def test_iter_variants_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 = iter_variants(p, m, cov, 'Rtab',
False, [], infile,
p.index, sample_order, False,
[], 0.01, 0.99, 1.0,
1, 1, None, None,
False, False)
# fist variant doesn't pass af filter
v = next(i_var)
for i in v:
self.assertEqual(i, None)
# lets' try again with lenient af filter
infile = open(PRES)
header = infile.readline().rstrip()
sample_order = header.split()[1:]
i_var = iter_variants(p, m, cov, 'Rtab',
False, [], infile,
p.index, sample_order, False,
[], 0.0, 1.0, 1.0,
1, 1, None, None,
False, False)
v = next(i_var)
self.assertEqual(v[0], 'COG_1')
self.assertTrue(abs((v[1] - p.values).max()) < 1E-7)
k = np.ones(50)
self.assertTrue(abs((v[2] - k).max()) < 1E-7)
self.assertEqual(v[3], None)
self.assertTrue(abs((v[4] - cov.values).max()) < 1E-7)
self.assertEqual(v[5], 1)
self.assertEqual(v[6], b'xxPKpdegG31U5Mx9EHcYXg==\n')
self.assertEqual(v[7], False)
self.assertEqual(v[8], [])
self.assertEqual(v[9], 1)
self.assertEqual(v[10], 1)
self.assertEqual(v[11], None)
self.assertEqual(v[12], None)
kstrains = sorted(['sample_%d' % x
for x in range(1, 51)])
nkstrains = []
self.assertEqual(v[13], kstrains)
self.assertEqual(v[14], nkstrains)
self.assertEqual(v[15], False)
# Read until the end
with self.assertRaises(StopIteration):
while True:
next(i_var)
def test_iter_variants_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 = iter_variants(p, m, cov, 'vcf',
False, [], infile,
p.index, [], False,
[], 0.2, 0.8, 1.0,
1, 1, None, None,
False, False)
# fist variant doesn't pass af filter
v = next(i_var)
for i in v:
self.assertEqual(i, None)
# let's try again with lenient af filter
infile = VariantFile(VCF)
i_var = iter_variants(p, m, cov, 'vcf',
False, [], infile,
p.index, [], False,
[], 0.0, 1.0, 1.0,
1, 1, None, None,
False, False)
v = next(i_var)
self.assertEqual(v[0], 'FM211187_16_G_A')
self.assertTrue(abs((v[1] - p.values).max()) < 1E-7)
k = np.zeros(50)
self.assertTrue(abs((v[2] - k).max()) < 1E-7)
self.assertEqual(v[3], None)
self.assertTrue(abs((v[4] - cov.values).max()) < 1E-7)
self.assertEqual(v[5], 0)
self.assertEqual(v[6], b'p119Qi/QC/MSCLAT502DlA==\n')
self.assertEqual(v[7], False)
self.assertEqual(v[8], [])
self.assertEqual(v[9], 1)
self.assertEqual(v[10], 1)
self.assertEqual(v[11], None)
self.assertEqual(v[12], None)
kstrains = []
nkstrains = sorted(['sample_%d' % x
for x in range(1, 51)])
self.assertEqual(v[13], kstrains)
self.assertEqual(v[14], nkstrains)
self.assertEqual(v[15], False)
# Read until the end
with self.assertRaises(StopIteration):
while True:
next(i_var)
def test_iter_variants_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 = iter_variants(p, m, cov, 'kmers', False, [], infile, p.index,
[], False, [], 0.2, 0.8, 1.0, 1, 1, None, None,
False, False)
# fist variant doesn't pass af filter
v = next(i_var)
for i in v:
self.assertEqual(i, None)
v = next(i_var)
v = next(i_var)
self.assertEqual(v[0], 'AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA')
self.assertTrue(abs((v[1] - p.values).max()) < 1E-7)
k = np.array([
1, 1, 0, 1, 0, 0, 0, 0, 1, 0, 0, 1, 1, 0, 1, 1, 0, 1, 1, 1, 0, 0,
0, 0, 0, 1, 0, 0, 1, 0, 0, 1, 1, 0, 1, 1, 1, 0, 1, 1, 0, 0, 0, 1,
0, 1, 1, 1, 0, 1
])
self.assertTrue(abs((v[2] - k).max()) < 1E-7)
self.assertEqual(v[3], None)
self.assertTrue(abs((v[4] - cov.values).max()) < 1E-7)
self.assertEqual(v[5], 0.5)
self.assertEqual(v[6], b'Rq/qSUjyLCAe/81lbP0wPA==\n')
self.assertEqual(v[7], False)
self.assertEqual(v[8], [])
self.assertEqual(v[9], 1)
self.assertEqual(v[10], 1)
self.assertEqual(v[11], None)
self.assertEqual(v[12], None)
kstrains = [
'sample_%d' % x for x in [
1, 12, 13, 15, 16, 18, 19, 2, 20, 26, 29, 32, 33, 35, 36, 37,
39, 4, 40, 44, 46, 47, 48, 50, 9
]
]
nkstrains = [
'sample_%d' % x for x in [
10, 11, 14, 17, 21, 22, 23, 24, 25, 27, 28, 3, 30, 31, 34, 38,
41, 42, 43, 45, 49, 5, 6, 7, 8
]
]
self.assertEqual(v[13], kstrains)
self.assertEqual(v[14], nkstrains)
self.assertEqual(v[15], False)
# Read until the end
with self.assertRaises(StopIteration):
while True:
next(i_var)