def test_load_var_block_rtab(self):
p = pd.read_csv(P, index_col=0, sep='\t')['binary']
m = None
cov = pd.DataFrame([0, 1])
infile = open(PRES)
header = infile.readline().rstrip()
sample_order = header.split()[1:]
i_var = load_var_block('Rtab', p.head(5), False, [], infile,
p.head(5).index, sample_order, 0.0, 1.0, 1.0,
False, 4)
variants, variant_mat, eof = next(i_var)
self.assertEqual(eof, False)
self.assertEqual(variant_mat.shape, (5, 4))
self.assertEqual(len(variants), 4)
t = np.array([[1., 1., 1., 1.], [1., 1., 1., 1.], [1., 1., 1., 1.],
[1., 1., 1., 1.], [1., 1., 1., 1.]])
self.assertTrue(abs((variant_mat - t).max()) < 1E-7)
t = [
b'2UFzg+SaUQpQxlmqSQ5lmQ==\n',
] * 4
self.assertEqual([x[0].pattern for x in variants], t)
# read until the end of the file
while not eof:
variants, variant_mat, eof = next(i_var)
variants, variant_mat, eof = next(i_var)
self.assertEqual(eof, True)
self.assertEqual(variants, None)
self.assertEqual(variant_mat, None)
def test_load_var_block_vcf(self):
p = pd.read_csv(P, index_col=0, sep='\t')['binary']
m = None
cov = pd.DataFrame([0, 1])
infile = VariantFile(VCF)
i_var = load_var_block('vcf', p.head(5), False, [], infile,
p.head(5).index, [], 0.0, 1.0, 1.0, False, 4)
variants, variant_mat, eof = next(i_var)
self.assertEqual(eof, False)
self.assertEqual(variant_mat.shape, (5, 4))
self.assertEqual(len(variants), 4)
t = np.array([[0., 0., 0., 0.], [0., 0., 0., 0.], [0., 0., 0., 0.],
[0., 0., 0., 0.], [0., 0., 0., 0.]])
self.assertTrue(abs((variant_mat - t).max()) < 1E-7)
t = [
b'/Us46UKS4AJRufOcR+5XEA==\n',
] + [
None,
] + [
b'/Us46UKS4AJRufOcR+5XEA==\n',
] * 2
self.assertEqual([x[0].pattern for x in variants], t)
# read until the end of the file
while not eof:
variants, variant_mat, eof = next(i_var)
variants, variant_mat, eof = next(i_var)
self.assertEqual(eof, True)
self.assertEqual(variants, None)
self.assertEqual(variant_mat, None)
def test_load_var_block_kmers(self):
p = pd.read_csv(P,
index_col=0,
sep='\t')['binary']
m = None
cov = pd.DataFrame([0, 1])
infile = gzip.open(KMER)
i_var = load_var_block('kmers', p.head(5), False, [], infile,
p.head(5).index, [], 0.2, 0.8, 1.0,
False, 4)
variants, variant_mat, eof = next(i_var)
self.assertEqual(eof, False)
self.assertEqual(variant_mat.shape, (5, 4))
self.assertEqual(len(variants), 4)
t = np.array([[0., 0., 1., 0.],
[0., 0., 1., 0.],
[0., 0., 0., 0.],
[0., 0., 1., 0.],
[0., 0., 0., 0.]])
self.assertTrue(abs((variant_mat - t).max()) < 1E-7)
t = [None, None, b'WZMmBpWOV4GTJ81l+lQgBA==\n', None]
self.assertEqual([x[0].pattern for x in variants], t)
# read until the end of the file
while not eof:
variants, variant_mat, eof = next(i_var)
variants, variant_mat, eof = next(i_var)
self.assertEqual(eof, True)
self.assertEqual(variants, None)
self.assertEqual(variant_mat, None)
