def test_load_all_vars_kmer(self):
p = pd.read_csv(P,
index_col=0,
sep='\t')['binary']
infile = gzip.open(KMER)
variants, sidx, vidx = load_all_vars('kmers', p, False, None,
infile, set(p.index), None,
0.45, 0.55, 1.0, False)
self.assertEqual(variants.shape, (20, 50))
self.assertEqual(variants.sum(), 474.0)
self.assertTrue(abs(variants.toarray()[0] -
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.])).max() < 1E-7)
self.assertEqual(len(sidx), 20)
self.assertEqual(sidx, [2, 6, 20, 32, 39, 54,
58, 60, 69, 89, 93,
123, 127, 134, 153,
156, 179, 180, 184, 194])
self.assertEqual(vidx, 200)
# not providing samples
infile = gzip.open(KMER)
with self.assertRaises(ZeroDivisionError):
_ = load_all_vars('kmers', p, False, None,
infile, set([]), None,
0.45, 0.55, 1.0, False)
# uncompressed option - only with python3+
if sys.version_info[0] >= 3:
infile = gzip.open(KMER)
with self.assertRaises(TypeError):
_ = load_all_vars('kmers', p, False, None,
infile, set(p.index), None,
0.45, 0.55, 1.0, True)
# different type
infile = gzip.open(KMER)
with self.assertRaises(ValueError):
_ = load_all_vars('Rtab', p, False, None,
infile, set([]), None,
0.45, 0.55, 1.0, False)
infile = gzip.open(KMER)
with self.assertRaises(AttributeError):
_ = load_all_vars('vcf', p, False, None,
infile, set([]), None,
0.45, 0.55, 1.0, False)
# different file
infile = gzip.open(PRES)
with self.assertRaises(IndexError):
_ = load_all_vars('kmers', p, False, None,
infile, set(p.index), None,
0.45, 0.55, 1.0, False)
infile = gzip.open(VCF)
with self.assertRaises(IndexError):
_ = load_all_vars('kmers', p, False, None,
infile, set(p.index), None,
0.45, 0.55, 1.0, False)
def test_load_all_vars_rtab(self):
p = pd.read_csv(P,
index_col=0,
sep='\t')['binary']
infile, sample_order = open_rtab(PRES)
variants, sidx, vidx = load_all_vars('Rtab', p, False, None,
infile, set(p.index),
sample_order,
0.25, 0.75, 1.0, False)
self.assertEqual(variants.shape, (7, 50))
self.assertEqual(variants.sum(), 103.0)
self.assertTrue(abs(variants.toarray()[0] -
np.array([0., 0., 1., 0., 0., 0., 1., 0., 1., 0.,
0., 0., 1., 0., 0., 0., 0.,
0., 1., 0., 0., 0., 0., 0., 0., 1., 0.,
0., 1., 1., 0., 0., 0., 0.,
0., 0., 0., 0., 1., 1., 0., 1., 0., 1.,
0., 1., 0., 0., 1., 0.
])).max() < 1E-7)
self.assertEqual(len(sidx), 7)
self.assertEqual(sidx, [1426, 1436, 1463, 1484, 1492, 1496, 1498])
self.assertEqual(vidx, 1499)
# too few OGs
with self.assertRaises(ValueError):
infile, sample_order = open_rtab(PRESSMALL, compressed=False)
_ = load_all_vars('Rtab', p, False, None,
infile, set(p.index), sample_order,
0.01, 0.99, 1.0, False)
# not providing samples
with self.assertRaises(ValueError):
infile, sample_order = open_rtab(PRESSMALL, compressed=False)
_ = load_all_vars('Rtab', p, False, None,
infile, set([]), [],
0.45, 0.55, 1.0, False)
# different type
with self.assertRaises(IndexError):
infile, sample_orders = open_rtab(PRES)
_ = load_all_vars('kmers', p, False, None,
infile, set(p.index), sample_order,
0.01, 0.99, 1.0, False)
with self.assertRaises(AttributeError):
infile, sample_orders = open_rtab(PRES)
_ = load_all_vars('vcf', p, False, None,
infile, set(p.index), sample_order,
0.01, 0.99, 1.0, False)
# different file
infile = gzip.open(KMER)
with self.assertRaises(ValueError):
_ = load_all_vars('Rtab', p, False, None,
infile, set(p.index), None,
0.45, 0.55, 1.0, False)
infile = gzip.open(VCF)
with self.assertRaises(ValueError):
_ = load_all_vars('Rtab', p, False, None,
infile, set(p.index), None,
0.45, 0.55, 1.0, False)
def test_no_file(self):
with self.assertRaises(AttributeError):
load_all_vars('kmers', None, None, None, None,
None, None, None, None, None, None)
with self.assertRaises(TypeError):
load_all_vars('vcf', None, None, None, None,
None, None, None, None, None, None)
with self.assertRaises(AttributeError):
load_all_vars('Rtab', None, None, None, None,
None, None, None, None, None, None)
def test_load_all_vars_vcf(self):
p = pd.read_csv(P,
index_col=0,
sep='\t')['binary']
infile = VariantFile(VCF)
variants, sidx, vidx = load_all_vars('vcf', p, False, None,
infile, set(p.index),
None,
0.25, 0.75, 1.0, False)
self.assertEqual(variants.shape, (8, 50))
self.assertEqual(variants.sum(), 140)
self.assertTrue(abs(variants.toarray()[0] -
np.array([
0., 0., 0., 0., 0., 0., 0., 0., 0.,
1., 1., 0., 1., 0., 0., 0., 0.,
1., 1., 1., 0., 0., 1., 0., 1., 1.,
0., 0., 0., 0., 1., 0., 0., 1.,
0., 1., 0., 0., 0., 1., 0., 0., 0.,
0., 1., 0., 0., 0., 0., 0.
])).max() < 1E-7)
self.assertEqual(len(sidx), 8)
self.assertEqual(sidx, [10, 29, 39, 95, 110, 153, 156, 164])
self.assertEqual(vidx, 254)
# not providing samples
with self.assertRaises(ZeroDivisionError):
infile = VariantFile(VCF)
_ = load_all_vars('vcf', p, False, None,
infile, set([]), None,
0.45, 0.55, 1.0, False)
# different type
with self.assertRaises(AttributeError):
infile = VariantFile(VCF)
_ = load_all_vars('kmers', p, False, None,
infile, set(p.index), None,
0.01, 0.99, 1.0, True)
with self.assertRaises(AttributeError):
infile = VariantFile(VCF)
_ = load_all_vars('Rtab', p, False, None,
infile, set(p.index), None,
0.01, 0.99, 1.0, False)
# different file
infile = gzip.open(KMER)
with self.assertRaises(AttributeError):
_ = load_all_vars('vcf', p, False, None,
infile, set(p.index), None,
0.45, 0.55, 1.0, False)
infile = gzip.open(PRES)
with self.assertRaises(AttributeError):
_ = load_all_vars('vcf', p, False, None,
infile, set(p.index), None,
0.45, 0.55, 1.0, True)
def test_unsupported(self):
with self.assertRaises(ValueError):
load_all_vars('test', None, None, None, None,
None, None, None, None, None, None)
