def test_specs__path_is_displayed_in_exception():
def _path_is_displayed_in_exception(spec, value):
assert_raises_regexp(MakefileError, _DUMMY_PATH_STR, spec, _DUMMY_PATH,
value)
yield _path_is_displayed_in_exception, IsInt(), "foo"
yield _path_is_displayed_in_exception, IsUnsignedInt(), -1
yield _path_is_displayed_in_exception, IsFloat(), "abc"
yield _path_is_displayed_in_exception, IsBoolean(), 1
yield _path_is_displayed_in_exception, IsStr(), 1
yield _path_is_displayed_in_exception, IsNone(), 1
yield _path_is_displayed_in_exception, ValueLT(0), 1
yield _path_is_displayed_in_exception, ValueLE(0), 1
yield _path_is_displayed_in_exception, ValueGE(0), -1
yield _path_is_displayed_in_exception, ValueGT(0), -1
yield _path_is_displayed_in_exception, ValueIn([1]), 2
yield _path_is_displayed_in_exception, ValuesIntersect([1]), [2]
yield _path_is_displayed_in_exception, ValuesSubsetOf([1]), [2]
yield _path_is_displayed_in_exception, ValueMissing(), True
yield _path_is_displayed_in_exception, And(IsStr), 1
yield _path_is_displayed_in_exception, Or(IsStr), 1
yield _path_is_displayed_in_exception, Xor(IsStr, IsInt), True
yield _path_is_displayed_in_exception, Not(IsInt), 1
yield _path_is_displayed_in_exception, StringIn("abc"), 1
yield _path_is_displayed_in_exception, StringsIntersect("abc"), [1]
yield _path_is_displayed_in_exception, StringsSubsetOf("abc"), [1]
yield _path_is_displayed_in_exception, StringIsUppercase(), 1
yield _path_is_displayed_in_exception, StringStartsWith("FOO"), 1
yield _path_is_displayed_in_exception, StringEndsWith("FOO"), 1
yield _path_is_displayed_in_exception, IsListOf(IsInt), "foo"
yield _path_is_displayed_in_exception, IsDictOf(IsInt, IsInt), 1
def test_string_in__default_set__valid_value():
spec = StringIn("ABCDEFGH", default="e")
assert_equal(spec.default, "e")
def test_string_in__case_insensitive__mixed_string__string_found():
spec = StringIn(("A", "c", "B", 1, 2, 3))
spec(_DUMMY_PATH, "a")
def test_string_in__default_not_set():
spec = StringIn("ABCDEFGH")
assert_is(spec.default, DEFAULT_NOT_SET)
def test_string_in__case_insensitive__value_not_set():
spec = StringIn(("Abc", "bCe", "cdE"))
assert_raises(MakefileError, spec, _DUMMY_PATH, "ABce")
def test_string_in__case_insensitive__value_in_set():
spec = StringIn(("Abc", "bCe", "cdE"))
spec(_DUMMY_PATH, "Bce")
for key in mkfile["Project"]["Regions"]:
msa[key] = fill_dict(msa.get(key, {}), defaults)
unknown_regions = set(msa) - set(mkfile["Project"]["Regions"])
if unknown_regions:
raise MakefileError("Unknown Regions of Interest in Genotyping: %s" \
% (", ".join(unknown_regions),))
# Recursive definition of sample tree
_VALIDATION_SUBSAMPLE_KEY = And(StringStartsWith("<"), StringEndsWith(">"))
_VALIDATION_SAMPLES_KEY = And(IsStr, Not(_VALIDATION_SUBSAMPLE_KEY))
_VALIDATION_SAMPLES = {
_VALIDATION_SAMPLES_KEY: {
"GenotypingMethod":
StringIn(("reference sequence", "random sampling", "samtools"),
default="samtools"),
"SpeciesName":
IsStr, # Not used; left for backwards compatibility
"CommonName":
IsStr, # Not used; left for backwards compatibility
"Gender":
IsStr(default=REQUIRED_VALUE),
}
}
_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),
return _validate_makefiles(config, makefiles)
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))
# Valid names for prefixes
_VALID_PREFIX_NAME = \
And(_alphanum_check(whitelist="._-*"),
Not(StringIn(["Options"] + [(s + "Reads") for s in _READ_TYPES])))
# Valid paths for prefixes; avoids some problems with e.g. Bowtie2
_VALID_PREFIX_PATH = \
And(IsStr(), Not(ValuesIntersect("\\:?\"<>|() \t\n\v\f\r")),
default=REQUIRED_VALUE)
# Valid strings for targets / samples / libraries / lanes
_VALID_TARGET_NAME = \
And(_alphanum_check(whitelist="._-"),
ValueGE(2, key=len, description="at least two characters long"))
_VALIDATION_OPTIONS = {
# Sequencing platform, used to tag read-groups.
"Platform":
StringIn(("CAPILLARY", "LS454", "ILLUMINA", "SOLID", "HELICOS",
_VALIDATION_NUCLEO = {
"Enabled": IsBoolean(default=False),
"Apply_GC_Correction": IsBoolean(default=True),
"ExcludeBed": EXCLUDEBED,
"--NucleosomeFlanks": IsUnsignedInt(default=25),
"--NucleosomeSize": IsUnsignedInt(default=147),
"--NucleosomeOffset": IsUnsignedInt(default=12)
}
_VALIDATION_METHYL = {
"Enabled": IsBoolean(default=False),
"ExcludeBed": EXCLUDEBED,
"--ReadBases": IsUnsignedInt(default=15),
"--MinBaseQuality": IsUnsignedInt(default=20),
"--SkipThreePrime": IsUnsignedInt(default=0),
"--SkipFivePrime": IsUnsignedInt(default=0),
"--Primes": StringIn(('five', 'three', 'both'), default='five')
}
_VALIDATION_PHASO = {
"Enabled": IsBoolean(default=False),
"ExcludeBed": EXCLUDEBED,
"Apply_GC_Correction": IsBoolean(default=False),
"--SubsetPileup": IsUnsignedInt(default=1),
"--MaxRange": IsUnsignedInt(default=1500)
}
_VALIDATION_WRITEDEPTH = {
"Enabled": IsBoolean(default=False),
"ExcludeBed": EXCLUDEBED,
"Apply_GC_Correction": IsBoolean(default=True)
}
_VALIDATION_TOOLS = {