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

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.