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.
