def test():
""" Test the results from R's build-in kruskal wallis function, R's matrix-based
kw test, and Python's matrix-based kw test
directory. Can be done in a nice way with rpy
"""
subprocess.call(['Rscript', 'test_kruX.R'])
outputFromR = numpy.genfromtxt('R.output',
dtype=[('SNP', 'i4'), ('gene', 'i4'),
('fd', 'i4'), ('chi', 'f4'),
('pvalue', 'f4')])
geno = numpy.genfromtxt('geno.tab.tmp', skip_header=1, missing_values='NA')
geno = geno[:, 1:]
mrna = numpy.genfromtxt('mrna.tab.tmp', skip_header=1, missing_values='NA')
mrna = mrna[:, 1:]
start = time.clock()
outputFromPython = kruX.calculateKruskalWallisWithMatrix(
geno, mrna, pValueThre=1, numTranscript=2000)
endTime = time.clock() - start
print('Total running time for Python matrix-based test: %.2f' % (endTime))
outputFromPython = outputFromPython[numpy.argsort(
outputFromPython['pvalue'])]
numpy.savetxt('python.output',
outputFromPython,
fmt='%i\t%i\t%i\t%.17e\t%.17e',
delimiter='\t')
if (numpy.all(outputFromR['pvalue'] - outputFromPython['pvalue'] < 1e-7)):
print(
'Passed: equal between R matrix-based and Python matrix-based test'
)
else:
print(
'Failed: not equal between R matrix-based and Python matrix-based test'
)
def test_python_performance():
"""Python's matrix-based kw test running time
"""
geno = numpy.genfromtxt('geno.tab.tmp', skip_header=1, missing_values='NA')
geno = geno[:, 1:]
mrna = numpy.genfromtxt('mrna.tab.tmp', skip_header=1, missing_values='NA')
mrna = mrna[:, 1:]
start = time.clock()
outputFromPython = kruX.calculateKruskalWallisWithMatrix(
geno, mrna, pValueThre=1, numTranscript=1000)
endTime = time.clock() - start
print('Total running time for Python matrix-based test: %.2f' % (endTime))
def test_python_performance():
"""Python's matrix-based kw test running time
"""
geno = numpy.genfromtxt('geno.tab.tmp', skip_header=1, missing_values='NA')
geno = geno[:,1:]
mrna = numpy.genfromtxt('mrna.tab.tmp', skip_header=1, missing_values='NA')
mrna = mrna[:,1:]
start = time.clock()
outputFromPython = kruX.calculateKruskalWallisWithMatrix(geno, mrna,
pValueThre = 1, numTranscript=1000)
endTime = time.clock() - start
print('Total running time for Python matrix-based test: %.2f'%(endTime))
def test():
""" Test the results from R's build-in kruskal wallis function, R's matrix-based
kw test, and Python's matrix-based kw test
directory. Can be done in a nice way with rpy
"""
subprocess.call(['Rscript','test_kruX.R'])
outputFromR = numpy.genfromtxt('R.output',
dtype=[('SNP','i4'),('gene','i4'),('fd','i4'),
('chi','f4'),('pvalue','f4') ] )
geno = numpy.genfromtxt('geno.tab.tmp', skip_header=1, missing_values='NA')
geno = geno[:,1:]
mrna = numpy.genfromtxt('mrna.tab.tmp', skip_header=1, missing_values='NA')
mrna = mrna[:,1:]
start = time.clock()
outputFromPython = kruX.calculateKruskalWallisWithMatrix(geno, mrna,
pValueThre = 1, numTranscript=2000)
endTime = time.clock() - start
print('Total running time for Python matrix-based test: %.2f'%(endTime))
outputFromPython = outputFromPython[numpy.argsort(outputFromPython['pvalue'])]
numpy.savetxt('python.output', outputFromPython, fmt='%i\t%i\t%i\t%.17e\t%.17e',delimiter='\t')
if (numpy.all(outputFromR['pvalue']-outputFromPython['pvalue']<1e-7)):
print('Passed: equal between R matrix-based and Python matrix-based test')
else:
print('Failed: not equal between R matrix-based and Python matrix-based test')