def test_remove_reaction_duplicates_V_shape(self):
N = np.array([[1, 2, 0, -1],
[0, 0, 1, 0],
[-2, -4, -1, 2]])
V = np.array([[-1, 0],
[1, 1],
[0, -1],
[2, -1]])
r_id2i = {'r1': 0, 'r2': 1, 'r3': 2, 'r4': 3}
r_duplicates = get_reaction_duplicates(N, r_id2i)
N_new, V_new, new_r_id2i, r_id2gr_id, _ = remove_reaction_duplicates(N, V, r_duplicates, r_id2i)
self.assertTupleEqual((2, 2), V_new.shape,
'Was supposed to get 2x2 V, got %s' % [str(it) for it in V_new.shape])
def test_remove_reaction_duplicates_NV(self):
N = np.array([[1, 2, 0, -1],
[0, 0, 1, 0],
[-2, -4, -1, 2]])
V = np.array([[-1, 0],
[1, 1],
[0, -1],
[2, -1]])
r_id2i = {'r1': 0, 'r2': 1, 'r3': 2, 'r4': 3}
r_duplicates = get_reaction_duplicates(N, r_id2i)
N_new, V_new, new_r_id2i, r_id2gr_id, _ = remove_reaction_duplicates(N, V, r_duplicates, r_id2i)
NV = np.dot(N, V)
NV_new = np.dot(N_new, V_new)
self.assertListEqual(list(NV.flatten()), list(NV_new.flatten()), 'NV was not supposed to change')
def test_remove_reaction_duplicates_N_content_1(self):
N = np.array([[1, 2, 0, -1],
[0, 0, 1, 0],
[-2, -4, -1, 2]])
V = np.array([[-1, 0],
[1, 1],
[0, -1],
[2, -1]])
r_id2i = {'r1': 0, 'r2': 1, 'r3': 2, 'r4': 3}
r_duplicates = get_reaction_duplicates(N, r_id2i)
N_new, V_new, new_r_id2i, r_id2gr_id, _ = remove_reaction_duplicates(N, V, r_duplicates, r_id2i)
m2_st = N[1, new_r_id2i[r_id2gr_id['r1']]]
self.assertEqual(0, m2_st,
'Was supposed to find no metabolite m2 in the grouped reaction, found %g' % m2_st)
def test_remove_reaction_duplicates_N_content_2(self):
N = np.array([[1, 2, 0, -1],
[0, 0, 1, 0],
[-2, -4, -1, 2]])
V = np.array([[-1, 0],
[1, 1],
[0, -1],
[2, -1]])
r_id2i = {'r1': 0, 'r2': 1, 'r3': 2, 'r4': 3}
r_duplicates = get_reaction_duplicates(N, r_id2i)
N_new, V_new, new_r_id2i, r_id2gr_id, _ = remove_reaction_duplicates(N, V, r_duplicates, r_id2i)
new_r_index = new_r_id2i[r_id2gr_id['r1']]
m1_st = N[0, new_r_index]
m3_st = N[2, new_r_index]
self.assertEqual(-2, m3_st / m1_st,
'Was supposed to get -2 as a proportion between m3 and m1 in the new reaction, found %g'
% (m3_st / m1_st))
def test_remove_reaction_duplicates_V_content(self):
N = np.array([[1, 2, 0, -1],
[0, 0, 1, 0],
[-2, -4, -1, 2]])
V = np.array([[-1, 0],
[1, 1],
[0, -1],
[2, -1]])
r_id2i = {'r1': 0, 'r2': 1, 'r3': 2, 'r4': 3}
r_duplicates = get_reaction_duplicates(N, r_id2i)
N_new, V_new, new_r_id2i, r_id2gr_id, _ = remove_reaction_duplicates(N, V, r_duplicates, r_id2i)
new_r_index = new_r_id2i[r_id2gr_id['r1']]
efm1_c = V_new[new_r_index, 0]
efm2_c = V_new[new_r_index, 1]
ratio = efm2_c / efm1_c
self.assertEqual(-3, ratio,
'Was supposed to get -3 as a ratio between the coefficients of the grouped reaction in EFMs 2 and 1, got %g'
% ratio)