Bio::PrimerDesigner::Result.3pm

Langue: en

Version: 2009-05-01 (debian - 07/07/09)

Section: 3 (Bibliothèques de fonctions)

Sommaire

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.