import random
from metagenomics.plugins.statisticalTests.Fishers import Fishers
from metagenomics.plugins.statisticalTests.ChiSquare import ChiSquare
from metagenomics.plugins.statisticalTests.ChiSquareYates import ChiSquareYates
from metagenomics.plugins.statisticalTests.GTest import GTest
from metagenomics.plugins.statisticalTests.GTestYates import GTestYates
from metagenomics.plugins.statisticalTests.Permutation import Permutation
from metagenomics.plugins.statisticalTests.DiffBetweenProp import DiffBetweenProp
from metagenomics.plugins.statisticalTests.Bootstrap import Bootstrap
from metagenomics.plugins.statisticalTests.Barnard import Barnard
fishers = Fishers()
chiSquare = ChiSquare()
chiSquareYates = ChiSquareYates()
gTest = GTest()
gTestYates = GTestYates()
permutation = Permutation()
diffBetweenProp = DiffBetweenProp()
bootstrap = Bootstrap()
barnard = Barnard()
sampleSizes = [5, 10, 15, 25]
def mean(x):
if len(x) == 0:
return 0
sum = 0.0
for i in xrange(0, len(x)):
sum += x[i]
import random
from metagenomics.plugins.statisticalTests.Fishers import Fishers
from metagenomics.plugins.statisticalTests.GTest import GTest
from metagenomics.plugins.statisticalTests.GTestYates import GTestYates
from metagenomics.plugins.statisticalTests.DiffBetweenProp import DiffBetweenProp
fishers = Fishers()
gTest = GTest()
gTestYates = GTestYates()
diffBetweenProp = DiffBetweenProp()
numReplicates = 10000 # number of samples to draw
popSize = 1000000 # size of underlying population
propInSS = [0.1] # proportion of sequences in subsystem (SS) of interest
sampleSize1 = [1000] # sample size for community 1
sampleSize2 = [2000] # sample size for community 2
for sampleSizeIndex in xrange(0, len(sampleSize1)):
print 'Considering communities with a sample size of: ' + str(sampleSize1[sampleSizeIndex]) + ' and ' + str(sampleSize2[sampleSizeIndex])
for prop in propInSS:
print ' Proportion of sequences in subsystem of interest: ' + str(prop)
totalSamples1 = sampleSize1[sampleSizeIndex]
totalSamples2 = sampleSize2[sampleSizeIndex]
fishersResults = []
gTestResults = []
gTestYatesResults = []