def test_array_to_bedgraph_span_zeros(self):
a = np.zeros((10000,1), dtype=np.float)
output, filename = make_temp()
array_to_bedgraph('chr1', a, output, span=1)
contents = getvalue(output)
self.assertTrue(np.array_equal(contents['chr1'], a[:,0]))
os.remove(filename)
def test_array_to_bedgraph_consecutive(self):
a = np.arange(0, 100, dtype=np.float)
a.resize((a.shape[0],1))
output, filename = make_temp()
array_to_bedgraph('chr1', a, output)
contents = getvalue(output)
self.assertTrue(np.array_equal(contents['chr1'], a[:,0]))
os.remove(filename)
def test_array_to_bedgraph_zeros(self):
a = np.array([0, 0, 0, 0, 0])
a.resize((a.shape[0],1))
output, filename = make_temp()
array_to_bedgraph('chr1', a, output)
contents = getvalue(output)
self.assertTrue(np.array_equal(contents['chr1'], a[:,0]))
os.remove(filename)
def test_array_to_bedgraph_sparse_spans(self):
a = np.zeros((10000,1), dtype=np.float)
a[6655] = 100
# check that spans work too
output, filename = make_temp()
array_to_bedgraph('chr1', a, output, span=10)
contents = getvalue(output)
correct = np.zeros(10000, dtype=np.float)
correct[6650:6660] = 10
self.assertTrue(np.array_equal(contents['chr1'], correct))
os.remove(filename)
def test_array_to_bedgraph_span_jumps(self):
a = np.array([0, 0, 2, 2, 0, 0, 4, 4, 0, 0, 0, 0, 10, 10, 10, 10], dtype=np.float)
a.resize((a.shape[0],1))
# span of 2
output, filename = make_temp()
array_to_bedgraph('chr1', a, output, span=2)
contents = getvalue(output)
self.assertTrue(np.array_equal(contents['chr1'], a[:,0]))
os.remove(filename)
# span of 4
output, filename = make_temp()
array_to_bedgraph('chr1', a, output, span=4)
contents = getvalue(output)
correct = np.array([1, 1, 1, 1, 2, 2, 2, 2, 0, 0, 0, 0, 10, 10, 10, 10])
self.assertTrue(np.array_equal(contents['chr1'], correct))
os.remove(filename)
def test_array_dtypes(self):
# float
a = np.array([1.25, 2.01, 3.98, 10.1, 4.02], dtype=np.float32)
a.resize((a.shape[0],1))
output, filename = make_temp()
array_to_bedgraph('chr1', a, output)
contents = getvalue(output)
self.assertTrue(np.array_equal(contents['chr1'], a[:,0]))
os.remove(filename)
# int
b = np.array([1.25, 2.01, 3.98, 10.1, 4.02], dtype=np.int32)
b.resize((b.shape[0],1))
bcorrect = np.array([1, 2, 3, 10, 4], dtype=np.int32)
bcorrect.resize((b.shape[0],1))
output, filename = make_temp()
array_to_bedgraph('chr1', b, output)
contents = getvalue(output)
self.assertTrue(np.array_equal(contents['chr1'], bcorrect[:,0]))
os.remove(filename)