def write_fixations(pops, fixationsFileName, repid):
x = fp.view_fixations(pops)
#hdf=pd.HDFStore(fixationsFileName,'a',complevel=6,complib='zlib')
con = sqlite3.connect(fixationsFileName)
df = [pd.DataFrame(i) for i in x]
for i in df:
i['rep'] = [repid] * len(i.index)
repid += 1
i.to_sql('fixations', con, if_exists='append', index=False)
#hdf.append('fixations',i)
con.close()
def testFixationViews(self):
temp = fwdpy.view_fixations(pops[0])
nlist = np.array([N]*10*N,dtype=np.uint32)
rng = fp.GSLrng(101)
pops = fp.evolve_regions(rng, #The random number generator
4, #The number of pops to simulate = number of threads to use.
N, #Initial population size for each of the 4 demes
nlist[0:], #List of population sizes over time.
0.005, #Neutral mutation rate (per gamete, per generation)
0.01, #Deleterious mutation rate (per gamete, per generation)
0.005, #Recombination rate (per diploid, per generation)
nregions, #Defined above
sregions, #Defined above
recregions)#Defined above
##Get fixation views:
fixations = [fp.view_fixations(i) for i in pops]
##Get mutation views:
mviews = fp.view_mutations(pops)
class test_sample_details(unittest.TestCase):
def test_CompareUsingView(self):
"""
Evolve some population, take samples,
get details of those samples, make sure
those details match up what 'views' think should
be in the population.
"""
samples = [fp.get_samples(rng,i,100) for i in pops]
details = [fp.get_sample_details(i[1],j) for i,j in zip(samples,pops)]
def testFixationViews(self):
temp = fwdpy.view_fixations(pops[0])