def test_term_init():
term = Term("AAF", None)
assert term.name == "AAF"
assert term.term == MACROS["AAF"]
assert term.samples == None
assert term.subsets == None
term = Term("AAF", items=[".05", ".95"])
assert term.subsets == [0.05, 0.95]
term = One()
assert term.name == "_ONE"
with pytest.raises(ValueError):
Term("NoSuchTerm", None)
MACROS["NOTYPE"] = {}
with pytest.raises(TypeError):
Term("NOTYPE", None)
del MACROS["NOTYPE"]
term = Term("AFs", samples=["1"])
assert term.samples == ["1"]
term = Term("AFs", [None, 0.5], ["sample2"])
term.set_samples(["sample1", "sample2"])
assert term.samples == [1]
assert term.subsets == [None, 0.5]
term2 = Term("AFs", [None, 0.5], ["sample2"])
term2.set_samples(["sample1", "sample2"])
assert term2.samples == [1]
assert term2.subsets == [None, 0.5]
assert repr(term2) == "<Term AFs(subsets=[None, 0.5], samples=[1])>"
assert term2 == term
assert term2 != 1
with pytest.raises(KeyError):
Term("AFs", [1, 2, 3], None)
def test_term_run(variants):
term = Term("FILTER", "PASS")
assert term.run(variants[0], passed=True) == False
assert term.run(variants[5], passed=True) == ["PASS"]
term = Term("FILTER2")
assert term.run(variants[5], passed=True) == False
term = Term("GTTYPEs", None, ["0"])
term.set_samples(variants[-1])
assert term.run(variants[0], passed=False) == ["HOM_REF"]
term = Term("AAF", [0.126, None])
# .125
assert term.run(variants[0], passed=False) == False
assert term.run(variants[2], passed=False) == [0.25]
term = Term("AAF", [None, 0.24])
# .25
assert term.run(variants[0], passed=False) == [0.125]
assert term.run(variants[2], passed=False) == False
term = Term("FILTER", "PASS")
assert term.run(variants[0], passed=False) == False
assert term.run(variants[5], passed=False) == ["PASS"]