/ 
Bio-PrimerDesigner-0.01
River stage zero No dependents
/ Bio::PrimerDesigner::Result

NAME

Bio::PrimerDesigner::Result - a class for handling primer design 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 the following keys: Native Boulder IO keys, Bio::PrimerDesigner alias keys, or e-PCR keys.

METHODS

keys

This handles result method calls made via the Bio::PrimerDesigner::Result object. Returns either a scalar or list dep. on context, e.g.:

------------------.------------------------
 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 four e-PCR-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

e-PCR keys

  • products -- number of e-PCR products

  • size -- product size

  • start -- product start coordinate

  • stop -- product stop coordinate

AUTHOR

Copyright (C) 2003 Sheldon McKay <smckay@bcgsc.bc.ca>, Ken Y 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 2.

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., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.

SEE ALSO

Bio::PrimerDesigner.