Bio::PrimerDesigner::Result - a class for handling primer design or validation results
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; }
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.
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)
Copyright (c) 2003-2008 Sheldon McKay <mckays@cshl.edu>, Ken Youens-Clark <kclark@cpan.org>.
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.
Bio::PrimerDesigner.
To install Bio::PrimerDesigner, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::PrimerDesigner
CPAN shell
perl -MCPAN -e shell install Bio::PrimerDesigner
For more information on module installation, please visit the detailed CPAN module installation guide.