def test_one():
# Just use the defaults
c = Configuration()
c.init()
p = Parser(c)
p.parse_configuration(test1)
assert len(c.user_subsets) == 9
assert len(c.user_schemes) == 6
def test_one():
# Just use the defaults
c = Configuration()
c.init()
p = Parser(c)
p.parse_configuration(test1)
assert len(c.user_subsets) == 9
assert len(c.user_schemes) == 6
def test_identity():
c = Configuration()
c.init()
s1 = Subset(c, set(range(10)))
s2 = Subset(c, set(range(20)))
s3 = Subset(c, set(range(10, 20)))
s4 = Subset(c, set(range(20)))
# Not just equal BUT THE SAME (see the __new__ member of the class Subset)
assert s1 is not s2
assert s1 is not s3
assert s2 is s4
def test_identity():
c = Configuration()
c.init()
s1 = Subset(c, set(range(10)))
s2 = Subset(c, set(range(20)))
s3 = Subset(c, set(range(10, 20)))
s4 = Subset(c, set(range(20)))
# Not just equal BUT THE SAME (see the __new__ member of the class Subset)
assert s1 is not s2
assert s1 is not s3
assert s2 is s4
def test_overlap(caplog):
c = Configuration()
c.init()
s1 = Subset(c, set(range(10)))
s2 = Subset(c, set(range(10, 20)))
s3 = Subset(c, set(range(9, 20)))
# This should be okay...
Scheme(c, 'a', [s1, s2])
# This isn't
with pytest.raises(SchemeError):
Scheme(c, 'a', [s1, s3])
assert "contains overlapping" in caplog.text()
def test_overlap(caplog):
c = Configuration()
c.init()
s1 = Subset(c, set(range(10)))
s2 = Subset(c, set(range(10, 20)))
s3 = Subset(c, set(range(9, 20)))
# This should be okay...
Scheme(c, 'a', [s1, s2])
# This isn't
with pytest.raises(SchemeError):
Scheme(c, 'a', [s1, s3])
assert "contains overlapping" in caplog.text()
def test_construction():
c = Configuration()
p1 = Partition(c, 'one', (1, 10))
Partition(c, 'two', (11, 20))
Partition(c, 'three', (21, 21))
assert p1.columnset == set(range(10))
assert c.partitions.columnset == set(range(0, 21))
def test_parse_aminoacid():
pth = os.path.join(MISC_PATH, 'raxml_aminoacid.output')
c = Configuration().init(datatype='protein', phylogeny_program="raxml")
p = raxml.Parser(c)
res = p.parse(open(pth).read())
expected = numpy.array([
0.046704, 0.017460, 0.068093, 0.030991, 0.003492, 0.021388, 0.027499,
0.064164, 0.027499, 0.131820, 0.121781, 0.019642, 0.061545, 0.073330,
0.035356, 0.102139, 0.048014, 0.025753, 0.035356, 0.037975
])
assert numpy.allclose(res.freqs[0], expected)
def test_parse_nucleotide():
pth = os.path.join(MISC_PATH, 'raxml_nucleotide.output')
c = Configuration().init(datatype='DNA', phylogeny_program="raxml")
p = raxml.Parser(c)
res = p.parse(open(pth).read())
expected = numpy.array([
0.315909,
0.232955,
0.190909,
0.260227,
])
assert numpy.allclose(res.freqs[0], expected)
def test_parse_lg4m():
pth = os.path.join(MISC_PATH, 'raxml_aminoacid_LG4M+G.output')
c = Configuration().init(datatype='protein', phylogeny_program="raxml")
p = raxml.Parser(c)
res = p.parse(open(pth).read())
# Make sure we got the first block of rates
expected = numpy.array([
0.082276, 0.055172, 0.043853, 0.053484, 0.018957, 0.028152, 0.046679,
0.15781701, 0.033297, 0.028284, 0.054284, 0.025275, 0.023665, 0.041874,
0.063071, 0.066501, 0.065424, 0.023837, 0.038633, 0.049465
])
assert numpy.allclose(res.freqs[0], expected)
def test_identity():
c = Configuration()
pa = Partition(c, 'a', (1, 10, 3))
pb = Partition(c, 'b', (2, 10, 3))
pc = Partition(c, 'c', (3, 10, 3))
s1 = Subset(pa, pb)
s2 = Subset(pa, pb)
s3 = Subset(pa, pc)
s4 = Subset(pa, pb)
# Not just equal BUT THE SAME
assert s1 is s2
assert s1 is s4
assert s1 is not s3
def test_overlap():
c = Configuration()
with pytest.raises(PartitionError):
Partition(c, 'one', (1, 10))
Partition(c, 'two', (10, 20))
