGC...TTCGC";
   my $seqID = "sequence 1";
 
   #
   # Define design parameters (native primer3 syntax)
   #
   my %params = ( 
       PRIMER_NUM_RETURN   => 2,
       PRIMER_SEQUENCE_ID  => $seqID,
       SEQUENCE            => $dna,
       PRIMER_PRODUCT_SIZE => '500-600'
   );
 
   #
   # Or use input aliases
   #
   %param = ( 
       num                 => 2,
       id                  => $seqID,
       seq                 => $dna,
       sizerange           => '500-600'
   ); 
 
   #
   # Design primers
   #
   my $results = $pd->design( %params ) or die $pd->error;
 
   #
   # Make sure the design was successful
   #
   if ( !$results->left ) {
       die "No primers found\n", $results->raw_data;
   }
 
   #
   # Get results (single primer set)
   #
   my $left_primer  = $results->left;
   my $right_primer = $results->right;
   my $left_tm      = $results->lefttm;
 
   #
   # Get results (multiple primer sets)
   #
   my @left_primers  = $results->left(1..3);
   my @right_primers = $results->right(1..3);
   my @left_tms      = $results->lefttm(1..3);
 
 

DESCRIPTION

Bio::PrimerDesigner provides a low-level interface to the primer3 and epcr binary executables and supplies methods to return the results. Because primer3 and e-PCR are only available for Unix-like operating systems, Bio::PrimerDesigner offers the ability to accessing the primer3 binary via a remote server. Local installations of primer3 or e-PCR on Unix hosts are also supported.

METHODS

binary_path

Gets/sets path to the primer3 binary.

design

Makes the primer design or e-PCR request. Returns an Bio::PrimerDesigner::Result object.

epcr_example

Run test e-PCR job. Returns an Bio::PrimerDesigner::Results object.

list_aliases

Lists aliases for primer3 input/output options

list_params

Lists input options for primer3 or epcr, depending on the context

method

Gets/sets method of accessing primer3 or epcr binaries.

os_is_unix

Returns 1 if it looks like the operating system is a Unix variant, otherwise returns 0.

primer3_example

Runs a sample design job for primers. Returns an Bio::PrimerDesigner::Results object.

program

Gets/sets which program to use.

run

Alias to ``design.''

url

Gets/sets the URL for accessing the remote binaries.

verify

Tests local installations of primer3 or e-PCR to ensure that they are working properly.

AUTHORS

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::primer3, Bio::PrimerDesigner::epcr.