def test_invalid_migration():
with pytest.raises(ValueError) as e:
options = Option_Parser.admixture_option_parser()\
.parse_args(['-g', 'AU_AF_1.5e-5'])
Demography_Models.Base_demography(options).simulate(1)
assert 'AU not a known population' in str(e)
with pytest.raises(ValueError) as e:
options = Option_Parser.admixture_option_parser()\
.parse_args(['-g', 'EU_AF_NUMBER'])
Demography_Models.Base_demography(options).simulate(1)
assert 'could not convert' in str(e)
def test_write_f4dstats():
parser = Option_Parser.admixture_option_parser()
opts = parser.parse_args([])
with File_Printer.file_printer(opts) as fp:
ind = io.StringIO()
fp.writers['ind'] = ind
eigen = io.BytesIO()
fp.writers['eigen'] = eigen
snp = io.StringIO()
fp.writers['snp'] = snp
model = Demography_Models.Tenn_demography(opts)
sim = model.simulate(1)
Admixture_Simulation.write_f4dstats(sim, fp, model)
ind = ind.getvalue().split('\n')
assert ind[0] == 'Sample_0\tU\tNeand1'
assert ind[9] == 'Sample_9\tU\tEUR'
snp = snp.getvalue().split('\n')
snp0 = snp[0].split('\t')
assert snp0[0] == 'rs1'
assert snp0[1] == '1'
assert snp0[3] == '129'
assert snp0[4] == 'A'
assert snp0[5] == 'T'
snp9 = snp[9].split('\t')
assert snp9[0] == 'rs10'
assert snp9[1] == '1'
assert snp9[3] == '965'
assert snp9[4] == 'A'
assert snp9[5] == 'T'
def test_construction():
parser = Option_Parser.admixture_option_parser()
options = parser.parse_args([])
Demography_Models.Base_demography(options).simulate(1)
Demography_Models.Tenn_demography(options).simulate(1)
Demography_Models.Tenn_no_modern_migration(options).simulate(1)
Demography_Models.Tenn_pulsed_migration(options).simulate(1)
Demography_Models.Sriram_demography(options).simulate(1)
Demography_Models.SplitPop_demography(options).simulate(1)
with pytest.raises(NotImplementedError):
Demography_Models.Out_of_africa_demography(options).simulate(1)
def test_get_model():
parser = Option_Parser.admixture_option_parser()
opts = parser.parse_args([])
assert type(Admixture_Simulation.get_model(opts)) == \
Demography_Models.Tenn_demography
opts.model = "SplitPop"
assert type(Admixture_Simulation.get_model(opts)) == \
Demography_Models.SplitPop_demography
with pytest.raises(ValueError) as e:
opts.model = "NONE"
Admixture_Simulation.get_model(opts)
assert "unsupported model: NONE" in str(e)
def test_get_samples():
parser = Option_Parser.admixture_option_parser()
opts = parser.parse_args([])
samp = Admixture_Simulation.get_human_samples(opts)
assert samp == range(6, 2020)
opts.pop = "AFR"
samp = Admixture_Simulation.get_human_samples(opts)
assert samp == range(4, 6)
with pytest.raises(ValueError) as e:
opts.pop = "NONE"
samp = Admixture_Simulation.get_human_samples(opts)
assert "unknown human sample: NONE" in str(e)
def nonDefault():
parser = Option_Parser.admixture_option_parser()
options = parser.parse_args([
'-s',
'4',
'-n',
'0.003',
'-d',
'0.001',
'--Neand1_sample_size',
'3',
'--Neand2_sample_size',
'1',
'-t',
'450',
'--time_N1_sample',
'50',
'--time_N2_sample',
'120',
'-l',
'1e4',
'-e',
'1007',
'-a',
'1007',
'-r',
'3',
'-g',
'AF_EU_1.5e-5',
'-g',
'EU_AF_1.5e-5',
'-g',
'AF_AS_0.78e-5',
'-g',
'AS_AF_0.79e-5',
'-g',
'EU_AS_3.11e-5',
])
return Demography_Models.Base_demography(options)
def default():
parser = Option_Parser.admixture_option_parser()
options = parser.parse_args([])
return Demography_Models.Base_demography(options)
def parser():
return Option_Parser.admixture_option_parser()
def test_tree_running():
parser = Option_Parser.admixture_option_parser()
opts = parser.parse_args([])
sim = Demography_Models.Tenn_demography(opts).simulate(1)
entries = Admixture_Simulation.get_haplo_entries(next(sim), opts)
assert entries == {}