def test_formula_init():
fmula = Formula("AAF", None, False, "title")
assert fmula.Y == Term("AAF", None)
assert fmula.X == One()
fmula = Formula("AAF~", None, False, "title")
assert fmula.Y == Term("AAF", None)
assert fmula.X == One()
fmula = Formula("MEAN(AAF) ~ CHROM", None, True, "title")
assert fmula.Y.group == Term("CHROM", None)
assert fmula.passed
fmula = Formula("MEAN(AAF) ~ FILTER", None, True, "title")
assert not fmula.passed
fmula = Formula("MEAN(AAF, FILTER[PASS], group=VARTYPE) ~ CHROM", None,
True, "title")
assert isinstance(fmula.Y, Aggr)
assert isinstance(fmula.X, Term)
def test_formula_init():
fmula = Formula('AAF', None, False, 'title')
assert fmula.Y == Term('AAF', None)
assert fmula.X == Term('1', None)
assert fmula._terms == {}
fmula = Formula('AAF~', None, False, 'title')
assert fmula.Y == Term('AAF', None)
assert fmula.X == Term('1', None)
assert fmula._terms == {}
fmula = Formula('MEAN(AAF) ~ CHROM', None, True, 'title')
assert fmula.Y.group == Term('CHROM', None)
assert fmula._terms == {'TERM0': Term('AAF', None)}
assert fmula.passed
fmula = Formula('MEAN(AAF) ~ FILTER', None, True, 'title')
assert not fmula.passed
with pytest.raises(ValueError):
Formula('MEAN(AAF, FILTER, CHROM, VARTYPE) ~ FILTER', None, True, 'title')
fmula = Formula('MEAN(AAF, FILTER[PASS], group=VARTYPE) ~ CHROM', None, True, 'title')
assert isinstance(fmula.Y, Aggr)
assert isinstance(fmula.X, Term)
with pytest.raises(ValueError):
Formula('MEAN(AAF, FILTER[PASS], group1=VARTYPE) ~ CHROM', None, True, 'title')
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_aggr_run(variants):
aggr = Aggr("COUNT",
One(),
filter=Term("FILTER", ["PASS"]),
group=Term("VARTYPE"))
aggr.run(variants[0], passed=True)
assert len(aggr.cache) == 0
aggr2 = Aggr("COUNT", One(), filter=Term("FILTER", ["PASS"]))
with pytest.raises(RuntimeError):
aggr2.run(variants[5], passed=True)
aggr3 = Aggr("COUNT",
One(),
filter=Term("FILTER", ["PASS"]),
group=Term("FILTER2"))
aggr3.run(variants[5], passed=False)
assert len(aggr3.cache) == 0
aggr4 = Aggr("COUNT", One(), Term("GTTYPEs"))
with pytest.raises(ValueError):
aggr4.run(variants[0], passed=False)
aggr5 = Aggr("COUNT", One(), Term("VARTYPE"))
aggr5.run(variants[0], passed=False)
assert aggr5.cache == {"snp": [1]}
aggr5.run(variants[1], passed=False)
assert aggr5.cache == {"snp": [1, 1]}
aggr5.run(variants[3], passed=False)
assert aggr5.cache == {"snp": [1, 1], "indel": [1]}
assert aggr5.dump() == {"snp": 2, "indel": 1}
aggr5.cache.clear()
aggr5.setxgroup(Term("FILTER", None))
aggr5.run(variants[0], passed=False)
assert aggr5.cache == {"MinMQ": {"snp": [1]}}
aggr5.cache.clear()
aggr5.setxgroup(Term("FILTER2", None))
aggr5.run(variants[0], passed=False)
assert aggr5.cache == {"MinMQ": {"snp": [1]}}
aggr5.run(variants[5], passed=False)
assert aggr5.cache == {"MinMQ": {"snp": [1]}}
aggr5.run(variants[1], passed=False)
assert aggr5.cache == {"MinMQ": {"snp": [1, 1]}}
assert aggr5.dump() == {"MinMQ": [(2, "snp")]}
aggr5.setxgroup(Term("GTTYPEs", ["HOM_REF", "HET"]))
with pytest.raises(ValueError):
aggr5.run(variants[0], passed=False)
aggr6 = Aggr("MEAN", Term("AAF", [".2", None]), Term("CHROM"))
aggr6.run(variants[0], passed=False) # .125
assert len(aggr6.cache) == 0
def test_aggr_init():
with pytest.raises(ValueError):
Aggr("COUNT", None)
with pytest.raises(ValueError):
Aggr("NoSuchAggr", "")
aggr = Aggr("COUNT", One())
assert aggr.term == One()
assert aggr.filter is None
assert aggr.group is None
assert not aggr.has_filter()
aggr = Aggr("COUNT", One(), Term("FILTER", ["PASS"]))
assert aggr.term == One()
assert aggr.group == Term("FILTER", ["PASS"])
assert aggr.filter is None
aggr = Aggr("COUNT", One(), filter=Term("FILTER", ["PASS"]))
assert aggr.term == One()
assert aggr.filter == Term("FILTER", ["PASS"])
assert aggr.group is None
assert aggr.has_filter()
aggr.setxgroup(Term("VARTYPE", None))
assert aggr.group == Term("VARTYPE", None)
assert aggr.xgroup is None
aggr = Aggr("COUNT",
One(),
filter=Term("FILTER", ["PASS"]),
group=Term("VARTYPE"))
assert aggr.term == One()
assert aggr.filter == Term("FILTER", ["PASS"])
assert aggr.group == Term("VARTYPE", None)
assert aggr.xgroup is None
aggr.setxgroup(Term("GTTYPEs", ["A"]))
assert aggr.xgroup == Term("GTTYPEs", ["A"])
assert (
repr(aggr) ==
"<Aggr COUNT(<Term _ONE()>, filter=<Term FILTER(subsets=['PASS'])>, group=<Term VARTYPE()>)>"
)
assert aggr.has_filter()
aggr = Aggr("COUNT", One(), filter=Term("FILTER"), group=Term("VARTYPE"))
assert aggr.term == One()
assert aggr.filter == Term("FILTER", None)
assert aggr.group == Term("VARTYPE", None)
aggr = Aggr("COUNT", One(), filter=Term("GTTYPEs"))
assert aggr.term == One()
assert aggr.filter == Term("GTTYPEs", None)
assert aggr.group == None
with pytest.raises(ValueError):
Aggr("Nosuchaggr", 1)
with pytest.raises(ValueError):
Aggr("COUNT", 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"]
def test_term_run(variants):
term = Term('FILTER[PASS]', None)
assert term.run(variants[0], passed = True) == False
assert term.run(variants[5], passed = True) == ['PASS']
term = Term('FILTER2', None)
assert term.run(variants[5], passed = True) == False
term = Term('GTTYPEs{0}', ['A', 'B', 'C', 'D'])
assert term.run(variants[0], passed = False) == ['HOM_REF']
term = Term('AAF[.126,]', None)
# .125
assert term.run(variants[0], passed = False) == False
assert term.run(variants[2], passed = False) == [.25]
term = Term('AAF[,.24]', None)
# .25
assert term.run(variants[0], passed = False) == [.125]
assert term.run(variants[2], passed = False) == False
term = Term('FILTER[PASS]', None)
assert term.run(variants[0], passed = False) == False
assert term.run(variants[5], passed = False) == ['PASS']
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[.05, .95]', None)
assert term.subsets == [.05, .95]
term = Term('1', None)
assert term.name == '1'
with pytest.raises(ValueError):
Term('NoSuchTerm', None)
MACROS['NOTYPE'] = {}
with pytest.raises(TypeError):
Term('NOTYPE', None)
del MACROS['NOTYPE']
term = Term('AFs{1}', ['sample1', 'sample2'])
assert term.samples == [1]
with pytest.raises(ValueError):
Term('AFs{sample2][,0.5]', ['sample1', 'sample2'])
term = Term('AFs{sample2}[,0.5]', ['sample1', 'sample2'])
assert term.samples == [1]
assert term.subsets == ['', 0.5]
with pytest.raises(ValueError):
Term('AFs[sample2}{,0.5}', ['sample1', 'sample2'])
term2 = Term('AFs[,.5]{sample2}', ['sample1', 'sample2'])
assert term2.samples == [1]
assert term2.subsets == ['', 0.5]
assert repr(term2) == "<Term AFs(subsets=['', 0.5], samples=[1])>"
assert term2 == term
assert term2 != 1
with pytest.raises(ValueError):
Term('AFs[)', None)
with pytest.raises(ValueError):
Term('AFs{sample}', ['sample1', 'sample2'])
with pytest.raises(KeyError):
Term('AFs[1,2,3]', None)
def test_aggr_run(variants):
aggr = Aggr('COUNT(1, filter = FILTER[PASS], group = VARTYPE)', {'1': Term('1', None), 'FILTER[PASS]': Term('FILTER[PASS]', None), 'VARTYPE': Term('VARTYPE', None)})
aggr.run(variants[0], passed = True)
assert len(aggr.cache) == 0
aggr2 = Aggr('COUNT(1, filter = FILTER[PASS])', {'1': Term('1', None), 'FILTER[PASS]': Term('FILTER[PASS]', None), 'VARTYPE': Term('VARTYPE', None)})
with pytest.raises(RuntimeError):
aggr2.run(variants[5], passed = True)
aggr3 = Aggr('COUNT(1, filter = FILTER[PASS], group = FILTER2)', {'1': Term('1', None), 'FILTER[PASS]': Term('FILTER[PASS]', None), 'FILTER2': Term('FILTER2', None)})
aggr3.run(variants[5], passed = False)
assert len(aggr3.cache) == 0
aggr4 = Aggr('COUNT(1, group = GTTYPEs)', {'1': Term('1', None), 'GTTYPEs': Term('GTTYPEs', None)})
with pytest.raises(ValueError):
aggr4.run(variants[0], passed = False)
aggr5 = Aggr('COUNT(1, group = VARTYPE)', {'1': Term('1', None), 'VARTYPE': Term('VARTYPE', None)})
aggr5.run(variants[0], passed = False)
assert aggr5.cache == {'snp': [1]}
aggr5.run(variants[1], passed = False)
assert aggr5.cache == {'snp': [1,1]}
aggr5.run(variants[3], passed = False)
assert aggr5.cache == {'snp': [1,1], 'indel': [1]}
assert aggr5.dump() == {'snp': 2, 'indel': 1}
aggr5.cache.clear()
aggr5.setxgroup(Term('FILTER', None))
aggr5.run(variants[0], passed = False)
assert aggr5.cache == {'MinMQ': {'snp': [1]}}
aggr5.cache.clear()
aggr5.setxgroup(Term('FILTER2', None))
aggr5.run(variants[0], passed = False)
assert aggr5.cache == {'MinMQ': {'snp': [1]}}
aggr5.run(variants[5], passed = False)
assert aggr5.cache == {'MinMQ': {'snp': [1]}}
aggr5.run(variants[1], passed = False)
assert aggr5.cache == {'MinMQ': {'snp': [1,1]}}
assert aggr5.dump() == {'MinMQ': [(2, 'snp')]}
aggr5.setxgroup(Term('GTTYPEs', ['A', 'B', 'C', 'D']))
with pytest.raises(ValueError):
aggr5.run(variants[0], passed = False)
aggr6 = Aggr('MEAN(AAF[.2,], group = CHROM)', {'AAF[.2,]': Term('AAF[.2,]', None), 'CHROM': Term('CHROM', None)})
aggr6.run(variants[0], passed = False) # .125
assert len(aggr6.cache) == 0
def test_aggr_init():
with pytest.raises(ValueError):
Aggr('COUNT', {})
with pytest.raises(ValueError):
Aggr('COUNT(', {})
with pytest.raises(ValueError):
Aggr('NoSuchAggr()', {})
aggr = Aggr('COUNT(1)', {'1': Term('1', None)})
assert aggr.term == Term('1', None)
assert aggr.filter is None
assert aggr.group is None
assert not aggr.hasFILTER()
aggr = Aggr('COUNT(1, FILTER[PASS])', {'1': Term('1', None), 'FILTER[PASS]': Term('FILTER[PASS]', None)})
assert aggr.term == Term('1', None)
assert aggr.filter == Term('FILTER[PASS]', None)
assert aggr.group is None
aggr = Aggr('COUNT(1, filter = FILTER[PASS])', {'1': Term('1', None), 'FILTER[PASS]': Term('FILTER[PASS]', None)})
assert aggr.term == Term('1', None)
assert aggr.filter == Term('FILTER[PASS]', None)
assert aggr.group is None
assert aggr.hasFILTER()
aggr.setxgroup(Term('VARTYPE', None))
assert aggr.group == Term('VARTYPE', None)
assert aggr.xgroup is None
aggr = Aggr('COUNT(1, filter = FILTER[PASS], group = VARTYPE)', {'1': Term('1', None), 'FILTER[PASS]': Term('FILTER[PASS]', None), 'VARTYPE': Term('VARTYPE', None)})
assert aggr.term == Term('1', None)
assert aggr.filter == Term('FILTER[PASS]', None)
assert aggr.group == Term('VARTYPE', None)
assert aggr.xgroup is None
aggr.setxgroup(Term('GTTYPEs{0}', ['A']))
assert aggr.xgroup == Term('GTTYPEs{0}', ['A'])
assert repr(aggr) == "<Aggr COUNT(<Term 1(subsets=None, samples=None)>, filter=<Term FILTER(subsets=['PASS'], samples=None)>, group=<Term VARTYPE(subsets=None, samples=None)>)>"
assert aggr.hasFILTER()
aggr = Aggr('COUNT(1, FILTER, VARTYPE)', {'1': Term('1', None), 'FILTER': Term('FILTER', None), 'VARTYPE': Term('VARTYPE', None)})
assert aggr.term == Term('1', None)
assert aggr.filter == Term('FILTER', None)
assert aggr.group == Term('VARTYPE', None)
aggr = Aggr('COUNT(1, GTTYPEs)', {'1': Term('1', None), 'GTTYPEs': Term('GTTYPEs', None)})
assert aggr.term == Term('1', None)
assert aggr.filter == Term('GTTYPEs', None)
assert aggr.group == None
with pytest.raises(TypeError):
Aggr('COUNT(FILTER)', {'FILTER': Term('FILTER', None)})
with pytest.raises(TypeError):
Aggr('COUNT(1, group = AAF)', {'AAF': Term('AAF', None), '1': Term('1', None)})