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_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 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_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_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)
log.log(
'The frequency file is unnecessary and is being ignored.'
)
args.frqfile = None
args.frqfile_chr = None
if args.overlap_annot and not args.not_M_5_50:
if not ((args.frqfile and args.ref_ld) or
(args.frqfile_chr and args.ref_ld_chr)):
raise ValueError(
'Must set either --frqfile and --ref-ld or --frqfile-chr and --ref-ld-chr'
)
if args.rg:
sumstats.estimate_rg(args, log)
elif args.h2:
sumstats.estimate_h2(args, log)
elif args.h2_cts:
sumstats.cell_type_specific(args, log)
# bad flags
else:
print header
print 'Error: no analysis selected.'
print 'ldsc.py -h describes options.'
except Exception:
ex_type, ex, tb = sys.exc_info()
log.log(traceback.format_exc(ex))
raise
finally:
log.log('Analysis finished at {T}'.format(T=time.ctime()))
time_elapsed = round(time.time() - start_time, 2)
if (args.samp_prev is not None) != (args.pop_prev is not None):
raise ValueError('Must set both or neither of --samp-prev and --pop-prev.')
if not args.overlap_annot or args.not_M_5_50:
if args.frqfile is not None or args.frqfile_chr is not None:
log.log('The frequency file is unnecessary and is being ignored.')
args.frqfile = None
args.frqfile_chr = None
if args.overlap_annot and not args.not_M_5_50:
if not ((args.frqfile and args.ref_ld) or (args.frqfile_chr and args.ref_ld_chr)):
raise ValueError ('Must set either --frqfile and --ref-ld or --frqfile-chr and --ref-ld-chr')
if args.rg:
sumstats.estimate_rg(args, log)
elif args.h2:
sumstats.estimate_h2(args, log)
# bad flags
else:
print header
print 'Error: no analysis selected.'
print 'ldsc.py -h describes options.'
except Exception:
ex_type, ex, tb = sys.exc_info()
log.log( traceback.format_exc(ex) )
raise
finally:
log.log('Analysis finished at {T}'.format(T=time.ctime()) )
time_elapsed = round(time.time()-start_time,2)
log.log('Total time elapsed: {T}'.format(T=sec_to_str(time_elapsed)))
