Python FamilyAllele.check_omission_trio Examples

Example #1

File: test_inheritance_checks.py Project: iossifovlab/gpf

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)

Example #2

File: test_inheritance_checks.py Project: iossifovlab/gpf

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)

Example #3

File: test_inheritance_checks.py Project: iossifovlab/gpf

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)

Example #4

File: test_inheritance_checks.py Project: iossifovlab/gpf

def test_omission_not_denovo():
    # AA,CC -> AA
    trio = [
        np.array([0, 0]),  # p1
        np.array([1, 1]),  # p2
        np.array([0, 0]),  # ch
    ]
    assert FV.check_omission_trio(*trio, allele_index=1)
    assert not FV.check_denovo_trio(*trio, allele_index=1)
    assert not FV.check_mendelian_trio(*trio, allele_index=1)

    # FIXME:
    assert not FV.check_omission_trio(*trio, allele_index=0)
    assert not FV.check_denovo_trio(*trio, allele_index=0)
    assert FV.check_mendelian_trio(*trio, allele_index=0)

Example #5

File: test_inheritance_checks.py Project: iossifovlab/gpf

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)

Example #6

File: test_inheritance_checks.py Project: iossifovlab/gpf

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)

Example #7

File: test_inheritance_checks.py Project: iossifovlab/gpf

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)

Example #8

File: test_inheritance_checks.py Project: iossifovlab/gpf

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)

Example #9

File: test_inheritance_checks.py Project: iossifovlab/gpf

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)