Bio::PrimerDesigner::epcr - A class for accessing the epcr binary
A low-level interface to the e-PCR binary. Uses supplied PCR primers, DNA
sequence and stringency parameters to predict both expected and unexpected PCR
Sets up the e-PCR request for a single primer combination and returns an
If the permute flag is true, all three possible primer combinations will be
tested (ie: forward + reverse, forward + forward, reverse + reverse)
Assembles the e-PCR config file and command-line arguments and send the e-PCR
request to the local e-PCR binary or remote server.
Check to make that the e-PCR binary is installed and functioning properly. Since
e-PCR returns nothing if no PCR product is found in the sequence, we have to
be able to distinguish between a valid, undefined output from a functioning
e-PCR and an undefined output for some other reason. verify uses sham e-PCR
data that is known to produce a PCR product.
Defines the binary's name on the system.
There are no aliases to list for epcr.
Returns a list of e-PCR configuration options. Required e-PCR input is a
sequence string or file and the left and right primers. Default values will be
used for the remaining options if none are supplied.
Copyright (C) 2003-2009 Sheldon McKay <email@example.com>, Ken Youens-Clark
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.