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

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object --+
         |
        FDistController
Known Subclasses:

Instance Methods [hide private]
 
__init__(self, fdist_dir='', ext=None)
Initializes the controller.
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_get_path(self, app)
Returns the path to an fdist application.
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_get_temp_file(self)
Gets a temporary file name.
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run_datacal(self, data_dir='.', version=1, crit_freq=0.99, p=0.5, beta=(0.25, 0.25))
Executes datacal.
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_generate_intfile(self, data_dir)
Generates an INTFILE.
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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.
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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.
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run_cplot(self, ci=0.95, data_dir='.', version=1, smooth=0.04)
Executes cplot.
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run_pv(self, out_file='probs.dat', data_dir='.', version=1, smooth=0.04)
Executes pv.
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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, fdist_dir='', ext=None)
(Constructor)

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Initializes the controller.

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

Overrides: object.__init__

_get_path(self, app)

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Returns the path to an fdist application.

Includes Path where fdist can be found plus executable extension.

_get_temp_file(self)

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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))

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Executes datacal.

data_dir - Where the data is found.

_generate_intfile(self, data_dir)

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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)

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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)

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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)

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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)

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Executes pv.

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