def tfunc_areabetween(self,
func_name: str,
f1: callable,
f2: callable,
are_intersects: bool = True,
maxerr: float = 0.001,
draw=False):
if (draw):
p_x = np.arange(0, 100)
p_y = f1(p_x) - f2(p_x)
plt.plot(p_x, p_y)
plt.show()
ass3 = Assignment3()
r = ass3.areabetween(f1, f2)
intersections = assignment2.Assignment2().intersections(f1, f2, 1, 100)
if ((not are_intersects)):
self.assertTrue(np.isnan(r))
if (len(intersections) < 2):
self.assertTrue(np.isnan(r))
else:
expect_area = 0
for i in range(0, len(intersections) - 1):
expect_area = expect_area + abs(
integrate.quad(lambda x: f1(x) - f2(x), intersections[i],
intersections[i + 1])[0])
# print(f"{expect_aera} {r}")
self.assertEqual(r.dtype, np.float32)
self.assertGreaterEqual(
maxerr, abs((r - expect_area) / expect_area),
f"\n{func_name}\n\t relative: {abs((r - expect_area) / expect_area)}\n\t actual {r}\n\t expect {expect_area}"
)
def tfunc_integrate(self,
func_name: str,
f1: callable,
s: float,
to: float,
n: int,
maxerr: float = 0.001,
draw=False):
if (draw):
p_x = np.arange(s * 1.1, to * 1.1, 0.1)
p_y = f1(p_x)
plt.plot(p_x, p_y)
plt.show()
expect_area = integrate.quad(lambda x: f1(x), s, to)
f1 = RESTRICT_INVOCATIONS(n)(f1)
ass3 = Assignment3()
r = ass3.integrate(f1, s, to, n)
# print(integrate.simps(f1(points), points))
# print(f"{expect_aera} {r}")
self.assertEqual(r.dtype, np.float32)
self.assertGreaterEqual(maxerr,
abs((r - expect_area[0]) / expect_area[0]),
f"{func_name}, {r}, {expect_area}")
def test_get_list_of_genes():
a3 = Assignment3()
assert os.path.exists(
"annotation_result.json"), "The annotation JSON file does not exist"
assert a3.get_list_of_genes() == 21 or len(a3.get_list_of_genes()) == 21
def test_get_number_of_annotated_variants():
a3 = Assignment3()
assert a3.get_number_of_annotated_variants() == 900
def test_view_vcf_in_browser():
a3 = Assignment3()
assert os.path.exists(
"annotation_result.json"), "The annotation JSON file does not exist"
assert "vcf.iobio.io" in a3.view_vcf_in_browser()
def test_get_num_variants_with_mutationtaster_annotation():
a3 = Assignment3()
assert os.path.exists(
"annotation_result.json"), "The annotation JSON file does not exist"
assert a3.get_num_variants_with_mutationtaster_annotation() == 5
def test_get_num_variants_modifier():
a3 = Assignment3()
assert os.path.exists(
"annotation_result.json"), "The annotation JSON file does not exist"
assert a3.get_num_variants_modifier() == 67
def test_integrate_float32(self):
ass3 = Assignment3()
f1 = np.poly1d([-1, 0, 1])
r = ass3.integrate(f1, -1, 1, 10)
self.assertEqual(r.dtype, np.float32)