def test_statistics_only_shapiro(self, statisticsArgs): statisticsArgs['genotype_folder'] = None statisticsArgs['type'] = 'shapiro' stats = pygwas.calculate_stats(statisticsArgs) assert stats['transformation'] == 'none' assert len(stats) == 2 np.testing.assert_allclose(stats['shapiro'],2.3893008814393317e-14,rtol=1e-5, atol=0)
def test_statistics_most_normal_only_shapiro(self, statisticsArgs): statisticsArgs['genotype_folder'] = None statisticsArgs['type'] = 'shapiro' statisticsArgs['transformation'] = 'most_normal' stats = pygwas.calculate_stats(statisticsArgs) assert stats['transformation'] == 'box_cox' assert len(stats) == 2 np.testing.assert_allclose(stats['shapiro'],3.551881553633118e-14,rtol=1e-5, atol=0)
def test_statistics_most_normal(self, statisticsArgs):
statisticsArgs['transformation'] = 'most_normal'
stats = pygwas.calculate_stats(statisticsArgs)
assert stats['transformation'] == 'box_cox'
assert len(stats) == 3
np.testing.assert_allclose(stats['shapiro'],
7.311389856176284e-14,
rtol=1e-5,
atol=0)
def test_statistics_only_shapiro_with_genotype(self, statisticsArgs):
statisticsArgs['type'] = 'shapiro'
stats = pygwas.calculate_stats(statisticsArgs)
assert stats['transformation'] == 'none'
assert len(stats) == 2
np.testing.assert_allclose(stats['shapiro'],
4.432536287882552e-14,
rtol=1e-5,
atol=0)
def test_statistics_only_shapiro(self, statisticsArgs):
statisticsArgs['genotype_folder'] = None
statisticsArgs['type'] = 'shapiro'
stats = pygwas.calculate_stats(statisticsArgs)
assert stats['transformation'] == 'none'
assert len(stats) == 2
np.testing.assert_allclose(stats['shapiro'],
2.3893008814393317e-14,
rtol=1e-5,
atol=0)
def on_post(self,req,resp,genotype_id,type):
phenotypes = zip(*req.context.get('doc',[]))
accessions = phenotypes[0]
values = phenotypes[1]
phen_data = phenotype.Phenotype(accessions,values,'phenotype')
genotype_folder = '%s/%s' % (self.storage_path,genotype_id)
arguments = {'type':type,'genotype_folder':genotype_folder,'phen_data':phen_data,'file':''}
statistics = pygwas.calculate_stats(arguments)
req.context['result'] = statistics
resp.status = falcon.HTTP_200
def test_statistics_most_normal_only_shapiro(self, statisticsArgs):
statisticsArgs['genotype_folder'] = None
statisticsArgs['type'] = 'shapiro'
statisticsArgs['transformation'] = 'most_normal'
stats = pygwas.calculate_stats(statisticsArgs)
assert stats['transformation'] == 'box_cox'
assert len(stats) == 2
np.testing.assert_allclose(stats['shapiro'],
3.551881553633118e-14,
rtol=1e-5,
atol=0)
def test_statistics(self, statisticsArgs):
stats = pygwas.calculate_stats(statisticsArgs)
assert len(stats) == 3
assert stats['transformation'] == 'none'
np.testing.assert_allclose(stats['shapiro'],
4.432536287882552e-14,
rtol=1e-5,
atol=0)
np.testing.assert_allclose(stats['pseudo_heritability'],
0.89686416775572486,
rtol=1e-5,
atol=0)
def test_statistics(self,statisticsArgs): stats = pygwas.calculate_stats(statisticsArgs) assert len(stats) == 3 assert stats['transformation'] == 'none' np.testing.assert_allclose(stats['shapiro'],4.432536287882552e-14,rtol=1e-5, atol=0) np.testing.assert_allclose(stats['pseudo_heritability'],0.89686416775572486,rtol=1e-5, atol=0)
def test_statistics_most_normal(self, statisticsArgs): statisticsArgs['transformation'] = 'most_normal' stats = pygwas.calculate_stats(statisticsArgs) assert stats['transformation'] == 'box_cox' assert len(stats) == 3 np.testing.assert_allclose(stats['shapiro'],7.311389856176284e-14,rtol=1e-5, atol=0)
def test_statistics_only_shapiro_with_genotype(self, statisticsArgs): statisticsArgs['type'] = 'shapiro' stats = pygwas.calculate_stats(statisticsArgs) assert stats['transformation'] == 'none' assert len(stats) == 2 np.testing.assert_allclose(stats['shapiro'],4.432536287882552e-14,rtol=1e-5, atol=0)