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_is_unsigned_int__default_set__valid_value():
spec = IsUnsignedInt(default=7913)
assert_equal(spec.default, 7913)
def test_is_unsigned_int__default_not_set():
spec = IsUnsignedInt()
assert_is(spec.default, DEFAULT_NOT_SET)
def test_is_unsigned_int__custom_description():
custom_desc = "any old unsigned integer"
spec = IsUnsignedInt(description=custom_desc)
assert_equal(spec.description, custom_desc)
def test_is_unsigned_int__default_description():
spec = IsUnsignedInt()
assert_equal(spec.description, "an unsigned integer")
def _reject_not_str(value):
spec = IsUnsignedInt()
assert_raises(MakefileError, spec, _DUMMY_PATH, value)
def test_is_unsigned_int__accepts_longs():
spec = IsUnsignedInt()
spec(_DUMMY_PATH, 1234L)
spec(_DUMMY_PATH, 0L)
def test_is_unsigned_int__accepts_non_negative_integers():
spec = IsUnsignedInt()
spec(_DUMMY_PATH, 1234)
spec(_DUMMY_PATH, 0)
# 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"),
}
}
},
"PAML": {
"codeml": {
"ExcludeSamples": [IsStr],
"SubsetRegions": {
IsStr: IsStr,
},
IsStr: {
"ControlFile": IsStr(default=REQUIRED_VALUE),
"TreeFile": IsStr(default=REQUIRED_VALUE),
},
# Format to use when compressing FASTQ files ("gz" or "bz2")
"CompressionFormat":
ValueIn(("gz", "bz2"), default="bz2"),
"AdapterRemoval": {
"Version": ValueIn(("v1.4", "v1.5+"), default="v1.5+"),
"--pcr1": IsStr,
"--pcr2": IsStr,
"--adapter1": IsStr,
"--adapter2": 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),
"--minalignmentlength": IsUnsignedInt,
"--shift": IsUnsignedInt,
"--5prime": IsStr,
},
# Which aliger/mapper to use (BWA/Bowtie2)
"Aligners": {
"Program": ValueIn(("BWA", "Bowtie2"), default="BWA"),
"BWA": {
# Mapping algorithm; availability depends on BWA version
"Algorithm":
StringIn(("backtrack", "mem", "bwasw"), default="backtrack"),
# Minimum mapping quality (PHREAD) of reads to retain
"MinQuality":
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_BED_NAME = _VALID_TARGET_NAME = \
And(_alphanum_check(whitelist=".-"),
ValueGE(2, key=len, description="at least two characters long"))
_VALIDATION_OPTIONS = {
"BamPath": IsStr,
"--MinMappingQuality": IsUnsignedInt(default=25),
"--MinAlignmentLength": IsUnsignedInt(default=25),
"--NoReadsChecked": IsUnsignedInt(default=5000)
}
_VALIDATION_GCCORRECT = {
"Enabled": IsBoolean(default=False),
"--NoRegions": Or(IsUnsignedInt, IsStr, default=200),
"--ChromUsed": Or(IsStr, IsUnsignedInt, default="all"), ## the is new
"--MappaUniqueness": IsFloat(default=0.9)
}
_VALIDATION_NUCLEO = {
"Enabled": IsBoolean(default=False),
"Apply_GC_Correction": IsBoolean(default=True),
"ExcludeBed": EXCLUDEBED,