Man pages sections > man3 > Bio::PrimerDesigner::Result

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

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

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.
2016-11-11 perl v5.24.1