/ 
Bio-PrimerDesigner-0.07
River stage zero No dependents
/ Bio::PrimerDesigner::Result

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.