Python compact_allele_name Examples

Example #1

File: test_mouse_class2.py Project: ikizhvatov/mhcnames

def test_mouse_class2_alleles():
    # H2-IAb
    eq_(parse_allele_name("H2-IAb"), AlleleName("H-2", "IA", "", "b"))
    eq_(normalize_allele_name("H2-IAb"), "H-2-IAb")
    eq_(compact_allele_name("H2-IAb"), "IAb")

    # with hyphen in "H-2"
    eq_(parse_allele_name("H-2-IAb"), AlleleName("H-2", "IA", "", "b"))
    eq_(normalize_allele_name("H-2-IAb"), "H-2-IAb")
    eq_(compact_allele_name("H-2-IAb"), "IAb")

Example #2

def test_mouse_class1_alleles_H2_Db():
    # H2-Db
    eq_(parse_allele_name("H2-Db"), AlleleName("H-2", "D", "", "b"))
    eq_(normalize_allele_name("H2-Db"), "H-2-Db")
    eq_(compact_allele_name("H2-Db"), "Db")

    # with hyphen in "H-2"
    eq_(parse_allele_name("H-2-Db"), AlleleName("H-2", "D", "", "b"))
    eq_(normalize_allele_name("H-2-Db"), "H-2-Db")
    eq_(compact_allele_name("H-2-Db"), "Db")

Example #3

def test_mouse_class1_alleles_H2_Kk():
    # H2-Kk
    eq_(parse_allele_name("H2-Kk"), AlleleName("H-2", "K", "", "k"))
    eq_(normalize_allele_name("H2-Kk"), "H-2-Kk")
    eq_(compact_allele_name("H-2-Kk"), "Kk")

    # with a hyphen in "H-2"
    eq_(parse_allele_name("H-2-Kk"), AlleleName("H-2", "K", "", "k"))
    eq_(normalize_allele_name("H-2-Kk"), "H-2-Kk")
    eq_(compact_allele_name("H-2-Kk"), "Kk")

Example #4

File: test_macaque.py Project: ikizhvatov/mhcnames

def test_macaque_alleles():
    allele_name = "Mamu-B*082:02"
    eq_(normalize_allele_name(allele_name), "Mamu-B*82:02")
    eq_(compact_allele_name(allele_name), "B8202")

    # expect 3rd zero in the family "007" to be trimmed in the normalized form
    # of this allele
    allele_name = "Mamu-B*007:02"
    eq_(normalize_allele_name(allele_name), "Mamu-B*07:02")
    eq_(compact_allele_name(allele_name), "B0702")

Example #5

File: test_mouse_class1.py Project: hammerlab/mhcnames

def test_mouse_class1_alleles_H2_Kk():
    # H2-Kk
    eq_(parse_allele_name("H2-Kk"),
        AlleleName("H-2", "K", "", "k"))
    eq_(normalize_allele_name("H2-Kk"), "H-2-Kk")
    eq_(compact_allele_name("H-2-Kk"), "Kk")

    # with a hyphen in "H-2"
    eq_(parse_allele_name("H-2-Kk"),
        AlleleName("H-2", "K", "", "k"))
    eq_(normalize_allele_name("H-2-Kk"), "H-2-Kk")
    eq_(compact_allele_name("H-2-Kk"), "Kk")

Example #6

File: test_mouse_class1.py Project: hammerlab/mhcnames

def test_mouse_class1_alleles_H2_Db():
    # H2-Db
    eq_(parse_allele_name("H2-Db"),
        AlleleName("H-2", "D", "", "b"))
    eq_(normalize_allele_name("H2-Db"), "H-2-Db")
    eq_(compact_allele_name("H2-Db"), "Db")

    # with hyphen in "H-2"
    eq_(parse_allele_name("H-2-Db"),
        AlleleName("H-2", "D", "", "b"))
    eq_(normalize_allele_name("H-2-Db"), "H-2-Db")
    eq_(compact_allele_name("H-2-Db"), "Db")

Example #7

File: test_mouse_class2.py Project: caperna/mhcnames

def test_mouse_class2_alleles():
    # H2-IAb
    eq_(parse_allele_name("H2-IAb"),
        AlleleName("H-2", "IA", "", "b"))
    eq_(normalize_allele_name("H2-IAb"), "H-2-IAb")
    eq_(compact_allele_name("H2-IAb"), "IAb")

    # with hyphen in "H-2"
    eq_(parse_allele_name("H-2-IAb"),
        AlleleName("H-2", "IA", "", "b"))
    eq_(normalize_allele_name("H-2-IAb"), "H-2-IAb")
    eq_(compact_allele_name("H-2-IAb"), "IAb")

Example #8

File: test_human_class1.py Project: ikizhvatov/mhcnames

def test_hla_with_3_digit_allele_code():
    # B*15:120
    eq_(normalize_allele_name("HLA-B*15:120"), "HLA-B*15:120")
    eq_(compact_allele_name("HLA-B*15:120"), "B15120")
    eq_(normalize_allele_name("B15120"), "HLA-B*15:120")
    eq_(compact_allele_name("B15120"), "B15120")

    # A*02*123
    eq_(normalize_allele_name("HLA-A*02:123"), "HLA-A*02:123")
    eq_(compact_allele_name("HLA-A*02:123"), "A02123")
    eq_(normalize_allele_name("A02123"), "HLA-A*02:123")
    eq_(compact_allele_name("A02123"), "A02123")

Example #9

File: test_human_class1.py Project: hammerlab/mhcnames

def test_hla_with_3_digit_allele_code():
    # B*15:120
    eq_(normalize_allele_name("HLA-B*15:120"), "HLA-B*15:120")
    eq_(compact_allele_name("HLA-B*15:120"), "B15120")
    eq_(normalize_allele_name("B15120"), "HLA-B*15:120")
    eq_(compact_allele_name("B15120"), "B15120")

    # A*02*123
    eq_(normalize_allele_name("HLA-A*02:123"), "HLA-A*02:123")
    eq_(compact_allele_name("HLA-A*02:123"), "A02123")
    eq_(normalize_allele_name("A02123"), "HLA-A*02:123")
    eq_(compact_allele_name("A02123"), "A02123")

Example #10

File: mhcnames_utils.py Project: bmmalone/pylifesci

def get_normalized_allele_name(raw_allele_name: str) -> Optional[str]:
    """ Try to parse `raw_allele_name` to a normalized compact allele name
    
    If `raw_allele_name` cannot be parsed, a warning is logged and `None` is
    returned.
    
    Parameters
    ----------
    raw_allele_name : str
        The unnormalized allele name
        
    Returns
    -------
    compact_allele_name : typing.Optional[str]
        The normalized, compact allele name, or `None`, if the allele name could
        not be parsed.
    """
    ret = None

    try:
        ret = mhcnames.compact_allele_name(raw_allele_name)
    except mhcnames.AlleleParseError as ape:
        logger.warning(ape)

    return ret

Example #11

File: test_human_class2.py Project: caperna/mhcnames

def test_human_class2_alpha_beta():
    expected = "HLA-DPA1*01:05-DPB1*100:01"
    expected_compact = "DPA10105-DPB110001"
    for name in ["DPA10105-DPB110001",
                 "HLA-DPA1*01:05-DPB1*100:01",
                 "hla-dpa1*0105-dpb1*10001",
                 "dpa1*0105-dpb1*10001",
                 "HLA-DPA1*01:05/DPB1*100:01"]:
        eq_(normalize_allele_name(name), expected)
        eq_(compact_allele_name(name), expected_compact)

Example #12

def test_human_class2_alpha_beta():
    expected = "HLA-DPA1*01:05-DPB1*100:01"
    expected_compact = "DPA10105-DPB110001"
    for name in ["DPA10105-DPB110001",
                 "HLA-DPA1*01:05-DPB1*100:01",
                 "hla-dpa1*0105-dpb1*10001",
                 "dpa1*0105-dpb1*10001",
                 "HLA-DPA1*01:05/DPB1*100:01",
                 "DPA10105/DPB110001"]:
        eq_(normalize_allele_name(name), expected)
        eq_(compact_allele_name(name), expected_compact)

Example #13

File: test_human_class2.py Project: caperna/mhcnames

def test_human_class2():
    expected = "HLA-DRB1*01:02"
    expected_compact = "DRB10102"
    for name in ["DRB1_0102",
                 "DRB101:02",
                 "HLA-DRB1_0102",
                 "DRB10102",
                 "DRB1*0102",
                 "HLA-DRB1*0102",
                 "HLA-DRB1*01:02"]:
        eq_(normalize_allele_name(name), expected)
        eq_(compact_allele_name(name), expected_compact)

Example #14

def test_human_class2():
    expected = "HLA-DRA1*01:01-DRB1*01:02"
    expected_compact = "DRB10102"
    for name in ["DRB1_0102",
                 "DRB101:02",
                 "HLA-DRB1_0102",
                 "DRB10102",
                 "DRB1*0102",
                 "HLA-DRB1*0102",
                 "HLA-DRB1*01:02",
                 "DRB0102"]:
        eq_(normalize_allele_name(name), expected)
        eq_(compact_allele_name(name), expected_compact)

Example #15

File: test_human_class1.py Project: ikizhvatov/mhcnames

def test_hla_short_names():
    expected = "A0201"
    for name in hla_02_01_names:
        result = compact_allele_name(name)
        eq_(result, expected)

Example #16

File: test_human_class1.py Project: hammerlab/mhcnames

def test_hla_short_names():
    expected = "A0201"
    for name in hla_02_01_names:
        result = compact_allele_name(name)
        eq_(result, expected)