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Bio::PrimerDesigner::Result.3pm
Langue: en
Version: 2009-05-01 (debian - 07/07/09)
Section: 3 (Bibliothèques de fonctions)
NAME
Bio::PrimerDesigner::Result - a class for handling primer design or validation resultsSYNOPSIS
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.Contenus ©2006-2024 Benjamin Poulain
Design ©2006-2024 Maxime Vantorre