NAME

       Bio::PrimerDesigner::Result - a class for handling primer design or validation results

SYNOPSIS

         use Bio::PrimerDesigner;

         #
         # primer3
         #
         my $primer3_obj = Bio::PrimerDesigner->new( program => 'primer3 );
         my $result = $primer3_obj->design( %hash_of_options );
         my $left_primer = $result->left;
         my @left_primers = $result->left(1..$num_primers);

         #
         # e-PCR -- first make a hash of options from primer3 results
         # then run e-PCR
         #
         my $epcr_obj = Bio::PrimerDesigner->new( program => 'primer3 );
         my $epcr_result = $epcr_obj->design( %hash_of_options );
         my $num_products = $epcr_result->products;

         #
         # one product
         #
         my $first_prod_size = $epcr_result->size;
         my $first_prod_start = $epcr_result->start;
         my $first_prod_stop = $epcr_result->start;

         #
         # more than one product
         #
         my @pcr_product_sizes = ();
         for (1..$num_products) {
             push @pcr_product_sizes, $epcr_result->size;
         }

DESCRIPTION

        Bio::PrimerDesigner::Result will autogenerate result access methods
        for for Native Boulder IO keys and Bio::PrimerDesigner keys for
        primer3, e-PCR, isPcr and ipcress.

METHODS

   keys
        This handles result method calls made via the
        Bio::PrimerDesigner::Result object.  Returns either a scalar or list
        depending on the on the arguments:

         ------------------+------------------------
          Args passed      |  Returns
         ------------------+------------------------
          none                scalar value for set 1
          numeric n           scalar value for set n
          numeric list 1..n   list with n elements

        The aliased output methods (below) return a string when called in a
        scalar context and a list when called in a list context.  The native
        primer3 (Boulder IO) keys can also be used.  There are also e-PCR,
        isPcr and ipcress specific methods

       Primer3 keys

       •   left        -- left primer sequence

       •   right       -- right primer sequence

       •   hyb_oligo   -- internal oligo sequence

       •   startleft   -- left primer 5' sequence coordinate

       •   startright  -- right primer 5' sequence coordinate

       •   tmleft      -- left primer tm

       •   tmright     -- right primer tm

       •   qual        -- primer pair penalty (Q value)

       •   lqual       -- left primer penalty

       •   rqual       -- right primer penalty

       •   leftgc      -- left primer % gc

       •   rightgc     -- right primer % gc

       •   lselfany    -- left primer self-complementarity (any)

       •   lselfend    -- left primer self-complementarity (end)

       •   rselfany    -- right primer self-complementarity (any)

       •   rselfend    -- right primer self-complementarity (end)

       •   pairanycomp -- primer pair complementarity (any)

       •   pairendcomp -- primer pair complementarity (end)

       •   lendstab    -- left primer end stability

       •   rendstab    -- right primer end stability

       •   amplicon    -- amplified PCR product

       Other keys

       •   products    -- number of PCR products

       •   size        -- product size

       •   start       -- product start coordinate

       •   stop        -- product stop coordinate

       •   end         -- synonymous with stop

       •   strand      -- strand of product relative to the ref. sequence (isPCR, ipcress)

       •   amplicon    -- returns the PCR product (isPCR only)

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.

perl v5.32.0                                       2020-11-16                   Bio::PrimerDesigner::Result(3pm)