Package Bio :: Package PopGen :: Package SimCoal :: Module Controller :: Class FastSimCoalController
[hide private]
[frames] | no frames]

Class FastSimCoalController

source code

object --+
         |
        FastSimCoalController

Instance Methods [hide private]
 
__init__(self, fastsimcoal_dir=None, bin_name='fastsimcoal21')
Initializes the controller.
source code
 
run_fastsimcoal(self, par_file, num_sims, par_dir='.', opts={})
Executes Fastsimcoal.
source code

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__init__(self, fastsimcoal_dir=None, bin_name='fastsimcoal21')
(Constructor)

source code 
Initializes the controller.

fastsimcoal_dir is the directory where fastsimcoal is.
By default the binary should be called fastsimcoal21.
bin_name specifies a different name for the binary.

The initializer checks for existence and executability of binaries
and sets up the command line controller.

Fastsimcoal2 is available here: http://cmpg.unibe.ch/software/fastsimcoal2/.
This wrapper was written and tested for fastsimcoal version 2.01.

Overrides: object.__init__

run_fastsimcoal(self, par_file, num_sims, par_dir='.', opts={})

source code 
Executes Fastsimcoal.

par_file is the input parameter file (--ifile) for fastsimcoal.
num_sims is the number of simulations to perform.
par_dir is the directory where par_file is and where output will be written.
opts is a dictionary of additional options to fastsimcoal.