_VALID_FEATURES_DICT = {
"Coverage":
IsBoolean(default=True),
"Depths":
IsBoolean(default=True),
"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),
}
ValueIn((33, 64, "Solexa"), default=33),
# Split a lane into multiple entries, one for each (pair of) file(s)
"SplitLanesByFilenames":
RemovedOption(),
"CompressionFormat":
RemovedOption(),
"AdapterRemoval": {
"Version": RemovedOption(),
"--pcr1": IsStr,
"--pcr2": IsStr,
"--adapter1": IsStr,
"--adapter2": IsStr,
"--adapter-list": IsStr,
"--maxns": IsUnsignedInt,
"--minquality": IsUnsignedInt,
"--trimns": Or(IsNone, IsBoolean),
"--trimqualities": Or(IsNone, IsBoolean),
"--collapse": Or(IsNone, IsBoolean, default=True),
"--mm": Or(IsFloat, IsUnsignedInt, default=3),
"--minlength": IsUnsignedInt(default=25),
"--maxlength": IsUnsignedInt,
"--minalignmentlength": IsUnsignedInt,
"--minadapteroverlap": IsUnsignedInt,
"--shift": IsUnsignedInt,
"--qualitymax": IsUnsignedInt,
"--mate-separator": IsStr,
},
# Which aliger/mapper to use (BWA/Bowtie2)
"Aligners": {
"Program": ValueIn(("BWA", "Bowtie2"), default="BWA"),
"BWA": {
default="samtools"),
"SpeciesName": IsStr, # Not used; left for backwards compatibility
"CommonName": IsStr, # Not used; left for backwards compatibility
"Sex": IsStr(),
"Gender": IsStr(),
}
}
_VALIDATION_SAMPLES[_VALIDATION_SUBSAMPLE_KEY] = _VALIDATION_SAMPLES
# Genotyping settings; note that explicit lists must not be used here, to allow
# proper inheritance of default values. Use IsListOf instead.
_VALIDATION_GENOTYPES = {
"Padding": IsUnsignedInt,
"GenotypeEntirePrefix": IsBoolean(default=False),
"MPileup": {
StringStartsWith("-"): Or(IsInt, IsStr, IsNone),
},
"BCFTools": {
StringStartsWith("-"): Or(IsInt, IsStr, IsNone),
},
"Random": {
"--min-distance-to-indels": IsUnsignedInt,
},
"VCF_Filter": {
"MaxReadDepth": Or(IsUnsignedInt, IsDictOf(IsStr, IsUnsignedInt),
StringIn(("auto",))),
"--keep-ambigious-genotypes": IsNone,
"--min-quality": IsUnsignedInt,
"--min-allele-frequency": IsFloat,
"--min-mapping-quality": IsUnsignedInt,
def test_or__default_set__must_meet_spec():
with pytest.raises(ValueError):
Or(IsInt, ValueIn((10, )), default=5.5)
def test_or__defaults_not_set_in_specs():
with pytest.raises(ValueError):
Or(IsInt(default=10), ValueIn((10, )))
def test_or__default_not_set():
spec = Or(IsInt, ValueIn((10, )))
assert spec.default is DEFAULT_NOT_SET
def test_or__default_set__valid_value():
spec = Or(IsInt, ValueIn((10, )), default=17)
assert spec.default == 17
def test_or__rejects_no_tests():
with pytest.raises(ValueError):
Or()
def test_or__rejects_non_spec_tests():
with pytest.raises(TypeError):
Or(id)
def test_or__rejects_if_both_specs_fail():
spec = Or(IsStr, IsBoolean)
with pytest.raises(MakefileError):
spec(_DUMMY_PATH, 1)
def test_or__accepts_second_test():
spec = Or(IsStr, IsBoolean)
spec(_DUMMY_PATH, False)
def test_or__accepts_first_test():
spec = Or(IsStr, IsBoolean)
spec(_DUMMY_PATH, "Foo")
###############################################################################
# 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):
spec(_DUMMY_PATH, value)
"GenotypingMethod": RemovedOption(),
"SpeciesName": RemovedOption(),
"CommonName": RemovedOption(),
"Sex": IsStr(),
"Gender": RemovedOption(),
}
}
_VALIDATION_SAMPLES[_VALIDATION_SUBSAMPLE_KEY] = _VALIDATION_SAMPLES
# Genotyping settings; note that explicit lists must not be used here, to allow
# proper inheritance of default values. Use IsListOf instead.
_VALIDATION_GENOTYPES = {
"Padding": IsUnsignedInt,
"GenotypeEntirePrefix": IsBoolean(default=False),
"MPileup": {
StringStartsWith("-"): Or(IsInt, IsStr, IsNone)
},
"BCFTools": {
StringStartsWith("-"): Or(IsInt, IsStr, IsNone)
},
"Random": {
"--min-distance-to-indels": IsUnsignedInt
},
"VCF_Filter": {
"MaxReadDepth":
Or(IsUnsignedInt, IsDictOf(IsStr, IsUnsignedInt), StringIn(
("auto", ))),
"--keep-ambigious-genotypes":
IsNone,
"--min-quality":
IsUnsignedInt,