Bio::PrimerDesigner::epcr3pm
A class for accessing the epcr binary
Usage
use Bio::PrimerDesigner::epcr;Overview
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 products.
Methods
run
Sets up the e-PCR request for a single primer combination and returns an Bio::PrimerDesigner::Result object
If the permute flag is true, all three possible primer combinations will be tested (ie: forward + reverse, forward + forward, reverse + reverse)
request
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.
verify
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.
binary_name
Defines the binary's name on the system.
list_aliases
There are no aliases to list for epcr.
list_params
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.
Releases
8 releases since Debian 6.0 (Squeeze); the text changed 4 times.