def _alphanum_check(whitelist):
description = "characters a-z, A-Z, 0-9%s allowed"
description %= (", and %r" % whitelist, ) if whitelist else ""
whitelist += string.ascii_letters + string.digits
return And(IsStr(), ValuesSubsetOf(whitelist, description=description))
"PhylogeneticInference": {
IsStr: {
# Which program to use; TODO: Add support for other programs
"Program": StringIn(("examl",), default="examl"),
# Exclude one or more samples from the phylogeny
"ExcludeSamples": [IsStr],
# Which samples to root the final trees on / or midpoint rooting
"RootTreesOn": [IsStr],
# Create a tree per gene, for each region of interest,
# or create a supermatrix tree from all regions specified.
"PerGeneTrees": IsBoolean(default=False),
# Selection of regions of interest / settings per region
"RegionsOfInterest": {
IsStr: {
"Partitions": Or(And(IsStr,
ValuesSubsetOf("123456789X")),
ValueIn([False]),
default=REQUIRED_VALUE),
"SubsetRegions": Or(IsStr, IsNone, default=None),
},
},
"SubsetRegions": {
IsStr: IsStr,
},
"ExaML": {
"Bootstraps": IsUnsignedInt(default=100),
"Replicates": IsUnsignedInt(default=1),
"Model": StringIn(("GAMMA", "PSR"),
default="gamma"),
}
}
def test_subset_of__handles_types(value):
spec = ValuesSubsetOf(list(range(5)))
with pytest.raises(MakefileError,
match="Expected value: subset of 0, 1, 2, 3, and 4"):
spec(_DUMMY_PATH, value)
def test_subset_of__default_set__must_meet_spec():
with pytest.raises(ValueError):
ValuesSubsetOf(list(range(5)), default=[4, 5])
def test_subset_of__default_set__valid_value():
spec = ValuesSubsetOf(list(range(5)), default=[3, 4])
assert spec.default == [3, 4]
def test_subset_of__default_not_set():
spec = ValuesSubsetOf(list(range(5)))
assert spec.default is DEFAULT_NOT_SET
def test_subset_of__chars__case_sensitive__rejects_differences_in_case():
spec = ValuesSubsetOf("abcdefghijkl ")
with pytest.raises(MakefileError):
spec(_DUMMY_PATH, "A big DEAL")
###############################################################################
###############################################################################
# Path is displayed in exception
_PATH_IN_EXCEPTION_VALUES = (
(IsInt(), "foo"),
(IsUnsignedInt(), -1),
(IsFloat(), "abc"),
(IsBoolean(), 1),
(IsStr(), 1),
(IsNone(), 1),
(ValueIn([1]), 2),
(ValuesIntersect([1]), [2]),
(ValuesSubsetOf([1]), [2]),
(ValueMissing(), True),
(And(IsStr), 1),
(Or(IsStr), 1),
(Not(IsInt), 1),
(StringIn("abc"), 1),
(StringStartsWith("FOO"), 1),
(StringEndsWith("FOO"), 1),
(IsListOf(IsInt), "foo"),
(IsDictOf(IsInt, IsInt), 1),
)
@pytest.mark.parametrize("spec, value", _PATH_IN_EXCEPTION_VALUES)
def test_specs__path_is_displayed_in_exception(spec, value):
with pytest.raises(MakefileError, match=_DUMMY_PATH_STR):
def test_subset_of__case_sensitive__value_in_not_set():
spec = ValuesSubsetOf(("Abc", "bCe", "cdE"))
with pytest.raises(MakefileError):
spec(_DUMMY_PATH, ["Bce"])
def test_subset_of__case_sensitive__value_in_set():
spec = ValuesSubsetOf(("Abc", "bCe", "cdE"))
spec(_DUMMY_PATH, ["bCe"])
def test_subset_of__empty_set():
spec = ValuesSubsetOf(list(range(5)))
spec(_DUMMY_PATH, [])
def test_subset_of__multiple_values_not_in_set():
spec = ValuesSubsetOf(list(range(5)))
with pytest.raises(MakefileError):
spec(_DUMMY_PATH, [4, 5])
def test_subset_of__multiple_values_in_set():
spec = ValuesSubsetOf(list(range(5)))
spec(_DUMMY_PATH, [1, 4])
def test_subset_of__single_value_in_set():
spec = ValuesSubsetOf(list(range(5)))
spec(_DUMMY_PATH, [1])
"DuplicateHist":
IsBoolean(default=False),
"RawBAM":
IsBoolean(default=False),
"RealignedBAM":
IsBoolean(default=True),
"Summary":
IsBoolean(default=True),
"mapDamage":
Or(IsBoolean,
StringIn(('rescale', 'model', 'plot', 'no', 'yes')),
default=True)
}
_VALID_FEATURES_LIST = ValuesSubsetOf(
("Coverage", "Depths", "DuplicateHist", "mapDamage", "Raw BAM", "RawBAM",
"Realigned BAM", "RealignedBAM", "Summary"))
_VALID_EXCLUDE_DICT = {
"Single": IsBoolean(default=False),
"Collapsed": IsBoolean(default=False),
"CollapsedTruncated": IsBoolean(default=False),
"Paired": IsBoolean(default=False),
"Singleton": IsBoolean(default=False),
}
_VALID_EXCLUDE_LIST = ValuesSubsetOf(_READ_TYPES)
class BAMFeatures(PreProcessMakefile):
"""Makefile pre-processor that converts convert an old-style 'Features'
def test_subset_of__chars__case_sensitive():
spec = ValuesSubsetOf("abcdefghijkl ")
spec(_DUMMY_PATH, "a big deal")
IsStr: {
# Which program to use; TODO: Add support for other programs
"Program": StringIn(("examl", ), default="examl"),
# Exclude one or more samples from the phylogeny
"ExcludeSamples": [IsStr],
# Which samples to root the final trees on / or midpoint rooting
"RootTreesOn": [IsStr],
# Create a tree per gene, for each region of interest,
# or create a supermatrix tree from all regions specified.
"PerGeneTrees": IsBoolean(default=False),
# Selection of regions of interest / settings per region
"RegionsOfInterest": {
IsStr: {
"Partitions":
Or(
And(IsStr, ValuesSubsetOf("123456789X")),
ValueIn([False]),
default=REQUIRED_VALUE,
),
"SubsetRegions":
Or(IsStr, IsNone, default=None),
}
},
"SubsetRegions": {
IsStr: IsStr
},
"ExaML": {
"Bootstraps": IsUnsignedInt(default=100),
"Replicates": IsUnsignedInt(default=1),
"Model": StringIn(("GAMMA", "PSR"), default="gamma"),
},