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_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 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_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_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 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_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_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)
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)
