def test_merge_genotypes(self):
expected = dict(X=dict(A=('1', '1'), B=('1', '2'), C=('2', '2')),
Y=dict(A=('1', '1'), D=('1', '2'), E=('2', '2')))
one = io.Genotype()
one.add('X', ['A', 'B', 'C'], [('1', '1'), ('1', '2'), ('2', '2')])
other = io.Genotype()
other.add('Y', ['A', 'D', 'E'], [('1', '1'), ('1', '2'), ('2', '2')])
one.merge(other)
assert one.n_loci == 5
assert one.n_samples == 2
for sample, geno in one:
assert sample in expected
assert geno == expected[sample]
def test_add_unique_loci(self):
genotype = io.Genotype()
loci = ["A", "B", "C", "D"]
genotype.add_loci(loci)
genotype.add_loci(loci)
assert genotype.n_loci == 4
def test_add_loci(self):
genotype = io.Genotype()
loci = ["A", "B", "C", "D"]
genotype.add_loci(loci)
# Check includes all
for locus in loci:
assert locus in genotype.loci
def test_combine(self):
expected = dict(X=dict(A=('1', '1'), B=('1', '2'), C=('2', '2')),
Y=dict(A=('1', '1'), D=('1', '2'), E=('2', '2')))
one = io.Genotype()
one.add('X', ['A', 'B', 'C'], [('1', '1'), ('1', '2'), ('2', '2')])
other = io.Genotype()
other.add('Y', ['A', 'D', 'E'], [('1', '1'), ('1', '2'), ('2', '2')])
merged = io.Genotype.combine(one, other)
# Check for side effects
assert one.n_loci == 3 and other.n_loci == 3
assert one.n_samples == 1 and other.n_samples == 1
assert merged.n_loci == 5
assert merged.n_samples == 2
for sample, geno in merged:
assert sample in expected
assert geno == expected[sample]
def test_add(self):
genotype = io.Genotype()
sample = "S0"
loci = ["A", "B", "C", "D"]
data = [[0, 1], [0, 2], [0, 1], [0, 2]]
genotype.add(sample, loci, data)
assert genotype.n_samples == 1
assert genotype.n_loci == 4
def test_write(self):
genotype = io.Genotype()
loci = ["A", "B", "C", "D", "E"]
genotype.add("X", loci, [('1', '1'), ('1', '1'), ('2', '2'),
('1', '2'), ('-9', '-9')])
genotype.add("Y", loci, [('2', '2'), ('1', '1'), ('1', '2'),
('-9', '-9'), ('1', '2')])
stream = StringIO("")
expected = "".join(STR_STREAM)
genotype.write(stream)
assert stream.getvalue() == expected
def test_iterate_genotypes(self):
genotype = io.Genotype()
name = "S0"
loci = ["A", "B", "C", "D"]
data = [[1, 1], [1, 2], [1, 1], [2, 2]]
genotype.add(name, loci, data)
count = 0
for sample, genotype in genotype:
assert sample == name # assert sample is the given
assert genotype == dict(A=[1, 1], B=[1, 2], C=[1, 1], D=[2, 2])
count += 1
assert count == 1 # Iterates over one item
def test_create_empty(self):
genotype = io.Genotype()
assert genotype.n_loci == 0
assert genotype.n_samples == 0
def test_create_empty(self):
reference = io.Reference(io.Genotype(), [], [])
assert reference.genotype.n_loci == 0
assert reference.genotype.n_samples == 0
assert reference.groups == []
assert reference.ranges == []
def test_merge_genotype_raises_error(self):
genotype = io.Genotype()
with pytest.raises(ValueError):
genotype.merge(1)