def run_fdist_force_fst(self, npops, nsamples, fst, sample_size,
mut = 0, num_sims = 50000, data_dir='.', try_runs = 5000):
"""Executes fdist (if not in cache).
Parameters
npops - Number of populations
nsamples - Number of populations sampled
fst - expected Fst
sample_size - Sample size per population
mut - 0=Stepwise, 1=Infinite allele
num_sims - number of simulations
dir - directory where fdist will be executed (must be rw)
try_runs - number of simulations on the part trying to get
Fst correct.
Important Note: This can take quite a while to run!
"""
cache_fst = str(round(fst, -int(log10(self.limit))))
cache_name = '_'.join([str(npops), str(nsamples), str(sample_size),
str(mut), cache_fst]) + '.bz2'
full_cache_name = self.cache_dir + os.sep + cache_name
full_final_name = data_dir + os.sep + 'out.dat'
if os.access(full_cache_name, os.R_OK):
bzf = BZ2File(full_cache_name, 'r')
of = open(full_final_name, 'w')
of.writelines(bzf.readlines())
of.close()
bzf.close()
return float(cache_fst)
else:
fdc = FDistController(self.fdist_dir)
real_fst = fdc.run_fdist_force_fst(npops, nsamples, fst,
sample_size, mut, num_sims, data_dir, try_runs, self.limit)
cache_name = '_'.join([str(npops), str(nsamples), str(sample_size),
str(mut), str(round(real_fst, -int(log10(self.limit))))]) \
+ '.bz2'
full_cache_name = self.cache_dir + os.sep + cache_name
if not os.access(full_cache_name, os.R_OK):
bzf = BZ2File(full_cache_name, 'w')
inf = open(data_dir + os.sep + 'out.dat')
bzf.writelines(inf.readlines())
inf.close()
bzf.close()
if real_fst < fst:
begin = real_fst
end = fst
else:
begin = fst
end = real_fst
while begin <= end + (self.limit/2):
interval_full_cache_name = self.cache_dir + os.sep + \
'_'.join([str(npops), str(nsamples), str(sample_size),
str(mut), str(round(begin, -int(log10(self.limit))))]) \
+ '.bz2'
try:
os.symlink(full_cache_name, interval_full_cache_name)
except OSError:
pass #safe to ignore
begin += self.limit
return real_fst
def run_pv(self, out_file='probs.dat', data_dir='.'):
fdc = FDistController(self.fdist_dir)
return fdc.run_pv(out_file, data_dir)
def run_cplot(self, ci = 0.95, data_dir='.'):
fdc = FDistController(self.fdist_dir)
return fdc.run_cplot(ci, data_dir)
def run_datacal(self, data_dir='.'):
fdc = FDistController(self.fdist_dir)
return fdc.run_datacal(data_dir)