def test_mendelian_from_ivan_2():
# AC AA AC mendel
assert FV.check_mendelian_trio(np.array([0, 1]), np.array([0, 0]),
np.array([0, 1]), 0)
assert FV.check_mendelian_trio(np.array([0, 1]), np.array([0, 0]),
np.array([0, 1]), 1)
def test_weird_mendel_from_ivan_4():
# AC AT CT mendel
assert not FV.check_mendelian_trio(np.array([0, 1]), np.array([0, 2]),
np.array([1, 2]), 0)
assert FV.check_mendelian_trio(np.array([0, 1]), np.array([0, 2]),
np.array([1, 2]), 1)
assert FV.check_mendelian_trio(np.array([0, 1]), np.array([0, 2]),
np.array([1, 2]), 2)
def test_denovo_check_5():
# GG, GG -> AC
assert FV.check_denovo_trio(np.array([2, 2]), np.array([2, 2]),
np.array([0, 1]), 0)
assert FV.check_denovo_trio(np.array([2, 2]), np.array([2, 2]),
np.array([0, 1]), 1)
assert not FV.check_denovo_trio(np.array([2, 2]), np.array([2, 2]),
np.array([0, 1]), 2)
def test_denovo_check_6():
# CC,CC -> GC
assert FV.check_denovo_trio(np.array([1, 1]), np.array([1, 1]),
np.array([2, 1]), 2)
assert not FV.check_denovo_trio(np.array([1, 1]), np.array([1, 1]),
np.array([2, 1]), 1)
assert not FV.check_denovo_trio(np.array([1, 1]), np.array([1, 1]),
np.array([2, 1]), 0)
def test_omission_check_1():
# CC, AA -> AA
assert FV.check_omission_trio(np.array([1, 1]), np.array([0, 0]),
np.array([0, 0]), 1)
assert not FV.check_omission_trio(np.array([1, 1]), np.array([0, 0]),
np.array([0, 0]), 0)
assert not FV.check_denovo_trio(np.array([1, 1]), np.array([0, 0]),
np.array([0, 0]), 0)
assert not FV.check_denovo_trio(np.array([1, 1]), np.array([0, 0]),
np.array([0, 0]), 1)
def test_omission_and_denovo():
# AA,CC -> AA
trio = [
np.array([1, 1]), # p1
np.array([1, 1]), # p2
np.array([0, 1]), # ch
]
# FIXME:
assert not FA.check_omission_trio(*trio, allele_index=1)
# assert not FA.check_denovo_trio(*trio, allele_index=0)
# assert FA.check_mendelian_trio(*trio, allele_index=0)
assert FA.check_denovo_trio(*trio, allele_index=0)
def test_mixed_check_1():
# AA,CC -> GG
trio = [
np.array([1, 1]),
np.array([0, 0]),
np.array([2, 2]),
]
assert not FV.check_denovo_trio(*trio, allele_index=0)
assert not FV.check_denovo_trio(*trio, allele_index=1)
assert FV.check_denovo_trio(*trio, allele_index=2)
assert FV.check_omission_trio(*trio, allele_index=0)
assert FV.check_omission_trio(*trio, allele_index=1)
assert not FV.check_omission_trio(*trio, allele_index=2)
assert not FV.check_mendelian_trio(*trio, allele_index=0)
assert not FV.check_mendelian_trio(*trio, allele_index=1)
assert not FV.check_mendelian_trio(*trio, allele_index=2)
def test_mixed_check_4():
# AA,CC -> AG
trio = [
np.array([1, 1]), # p1
np.array([0, 0]), # p2
np.array([0, 2]), # ch
]
assert not FV.check_denovo_trio(*trio, allele_index=0)
assert not FV.check_denovo_trio(*trio, allele_index=1)
assert FV.check_denovo_trio(*trio, allele_index=2)
assert not FV.check_omission_trio(*trio, allele_index=0)
assert FV.check_omission_trio(*trio, allele_index=1)
assert not FV.check_omission_trio(*trio, allele_index=2)
assert FV.check_mendelian_trio(*trio, allele_index=0)
assert not FV.check_mendelian_trio(*trio, allele_index=1)
assert not FV.check_mendelian_trio(*trio, allele_index=2)
def test_allele_best_state(
chromosome,
position,
reference,
alternative,
allele_index,
allele_count,
genotype,
expected,
sample_family,
):
fa = FamilyAllele(
SummaryAllele(
chromosome, position, reference, alternative, 0, allele_index, {},
),
sample_family,
genotype,
None,
)
fa.update_attributes({"allele_count": allele_count})
assert np.array_equal(fa.best_state, expected)
def test_super_weird_denovo_omission_mix_from_ivan_2():
# AA AC TG denovo
trio = [
np.array([0, 0]),
np.array([0, 1]),
np.array([2, 3]),
]
assert FV.check_omission_trio(*trio, allele_index=0)
assert not FV.check_omission_trio(*trio, allele_index=1)
assert not FV.check_omission_trio(*trio, allele_index=2)
assert not FV.check_omission_trio(*trio, allele_index=3)
assert not FV.check_denovo_trio(*trio, allele_index=0)
assert not FV.check_denovo_trio(*trio, allele_index=1)
assert FV.check_denovo_trio(*trio, allele_index=2)
assert FV.check_denovo_trio(*trio, allele_index=3)
def test_weird_denovo_from_ivan_1_4():
# AC AA GA denovo
assert FV.check_denovo_trio(np.array([0, 1]), np.array([0, 0]),
np.array([2, 0]), 2)
assert not FV.check_denovo_trio(np.array([0, 1]), np.array([0, 0]),
np.array([2, 0]), 0)
assert not FV.check_denovo_trio(np.array([0, 1]), np.array([0, 0]),
np.array([2, 0]), 1)
assert not FV.check_omission_trio(np.array([0, 1]), np.array([0, 0]),
np.array([2, 0]), 2)
assert not FV.check_omission_trio(np.array([0, 1]), np.array([0, 0]),
np.array([2, 0]), 0)
assert not FV.check_omission_trio(np.array([0, 1]), np.array([0, 0]),
np.array([2, 0]), 1)
def test_weird_denovo_from_ivan_4():
# AC AC CG denovo
assert FV.check_denovo_trio(np.array([0, 1]), np.array([0, 1]),
np.array([1, 2]), 2)
assert not FV.check_denovo_trio(np.array([0, 1]), np.array([0, 1]),
np.array([1, 2]), 0)
assert not FV.check_denovo_trio(np.array([0, 1]), np.array([0, 1]),
np.array([1, 2]), 1)
assert not FV.check_omission_trio(np.array([0, 1]), np.array([0, 1]),
np.array([1, 2]), 2)
assert not FV.check_omission_trio(np.array([0, 1]), np.array([0, 1]),
np.array([1, 2]), 0)
assert not FV.check_omission_trio(np.array([0, 1]), np.array([0, 1]),
np.array([1, 2]), 1)
def test_denovo_check_4():
# CC, CC -> AA
assert FV.check_denovo_trio(np.array([1, 1]), np.array([1, 1]),
np.array([0, 0]), 0)
assert not FV.check_denovo_trio(np.array([1, 1]), np.array([1, 1]),
np.array([0, 0]), 1)
def test_denovo_check_1():
# AA, AA -> AC
assert FV.check_denovo_trio(np.array([0, 0]), np.array([0, 0]),
np.array([0, 1]), 1)
assert not FV.check_denovo_trio(np.array([0, 0]), np.array([0, 0]),
np.array([0, 1]), 0)
def test_omission_check_4():
# AA,CC -> CC
assert FV.check_omission_trio(np.array([1, 1]), np.array([0, 0]),
np.array([1, 1]), 0)
assert not FV.check_omission_trio(np.array([1, 1]), np.array([0, 0]),
np.array([1, 1]), 1)
def test_mendelian_from_ivan_5():
# AC AC CC mendel
assert FV.check_mendelian_trio(np.array([0, 1]), np.array([0, 1]),
np.array([1, 1]), 1)
assert not FV.check_mendelian_trio(np.array([0, 1]), np.array([0, 1]),
np.array([1, 1]), 0)
def test_denovo_and_omission_from_ivan_1():
# AA AA AC denovo
assert FV.check_denovo_trio(np.array([0, 0]), np.array([0, 0]),
np.array([0, 1]), 1)
assert not FV.check_denovo_trio(np.array([0, 0]), np.array([0, 0]),
np.array([0, 1]), 0)
def test_denovo_check_2():
# AA, AA -> CA
assert FV.check_denovo_trio(np.array([0, 0]), np.array([0, 0]),
np.array([1, 0]), 1)
assert not FV.check_denovo_trio(np.array([0, 0]), np.array([0, 0]),
np.array([1, 0]), 0)
def test_denovo_and_omission_from_ivan_4():
# AA CC CC omission
assert FV.check_omission_trio(np.array([0, 0]), np.array([1, 1]),
np.array([1, 1]), 0)
assert not FV.check_omission_trio(np.array([0, 0]), np.array([1, 1]),
np.array([1, 1]), 1)