Bio::PrimerDesigner::ispcr3pm
A class for accessing the ispcr (in-silico pcr) binary
Usage
use Bio::PrimerDesigner::ispcr;Overview
A low-level interface to the isPcr program. Uses supplied PCR primers, DNA sequence and stringency parameters to predict both expected and unexpected PCR products.
Methods
run
Sets up the isPcr 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 config file and command-line arguments and sends the request to the local binary or remote server.
verify
Check to make that the isPCR binary is installed and functioning properly. Since ispcr 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 ispcr and an undefined output for some other reason. verify uses sham ispcr 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 ispcr.
list_params
Returns a list of ispcr configuration options. Required ispcr 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.