Python GTest示例

示例#1

文件： pValueBarnardTest.py 项目： mlangill/STAMP

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]

示例#2

文件： alphaTest.py 项目： Mohamed-Fares/AutoMetagen

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 = []