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Package Bio :: Package PopGen :: Package FDist :: Module Controller :: Class FDistController
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Class FDistController

source code

Known Subclasses:
Instance Methods [hide private]
 
__init__(self, fdist_dir='', ext=None)
Initializes the controller.		 source code
 
_get_path(self, app)
Returns the path to an fdist application.		 source code
 
_get_temp_file(self)
Gets a temporary file name.		 source code
 
run_datacal(self, data_dir='.', version=1, crit_freq=0.99, p=0.5, beta=(0.25, 0.25))
Executes datacal.		 source code
 
_generate_intfile(self, data_dir)
Generates an INTFILE.		 source code
 
run_fdist(self, npops, nsamples, fst, sample_size, mut=0, num_sims=50000, data_dir='.', is_dominant=False, theta=0.06, beta=(0.25, 0.25), max_freq=0.99)
Executes (d)fdist.		 source code
 
run_fdist_force_fst(self, npops, nsamples, fst, sample_size, mut=0, num_sims=50000, data_dir='.', try_runs=5000, limit=0.001, is_dominant=False, theta=0.06, beta=(0.25, 0.25), max_freq=0.99)
Executes fdist trying to force Fst.		 source code
 
run_cplot(self, ci=0.95, data_dir='.', version=1, smooth=0.04)
Executes cplot.		 source code
 
run_pv(self, out_file='probs.dat', data_dir='.', version=1, smooth=0.04)
Executes pv.		 source code
Method Details [hide private]

__init__(self, fdist_dir='', ext=None)
(Constructor)

source code  
Initializes the controller.

fdist_dir is the directory where fdist2 is.
ext is the extension of binaries (.exe on windows, 
  none on Unix)

_get_path(self, app)

source code 

Returns the path to an fdist application.

Includes Path where fdist can be found plus executable extension.

_get_temp_file(self)

source code 

Gets a temporary file name.

Returns a temporary file name, if executing inside jython tries to replace unexisting tempfile.mkstemp().

run_datacal(self, data_dir='.', version=1, crit_freq=0.99, p=0.5, beta=(0.25, 0.25))

source code 

Executes datacal.

data_dir - Where the data is found.

_generate_intfile(self, data_dir)

source code 

Generates an INTFILE.

Parameter: data_dir - data directory

run_fdist(self, npops, nsamples, fst, sample_size, mut=0, num_sims=50000, data_dir='.', is_dominant=False, theta=0.06, beta=(0.25, 0.25), max_freq=0.99)

source code  
Executes (d)fdist.

Parameters:
npops - Number of populations
nsamples - Number of populations sampled
fst - expected Fst
sample_size - Sample size per population
        For dfdist: if zero a sample size file has to be provided 
mut - 1=Stepwise, 0=Infinite allele
num_sims - number of simulations
data_dir - Where the data is found
is_dominant - If true executes dfdist
theta - Theta (=2Nmu)
beta - Parameters for the beta prior
max_freq - Maximum allowed frequency of the commonest allele

Returns:
fst - Average Fst

Important Note: This can take quite a while to run!

run_fdist_force_fst(self, npops, nsamples, fst, sample_size, mut=0, num_sims=50000, data_dir='.', try_runs=5000, limit=0.001, is_dominant=False, theta=0.06, beta=(0.25, 0.25), max_freq=0.99)

source code  
Executes fdist trying to force Fst.

Parameters:
try_runs - Number of simulations on the part trying to get
           Fst correct
limit - Interval limit
Other parameters can be seen on run_fdist.

run_cplot(self, ci=0.95, data_dir='.', version=1, smooth=0.04)

source code 

Executes cplot.

ci - Confidence interval. data_dir - Where the data is found.

run_pv(self, out_file='probs.dat', data_dir='.', version=1, smooth=0.04)

source code 

Executes pv.

out_file - Name of output file. data_dir - Where the data is found.


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