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")