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
o left -- left primer sequence
o right -- right primer sequence
o hyb_oligo -- internal oligo sequence
o startleft -- left primer 5' sequence coordinate
o startright -- right primer 5' sequence coordinate
o tmleft -- left primer tm
o tmright -- right primer tm
o qual -- primer pair penalty (Q value)
o lqual -- left primer penalty
o rqual -- right primer penalty
o leftgc -- left primer % gc
o rightgc -- right primer % gc
o lselfany -- left primer self-complementarity (any)
o lselfend -- left primer self-complementarity (end)
o rselfany -- right primer self-complementarity (any)
o rselfend -- right primer self-complementarity (end)
o pairanycomp -- primer pair complementarity (any)
o pairendcomp -- primer pair complementarity (end)
o lendstab -- left primer end stability
o rendstab -- right primer end stability
o amplicon -- amplified PCR product
Other keys
o products -- number of PCR products
o size -- product size
o start -- product start coordinate
o stop -- product stop coordinate
o end -- synonymous with stop
o strand -- strand of product relative to the ref. sequence (isPCR, ipcress)
o 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.
perl v5.10.0 2009-08-04 Bio::PrimerDesigner::Result(3pm)