mpl.rc('font', **{'family': 'serif', 'serif': ['Computer Modern'], 'size': 20});
mpl.rc('text', usetex=True)
reload(Simulation)
reload(utl)
reload(est)
s=1; nu0=-1 # if zero is given it sets selection on A site with Minimum Allele Frequency. i.e. 1/F
FounderLines=150; numReplicates=4
PopulationSize=1000;L=50000
ModelName='SeasonalSNPs'
i = 0;
filename = '{}/{}/msms/L{:.0f}K.{:04.0f}.msms'.format(popgen.Utils.simoutpath, ModelName, L / 1000, i)
initialNeutralGenerations=10
maxGeneration=10
i=0
fig=plt.figure(figsize=(30,35), dpi=60)
for i in range(20):
plt.subplot(5,4,i+1)
sim = Simulation.Simulation(initialNeutralGenerations=initialNeutralGenerations, s=s, L=L,
numReplicates=numReplicates, initialCarrierFreq=nu0, msmsFile=filename, F=FounderLines,
maxGeneration=maxGeneration, generationStep=1, N=PopulationSize, experimentID=i,
ModelName=ModelName, ignoreInitialNeutralGenerations=not True, foldInitialAFs=False)
utl.plotNu(sim,fig=fig,show=False)
plt.suptitle('Four simulations window of {:.0f}Kbp (roughly {:.0f} variants)'.format(L/1000 , round(sim.theta*sum(1./np.arange(1,150)),0)//100 *100))
plt.savefig('/home/arya/Dropbox/SeasonalSNPs/notes/simulationModel.png')
# plt.show()
import matplotlib as mpl;
import popgen.Estimate as est
import popgen.TimeSeries.RNN.Utils as utl
import popgen.Utils
from popgen.Utils import Simulation
mpl.rc('font', **{'family': 'serif', 'serif': ['Computer Modern'], 'size': 20});
mpl.rc('text', usetex=True)
reload(Simulation)
reload(utl)
reload(est)
s=1; nu0=-1 # if zero is given it sets selection on A site with Minimum Allele Frequency. i.e. 1/F
FounderLines=150; numReplicates=4
PopulationSize=1000;L=50000
ModelName='SeasonalSNPs'
i = 0;
filename = '{}/{}/msms/L{:.0f}K.{:04.0f}.msms'.format(popgen.Utils.simoutpath, ModelName, L / 1000, i)
initialNeutralGenerations=10
maxGeneration=10
sim = Simulation.Simulation(initialNeutralGenerations=initialNeutralGenerations, s=s, L=L, numReplicates=numReplicates,
initialCarrierFreq=nu0, msmsFile=filename, F=FounderLines, maxGeneration=maxGeneration,
generationStep=1, N=PopulationSize, experimentID=i, ModelName=ModelName,
ignoreInitialNeutralGenerations=True);
utl.plotNu(sim)
