def test_load_hut_and_recode(self):
"""Load hutterites pedigree from file; recode to consecutive IDs based on a genotyped
ID list."""
p = itu.read_pedigree_from_test_file(itu.HUTT_PED, genotyped_id_file=itu.GENOTYPE_SAMPLE + ".tfam")
assert_equal(p.graph.number_of_edges(), 7200, "Incorrect number of edges")
assert_equal(p.n, 3671, "Incorrect number of nodes")
assert_equal(p.graph.nodes(), range(0, p.n), "Incorrect node IDs")
def test_load_hut(self):
'''Load hutterites pedigree from file.'''
# Load data from text file to compare with the load result
p = itu.read_pedigree_from_test_file(itu.HUTT_PED)
assert_equal(p.graph.number_of_edges(), 7200,
'Incorrect number of edges')
assert_equal(p.n, 3671, 'Incorrect number of nodes')
def test_matrices(self):
'''Test adjacency and Laplacian matrix computation.'''
# Load data from text file to compare with the load result
p = itu.read_pedigree_from_test_file(itu.HUTT_PED)
A = sym_adjacency(p.graph)
L = laplacian(p.graph)
assert not np.nonzero(A-A.T)[0], 'Adjacency matrix returned from sym_adjacency() should be symmetric'
assert not np.nonzero(L-L.T)[0], 'Laplacian matrix should be symmetric'
assert (abs(L.sum(axis=1)) < 1e-8).all(), 'Laplacian matrix should be zero-row-sum'
def test_load_hut_and_recode(self):
'''Load hutterites pedigree from file; recode to consecutive IDs based on a genotyped
ID list.'''
p = itu.read_pedigree_from_test_file(
itu.HUTT_PED, genotyped_id_file=itu.GENOTYPE_SAMPLE + '.tfam')
assert_equal(p.graph.number_of_edges(), 7200,
'Incorrect number of edges')
assert_equal(p.n, 3671, 'Incorrect number of nodes')
assert_equal(p.graph.nodes(), range(0, p.n), 'Incorrect node IDs')
def test_matrices(self):
'''Test adjacency and Laplacian matrix computation.'''
# Load data from text file to compare with the load result
p = itu.read_pedigree_from_test_file(itu.HUTT_PED)
A = sym_adjacency(p.graph)
L = laplacian(p.graph)
assert not np.nonzero(
A - A.T
)[0], 'Adjacency matrix returned from sym_adjacency() should be symmetric'
assert not np.nonzero(L -
L.T)[0], 'Laplacian matrix should be symmetric'
assert (abs(L.sum(axis=1)) <
1e-8).all(), 'Laplacian matrix should be zero-row-sum'
def test_load_hut(self):
"""Load hutterites pedigree from file."""
# Load data from text file to compare with the load result
p = itu.read_pedigree_from_test_file(itu.HUTT_PED)
assert_equal(p.graph.number_of_edges(), 7200, "Incorrect number of edges")
assert_equal(p.n, 3671, "Incorrect number of nodes")
