def test_get_single(self):
lateral_map = MapLateral(self.ham_analysis)
map_human_euarc = HOGsMap(self.ham_analysis, self.human,
self.euarchontoglires)
self.assertTrue(map_human_euarc.consistent)
lateral_map.add_map(map_human_euarc)
map_rat_euarc = HOGsMap(self.ham_analysis, self.rat,
self.euarchontoglires)
self.assertTrue(map_rat_euarc.consistent)
lateral_map.add_map(map_rat_euarc)
single = lateral_map.get_retained()
for hog in single.keys():
if str(hog) == "<HOG(3.E.1)>":
H3_E_1 = hog
elif str(hog) == "<HOG(1.M.E)>":
H1_M_E = hog
elif str(hog) == "<HOG(2.E)>":
H2_E = hog
self.assertDictEqual({str(self.human): "Gene(3)"},
_str_dict_one_value(single[H3_E_1]))
self.assertDictEqual(
{
str(self.human): "Gene(1)",
str(self.rat): "Gene(41)"
}, _str_dict_one_value(single[H1_M_E]))
self.assertDictEqual({str(self.human): "Gene(2)"},
_str_dict_one_value(single[H2_E]))
def test_get_lost(self):
lateral_map = MapLateral(self.ham_analysis)
map_human_euarc = HOGsMap(self.ham_analysis, self.human,
self.euarchontoglires)
self.assertTrue(map_human_euarc.consistent)
lateral_map.add_map(map_human_euarc)
map_rat_euarc = HOGsMap(self.ham_analysis, self.rat,
self.euarchontoglires)
self.assertTrue(map_rat_euarc.consistent)
lateral_map.add_map(map_rat_euarc)
loss = lateral_map.get_lost()
for hog in loss.keys():
if str(hog) == "<HOG(3.E.2)>":
H3_E_2 = hog
elif str(hog) == "<HOG(3.E.1)>":
H3_E_1 = hog
elif str(hog) == "<HOG(2.E)>":
H2_E = hog
self.assertEqual({self.rat}, set(loss[H2_E]))
self.assertEqual({self.rat}, set(loss[H3_E_1]))
self.assertEqual({self.rat, self.human}, set(loss[H3_E_2]))
# trying if lazy property work
loss2 = lateral_map.get_lost()
self.assertEqual({self.rat}, set(loss2[H2_E]))
self.assertEqual({self.rat}, set(loss2[H3_E_1]))
self.assertEqual({self.rat, self.human}, set(loss2[H3_E_2]))
def test_can_only_add_HOGMAP_as_map(self):
lateral_map = MapLateral(self.ham_analysis)
with self.assertRaises(TypeError):
lateral_map.add_map("111")
with self.assertRaises(TypeError):
lateral_map.add_map("")
def test_cannot_add_map_with_different_ancestor(self):
lateral_map = MapLateral(self.ham_analysis)
map = HOGsMap(self.ham_analysis, self.human, self.euarchontoglires)
self.assertTrue(map.consistent)
lateral_map.add_map(map)
map2 = HOGsMap(self.ham_analysis, self.human, self.vertebrates)
self.assertTrue(map2.consistent)
with self.assertRaises(TypeError):
lateral_map.add_map(map2)
def test_create_correctly_lateral_map(self):
lateral_map = MapLateral(self.ham_analysis)
map = HOGsMap(self.ham_analysis, self.human, self.euarchontoglires)
self.assertTrue(map.consistent)
lateral_map.add_map(map)
map2 = HOGsMap(self.ham_analysis, self.rodents, self.euarchontoglires)
self.assertTrue(map2.consistent)
lateral_map.add_map(map2)
self.assertEqual(self.euarchontoglires, lateral_map.ancestor)
self.assertEqual([self.human, self.rodents], lateral_map.descendants)
self.assertEqual(self.ham_analysis, lateral_map.HAM)
def test_get_gained(self):
lateral_map = MapLateral(self.ham_analysis)
map_frog_vertebrate = HOGsMap(self.ham_analysis, self.frog,
self.vertebrates)
self.assertTrue(map_frog_vertebrate.consistent)
lateral_map.add_map(map_frog_vertebrate)
map_human_euarc = HOGsMap(self.ham_analysis, self.human,
self.vertebrates)
self.assertTrue(map_human_euarc.consistent)
lateral_map.add_map(map_human_euarc)
gain = lateral_map.get_gained()
self.assertEqual(set(), set(_str_array(gain[self.frog])))
self.assertEqual({"Gene(2)", "Gene(5)"},
set(_str_array(gain[self.human])))
def test_get_duplicated(self):
lateral_map = MapLateral(self.ham_analysis)
map_human_vert = HOGsMap(self.ham_analysis, self.human,
self.vertebrates)
self.assertTrue(map_human_vert.consistent)
lateral_map.add_map(map_human_vert)
map_mouse_vert = HOGsMap(self.ham_analysis, self.mouse,
self.vertebrates)
self.assertTrue(map_mouse_vert.consistent)
lateral_map.add_map(map_mouse_vert)
duplicate = lateral_map.get_duplicated()
for hog in duplicate.keys():
if str(hog) == "<HOG(3)>":
H = hog
self.assertDictEqual(
{
str(self.human): {"Gene(3)"},
str(self.mouse): {'Gene(33)', 'Gene(34)'}
}, _str_dict_array_value(duplicate[H]))