def setUpClass(cls): args = parser.parse_args('') args.ref_ld = DIR + '/simulate_test/ldscore/twold_onefile' args.w_ld = DIR + '/simulate_test/ldscore/w' args.rg = ','.join( (DIR + '/simulate_test/sumstats/' + str(i) for i in xrange(N_REP))) args.out = DIR + '/simulate_test/1' x = s.estimate_rg(args, log) args.intercept_gencov = ','.join(('0' for _ in xrange(N_REP))) args.intercept_h2 = ','.join(('1' for _ in xrange(N_REP))) y = s.estimate_rg(args, log) cls.rg = x cls.rg_noint = y
def test_no_check_alleles(self): args = parser.parse_args('') args.ref_ld = DIR + '/simulate_test/ldscore/oneld_onefile' args.w_ld = DIR + '/simulate_test/ldscore/w' args.rg = ','.join( [DIR + '/simulate_test/sumstats/1' for _ in xrange(2)]) args.out = DIR + '/simulate_test/1' x = s.estimate_rg(args, log)[0] args.no_check_alleles = True y = s.estimate_rg(args, log)[0] assert_equal(x.rg_ratio, y.rg_ratio) assert_almost_equal(x.rg_jknife, y.rg_jknife) assert_equal(x.rg_se, y.rg_se)
def test_twostep_rg(self): # make sure two step isn't going crazy args = parser.parse_args('') args.ref_ld_chr = DIR + '/simulate_test/ldscore/oneld_onefile' args.w_ld = DIR + '/simulate_test/ldscore/w' args.rg = ','.join( [DIR + '/simulate_test/sumstats/1' for _ in xrange(2)]) args.out = DIR + '/simulate_test/rg' args.two_step = 999 x = s.estimate_rg(args, log)[0] args.two_step = 99999 y = s.estimate_rg(args, log)[0] assert_allclose(x.rg_ratio, y.rg_ratio, atol=1e-5) assert_allclose(x.gencov.tot, y.gencov.tot, atol=1e-5)
def test_twostep_h2(self): # make sure two step isn't going crazy args = parser.parse_args('') args.ref_ld = DIR + '/simulate_test/ldscore/oneld_onefile' args.w_ld = DIR + '/simulate_test/ldscore/w' args.h2 = DIR + '/simulate_test/sumstats/1' args.out = DIR + '/simulate_test/1' args.chisq_max = 9999999 args.two_step = 999 x = s.estimate_h2(args, log) args.chisq_max = 9999 args.two_step = 99999 y = s.estimate_h2(args, log) assert_allclose(x.tot, y.tot, atol=1e-5)
def test_rg_M(self): args = parser.parse_args('') args.ref_ld = DIR + '/simulate_test/ldscore/oneld_onefile' args.w_ld = DIR + '/simulate_test/ldscore/w' args.rg = ','.join( [DIR + '/simulate_test/sumstats/1' for _ in xrange(2)]) args.out = DIR + '/simulate_test/1' x = s.estimate_rg(args, log)[0] args.M = open(DIR + '/simulate_test/ldscore/oneld_onefile.l2.M_5_50', 'rb').read().rstrip('\n') y = s.estimate_rg(args, log)[0] assert_array_almost_equal(x.rg_ratio, y.rg_ratio) assert_array_almost_equal(x.rg_se, y.rg_se) args.M = '1,2' assert_raises(ValueError, s.estimate_rg, args, log) args.M = 'foo_bar' assert_raises(ValueError, s.estimate_rg, args, log)
def setUpClass(cls): args = parser.parse_args('') args.ref_ld = DIR + '/simulate_test/ldscore/twold_onefile' args.w_ld = DIR + '/simulate_test/ldscore/w' args.chisq_max = 99999 h2 = [] h2_noint = [] for i in xrange(N_REP): args.intercept_h2 = None args.h2 = DIR + '/simulate_test/sumstats/' + str(i) args.out = DIR + '/simulate_test/1' h2.append(s.estimate_h2(args, log)) args.intercept_h2 = 1 h2_noint.append(s.estimate_h2(args, log)) cls.h2 = h2 cls.h2_noint = h2_noint
def test_rg_M(self): args = parser.parse_args('') args.ref_ld = DIR + '/simulate_test/ldscore/oneld_onefile' args.w_ld = DIR + '/simulate_test/ldscore/w' args.rg = ','.join( [DIR + '/simulate_test/sumstats/1' for _ in xrange(2)]) args.out = DIR + '/simulate_test/1' x = s.estimate_rg(args, log)[0] args.M = open( DIR + '/simulate_test/ldscore/oneld_onefile.l2.M_5_50', 'rb').read().rstrip('\n') y = s.estimate_rg(args, log)[0] assert_array_almost_equal(x.rg_ratio, y.rg_ratio) assert_array_almost_equal(x.rg_se, y.rg_se) args.M = '1,2' assert_raises(ValueError, s.estimate_rg, args, log) args.M = 'foo_bar' assert_raises(ValueError, s.estimate_rg, args, log)
def test_h2_M(self): # check --M works args = parser.parse_args('') args.ref_ld = DIR + '/simulate_test/ldscore/oneld_onefile' args.w_ld = DIR + '/simulate_test/ldscore/w' args.h2 = DIR + '/simulate_test/sumstats/1' args.out = DIR + '/simulate_test/1' args.print_cov = True # right now just check no runtime errors args.print_delete_vals = True x = s.estimate_h2(args, log) args.M = str( float(open(DIR + '/simulate_test/ldscore/oneld_onefile.l2.M_5_50').read())) y = s.estimate_h2(args, log) assert_array_almost_equal(x.tot, y.tot) assert_array_almost_equal(x.tot_se, y.tot_se) args.M = '1,2' assert_raises(ValueError, s.estimate_h2, args, log) args.M = 'foo_bar' assert_raises(ValueError, s.estimate_h2, args, log)
def test_rg_ref_ld(self): args = parser.parse_args('') args.ref_ld_chr = DIR + '/simulate_test/ldscore/twold_onefile' args.w_ld = DIR + '/simulate_test/ldscore/w' args.rg = ','.join( [DIR + '/simulate_test/sumstats/1' for _ in xrange(2)]) args.out = DIR + '/simulate_test/1' args.print_cov = True # right now just check no runtime errors args.print_delete_vals = True x = s.estimate_rg(args, log)[0] args.ref_ld = DIR + '/simulate_test/ldscore/twold_firstfile,' + \ DIR + '/simulate_test/ldscore/twold_secondfile' y = s.estimate_rg(args, log)[0] args.ref_ld_chr = DIR + '/simulate_test/ldscore/twold_firstfile,' + \ DIR + '/simulate_test/ldscore/twold_secondfile' z = s.estimate_rg(args, log)[0] assert_almost_equal(x.rg_ratio, y.rg_ratio) assert_almost_equal(y.rg_jknife, z.rg_jknife) assert_almost_equal(x.rg_se, y.rg_se)
def test_h2_ref_ld(self): # test different ways of reading ref ld args = parser.parse_args('') args.ref_ld_chr = DIR + '/simulate_test/ldscore/twold_onefile' args.w_ld = DIR + '/simulate_test/ldscore/w' args.h2 = DIR + '/simulate_test/sumstats/555' args.out = DIR + '/simulate_test/' x = s.estimate_h2(args, log) args.ref_ld = DIR + '/simulate_test/ldscore/twold_firstfile,' + \ DIR + '/simulate_test/ldscore/twold_secondfile' y = s.estimate_h2(args, log) args.ref_ld_chr = DIR + '/simulate_test/ldscore/twold_firstfile,' + \ DIR + '/simulate_test/ldscore/twold_secondfile' z = s.estimate_h2(args, log) assert_almost_equal(x.tot, y.tot) assert_array_almost_equal(y.cat, z.cat) assert_array_almost_equal(x.prop, y.prop) assert_array_almost_equal(y.coef, z.coef) assert_array_almost_equal(x.tot_se, y.tot_se) assert_array_almost_equal(y.cat_se, z.cat_se) assert_array_almost_equal(x.prop_se, y.prop_se) assert_array_almost_equal(y.coef_se, z.coef_se)