def test_select_samples(self): '''Create sub-problem by selecting samples/family..''' p = io.read_npz(itu.FAMILY13_STAGE3) f = p.families()[0] ps = p.sub_problem(f.member_list) pf = p.sub_problem_of_parents(f.father, f.mother) # pf has family_info entry, ps doesn't assert_equal(ps.pedigree.graph.nodes(), pf.pedigree.graph.nodes(), 'Incorrect pedigree graph nodes') assert_equal(set(ps.pedigree.graph.edges()), set(pf.pedigree.graph.edges()), 'Incorrect pedigree graph edges') assert_equal(ps.pedigree.sample_id.tolist(), pf.pedigree.sample_id.tolist(), 'Incorrect pedigree sample ID array') assert_equal(ps.pedigree, pf.pedigree, 'Incorrect pedigree') assert_equal(ps.genotype, pf.genotype, 'Incorrect genotype') assert_equal(ps.haplotype, pf.haplotype, 'Incorrect haplotype') self.assertTrue(ps.info.family_info != pf.info.family_info, 'Incorrect info family') assert_not_equal(ps.info, pf.info, 'Incorrect info') assert_not_equal(ps, pf, 'pf should have a family_info entry, ps shouldn' 't')
def testMatrixDecompose(self): matrix = Matrix("[1,2;3,4]") assert (matrix.decompose() == None) assert_not_equal(matrix.decompose('D'), matrix.decompose('U')) assert_equal(matrix.decompose('D'), Matrix('[1,0;0,4]')) assert_equal(matrix.decompose('U'), Matrix('[0,2;0,0]')) assert_equal(matrix.decompose('L'), Matrix('[0,0;3,0]')) assert_equal(matrix.decompose('LU'), Matrix('[0,2;3,0]')) assert_equal(matrix.decompose('DL'), Matrix('[1,0;3,4]'))
def test_select_samples(self): '''Create sub-problem by selecting samples/family..''' p = io.read_npz(itu.FAMILY13_STAGE3) f = p.families()[0] ps = p.sub_problem(f.member_list) pf = p.sub_problem_of_parents(f.father, f.mother) # pf has family_info entry, ps doesn't assert_equal(ps.pedigree.graph.nodes(), pf.pedigree.graph.nodes(), 'Incorrect pedigree graph nodes') assert_equal(set(ps.pedigree.graph.edges()), set(pf.pedigree.graph.edges()), 'Incorrect pedigree graph edges') assert_equal(ps.pedigree.sample_id.tolist(), pf.pedigree.sample_id.tolist(), 'Incorrect pedigree sample ID array') assert_equal(ps.pedigree, pf.pedigree, 'Incorrect pedigree') assert_equal(ps.genotype, pf.genotype, 'Incorrect genotype') assert_equal(ps.haplotype, pf.haplotype, 'Incorrect haplotype') self.assertTrue(ps.info.family_info != pf.info.family_info, 'Incorrect info family') assert_not_equal(ps.info, pf.info, 'Incorrect info') assert_not_equal(ps, pf, 'pf should have a family_info entry, ps shouldn''t')