def test3(self):
btg = BTG(
gencode_path='src/tests/gencode_example.csv', extend=None)
bin_names = np.array([
'chr1:0-100', # 0 -> 0
'chr2:201-300', # 5 -> 1
'chr2:301-400', # 6 -> 2
'chr1:101-200', # 1 -> 3
'chr3:0-100', # 7 -> 4
'chr3:101-200', # 8 -> 5
'chr2:0-100', # 3 -> 6
'chr2:101-200', # 4 -> 7
'chr3:201-300', # 9 -> 8
'chr3:301-400', # 10 -> 9
'chr1:201-300', # 2 -> 10
'chr3:401-500', # 11 -> 11
'chr3:501-600' # 12 -> 12
])
x = np.random.random((1000, len(bin_names)))
counts, ids = btg.convert(x, bin_names, prefix='chr')
ae(ids, ["gene" + str(i) for i in range(1, 8)])
ground_counts = np.zeros((1000, 7))
ground_counts[:, 0] += x[:, 0]
ground_counts[:, 1] += x[:, 3]
ground_counts[:, 2] += x[:, 7] + x[:, 1]
ground_counts[:, 3] += x[:, 6] + x[:, 7] + x[:, 1]
ground_counts[:, 4] += x[:, 5] + x[:, 8]
ground_counts[:, 5] += x[:, 8] + x[:, 9] + x[:, 11] + x[:, 12]
ground_counts[:, 6] += x[:, 8] + x[:, 9] + x[:, 11] + x[:, 12]
aae(ground_counts, counts)
def test8(self):
btg = BTG(
gencode_path='src/tests/gencode_example.csv',
extend=None, n_jobs=4)
bin_names = np.array([
'chr1:0-100', # 0
'chr3:501-600', # 1
'chr2:201-300', # 2
'chr2:301-400', # 3
'chr1:101-200', # 4
'chr2:601-700', # 5
'chr3:700-900' # 6
])
x = np.random.random((1000, len(bin_names)))
counts, ids = btg.convert(x, bin_names, prefix='chr')
ae(ids, ["gene1", "gene2", "gene3", "gene4", "gene6", "gene7"])
ground_counts = np.zeros((1000, 6))
ground_counts[:, 0] += x[:, 0]
ground_counts[:, 1] += x[:, 4]
ground_counts[:, 2] += x[:, 2]
ground_counts[:, 3] += x[:, 2]
ground_counts[:, 4] += x[:, 1]
ground_counts[:, 5] += x[:, 1] + x[:, 6]
aae(ground_counts, counts)
def test10(self):
btg = BTG(
gencode_path='src/tests/gencode_example.csv',
extend=None, n_jobs=4)
bin_names = np.array([
'chr1:1000-2000', # 0
])
x = np.random.random((1000, len(bin_names)))
counts, ids = btg.convert(x, bin_names, prefix='chr')
ae(ids, [])
aae([], counts)
def test9(self):
btg = BTG(
gencode_path='src/tests/gencode_example.csv',
extend=None, n_jobs=4)
bin_names = np.array([
'chr1:0-100', # 0
])
x = np.random.random((1000, len(bin_names)))
counts, ids = btg.convert(x, bin_names, prefix='chr')
ae(ids, ["gene1"])
aae(x[:, 0].reshape(-1, 1), counts)
def test2(self):
btg = BTG(
gencode_path='src/tests/gencode_example.csv',
operation='mean', extend=None)
bin_names = np.array([
'chr1:0-100', # 0
'chr1:101-200', # 1
'chr1:201-300', # 2
'chr2:0-100', # 3
'chr2:101-200', # 4
'chr2:201-300', # 5
'chr2:301-400', # 6
'chr3:0-100', # 7
'chr3:101-200', # 8
'chr3:201-300', # 9
'chr3:301-400', # 10
'chr3:401-500', # 11
'chr3:501-600' # 12
])
x = np.random.random((1000, len(bin_names)))
counts, ids = btg.convert(x, bin_names, prefix='chr')
ae(ids, ["gene" + str(i) for i in range(1, 8)])
ground_counts = np.zeros((1000, 7))
ground_counts[:, 0] += x[:, 0]
ground_counts[:, 1] += x[:, 1]
ground_counts[:, 2] += (x[:, 4] + x[:, 5]) / 2
ground_counts[:, 3] += (x[:, 3] + x[:, 4] + x[:, 5]) / 3
ground_counts[:, 4] += (x[:, 8] + x[:, 9]) / 2
ground_counts[:, 5] += x[:, 9:13].mean(axis=1)
ground_counts[:, 6] += x[:, 9:13].mean(axis=1)
aae(ground_counts, counts)
def test4(self):
b = BinToGene()
bin_list = [
Bin("s", 0, 10, 0),
Bin("s", 21, 30, 0),
Bin("s", 31, 40, 0),
Bin("s", 41, 50, 0),
Bin("s", 71, 90, 0)
]
result = b.binary_search(bin_list, 2, 13, True)
assert result == 0
result = b.binary_search(bin_list, 2, 13, False)
assert result == 0
result = b.binary_search(bin_list, 12, 22, True)
assert result == 1
result = b.binary_search(bin_list, 12, 22, False)
assert result == 1
result = b.binary_search(bin_list, 41, 62, True)
assert result == 3
result = b.binary_search(bin_list, 41, 62, False)
assert result == 3
result = b.binary_search(bin_list, 41, 92, False)
assert result == 4
result = b.binary_search(bin_list, 11, 20, True)
assert result == -1
result = b.binary_search(bin_list, 11, 20, False)
assert result == -1
result = b.binary_search(bin_list, 51, 60, True)
assert result == -1
result = b.binary_search(bin_list, 51, 60, False)
assert result == -1
def test1(self):
b = BinToGene()
bin_list = [
Bin("s", 0, 10, 0),
Bin("s", 11, 20, 0),
Bin("s", 21, 30, 0),
Bin("s", 31, 40, 0),
Bin("s", 41, 50, 0)
]
result = b.binary_search(bin_list, 2, 21, True)
assert result == 0
result = b.binary_search(bin_list, 12, 22, True)
assert result == 1
result = b.binary_search(bin_list, 22, 32, True)
assert result == 2
result = b.binary_search(bin_list, 32, 42, True)
assert result == 3
result = b.binary_search(bin_list, 42, 52, True)
assert result == 4
result = b.binary_search(bin_list, 12, 71, True)
assert result == 1
result = b.binary_search(bin_list, -10, 21, True)
assert result == 0
result = b.binary_search(bin_list, -10, 71, True)
assert result == 0
result = b.binary_search(bin_list, -20, -10, True)
assert result == -1
result = b.binary_search(bin_list, 61, 81, True)
assert result == -1