def testLoadPeople(self):
#Shouldn't work when wrong delimiter is specified
thrown = False
try:
person = Person.loadPeople("tests/_td/dosage_set_1/set.sample",
delim=",")
except:
thrown = True
self.assertEqual(thrown, True)
#default load
people = Person.loadPeople("tests/_td/dosage_set_1/set.sample")
self.assertIsNotNone(people)
self.assertEqual(len(people), 5)
self.assertPerson(people[0], "ID1", "K", "HERO", "male")
self.assertPerson(people[1], "ID2", "K", "HERO", "female")
self.assertPerson(people[2], "DI5", "K", "HERO", "male")
self.assertPerson(people[3], "ID3", "K", "HERO", "female")
self.assertPerson(people[4], "B1", "L", "T", "female")
#let's pretend the file header is a person entry
people = Person.loadPeople("tests/_td/dosage_set_1/set.sample",
skip_header=False)
self.assertIsNotNone(people)
self.assertEqual(len(people), 6)
self.assertPerson(people[0], "ID", "POP", "GROUP", "SEX")
self.assertPerson(people[1], "ID1", "K", "HERO", "male")
self.assertPerson(people[2], "ID2", "K", "HERO", "female")
self.assertPerson(people[3], "DI5", "K", "HERO", "male")
self.assertPerson(people[4], "ID3", "K", "HERO", "female")
self.assertPerson(people[5], "B1", "L", "T", "female")
def testLoadPeople(self):
# Shouldn't work when wrong delimiter is specified
thrown = False
try:
person = Person.loadPeople("tests/_td/dosage_set_1/set.sample", delim=",")
except:
thrown = True
self.assertEqual(thrown, True)
# default load
people = Person.loadPeople("tests/_td/dosage_set_1/set.sample")
self.assertIsNotNone(people)
self.assertEqual(len(people), 5)
self.assertPerson(people[0], "ID1", "K", "HERO", "male")
self.assertPerson(people[1], "ID2", "K", "HERO", "female")
self.assertPerson(people[2], "DI5", "K", "HERO", "male")
self.assertPerson(people[3], "ID3", "K", "HERO", "female")
self.assertPerson(people[4], "B1", "L", "T", "female")
# let's pretend the file header is a person entry
people = Person.loadPeople("tests/_td/dosage_set_1/set.sample", skip_header=False)
self.assertIsNotNone(people)
self.assertEqual(len(people), 6)
self.assertPerson(people[0], "ID", "POP", "GROUP", "SEX")
self.assertPerson(people[1], "ID1", "K", "HERO", "male")
self.assertPerson(people[2], "ID2", "K", "HERO", "female")
self.assertPerson(people[3], "DI5", "K", "HERO", "male")
self.assertPerson(people[4], "ID3", "K", "HERO", "female")
self.assertPerson(people[5], "B1", "L", "T", "female")
def testPersonLoadFromRowIfFilter(self):
row1 = ["a", "b", "c", "d"]
p = Person.loadPersonFromSampleRowIfFilter(
row1, group_filters=["None", "EUR"], individual_filters=[])
self.assertPerson(p)
p = Person.loadPersonFromSampleRowIfFilter(row1,
group_filters=["EUR"],
individual_filters=[])
self.assertIsNone(p)
p = Person.loadPersonFromSampleRowIfFilter(row1,
group_filters=["c", "EUR"],
individual_filters=[])
self.assertPerson(p)
p = Person.loadPersonFromSampleRowIfFilter(
row1,
group_filters=["c", "EUR"],
individual_filters=[re.compile("Nope")])
self.assertIsNone(p)
p = Person.loadPersonFromSampleRowIfFilter(
row1,
group_filters=["c", "EUR"],
individual_filters=[re.compile("Nope"),
re.compile("a")])
self.assertPerson(p)
def testPersonLoadFromRowIfFilter(self):
row1 = ["a", "b", "c", "d"]
p = Person.loadPersonFromSampleRowIfFilter(row1, group_filters=["None", "EUR"], individual_filters=[])
self.assertPerson(p)
p = Person.loadPersonFromSampleRowIfFilter(row1, group_filters=["EUR"], individual_filters=[])
self.assertIsNone(p)
p = Person.loadPersonFromSampleRowIfFilter(row1, group_filters=["c", "EUR"], individual_filters=[])
self.assertPerson(p)
p = Person.loadPersonFromSampleRowIfFilter(
row1, group_filters=["c", "EUR"], individual_filters=[re.compile("Nope")]
)
self.assertIsNone(p)
p = Person.loadPersonFromSampleRowIfFilter(
row1, group_filters=["c", "EUR"], individual_filters=[re.compile("Nope"), re.compile("a")]
)
self.assertPerson(p)
def testLoadFilteredPeople(self):
#Shouldn't work when wrong delimiter is specified
thrown = False
try:
person = Person.loadFilteredPeople(
"tests/_td/dosage_set_1/set.sample", delim=",")
except:
thrown = True
self.assertEqual(thrown, True)
#default load
people = Person.loadFilteredPeople("tests/_td/dosage_set_1/set.sample")
self.assertIsNotNone(people)
self.assertEqual(len(people), 0)
people = Person.loadFilteredPeople("tests/_td/dosage_set_1/set.sample",
group_filters=["HERO"])
self.assertIsNotNone(people)
self.assertEqual(len(people), 4)
self.assertPerson(people[0], "ID1", "K", "HERO", "male")
self.assertPerson(people[1], "ID2", "K", "HERO", "female")
self.assertPerson(people[2], "DI5", "K", "HERO", "male")
self.assertPerson(people[3], "ID3", "K", "HERO", "female")
people = Person.loadFilteredPeople("tests/_td/dosage_set_1/set.sample",
group_filters=["HERO", "T"])
self.assertIsNotNone(people)
self.assertEqual(len(people), 5)
self.assertPerson(people[0], "ID1", "K", "HERO", "male")
self.assertPerson(people[1], "ID2", "K", "HERO", "female")
self.assertPerson(people[2], "DI5", "K", "HERO", "male")
self.assertPerson(people[3], "ID3", "K", "HERO", "female")
self.assertPerson(people[4], "B1", "L", "T", "female")
people = Person.loadFilteredPeople("tests/_td/dosage_set_1/set.sample",
group_filters=["T"])
self.assertIsNotNone(people)
self.assertEqual(len(people), 1)
self.assertPerson(people[0], "B1", "L", "T", "female")
people = Person.loadFilteredPeople(
"tests/_td/dosage_set_1/set.sample",
group_filters=["HERO"],
individual_filters=[re.compile("ID")])
self.assertIsNotNone(people)
self.assertEqual(len(people), 3)
self.assertPerson(people[0], "ID1", "K", "HERO", "male")
self.assertPerson(people[1], "ID2", "K", "HERO", "female")
self.assertPerson(people[2], "ID3", "K", "HERO", "female")
people = Person.loadFilteredPeople(
"tests/_td/dosage_set_1/set.sample",
group_filters=["HERO"],
individual_filters=[re.compile("ID"),
re.compile("DI")])
self.assertIsNotNone(people)
self.assertEqual(len(people), 4)
self.assertPerson(people[0], "ID1", "K", "HERO", "male")
self.assertPerson(people[1], "ID2", "K", "HERO", "female")
self.assertPerson(people[2], "DI5", "K", "HERO", "male")
self.assertPerson(people[3], "ID3", "K", "HERO", "female")
people = Person.loadFilteredPeople(
"tests/_td/dosage_set_1/set.sample",
group_filters=["HERO"],
individual_filters=[re.compile("DI")])
self.assertIsNotNone(people)
self.assertEqual(len(people), 1)
self.assertPerson(people[0], "DI5", "K", "HERO", "male")
def testPersonLoadFromRow(self):
row = ["a", "b", "c", "d"]
p = Person.loadPersonFromSampleRow(row)
self.assertPerson(p)
def testPersonToLine(self):
p = Person("a", "b", "c", "d")
l = p.toTextLine()
self.assertEqual("a b c d", l)
def testBuildFilteredSamples(self):
if os.path.exists("_test"):
shutil.rmtree("_test")
os.makedirs("_test")
Person.buildFilteredSamples("tests/_td/dosage_set_1/set.sample",
"_test/s.sample")
expected = ["ID POP GROUP SEX"]
self.assertSamplesFile("_test/s.sample", expected)
Person.buildFilteredSamples("tests/_td/dosage_set_1/set.sample",
"_test/s.sample",
group_filters=["HERO"])
expected = [
"ID POP GROUP SEX", "ID1 K HERO male", "ID2 K HERO female",
"DI5 K HERO male", "ID3 K HERO female"
]
self.assertSamplesFile("_test/s.sample", expected)
Person.buildFilteredSamples("tests/_td/dosage_set_1/set.sample",
"_test/s.sample",
group_filters=["HERO", "T"])
expected = [
"ID POP GROUP SEX", "ID1 K HERO male", "ID2 K HERO female",
"DI5 K HERO male", "ID3 K HERO female", "B1 L T female"
]
self.assertSamplesFile("_test/s.sample", expected)
Person.buildFilteredSamples("tests/_td/dosage_set_1/set.sample",
"_test/s.sample",
group_filters=["T"])
expected = ["ID POP GROUP SEX", "B1 L T female"]
self.assertSamplesFile("_test/s.sample", expected)
Person.buildFilteredSamples("tests/_td/dosage_set_1/set.sample",
"_test/s.sample",
group_filters=["HERO"],
individual_filters=[re.compile("ID")])
expected = [
"ID POP GROUP SEX", "ID1 K HERO male", "ID2 K HERO female",
"ID3 K HERO female"
]
self.assertSamplesFile("_test/s.sample", expected)
Person.buildFilteredSamples("tests/_td/dosage_set_1/set.sample",
"_test/s.sample",
group_filters=["HERO"],
individual_filters=[re.compile("DI")])
expected = ["ID POP GROUP SEX", "DI5 K HERO male"]
self.assertSamplesFile("_test/s.sample", expected)
Person.buildFilteredSamples(
"tests/_td/dosage_set_1/set.sample",
"_test/s.sample",
group_filters=["HERO"],
individual_filters=[re.compile("DI"),
re.compile("ID")])
expected = [
"ID POP GROUP SEX", "ID1 K HERO male", "ID2 K HERO female",
"DI5 K HERO male", "ID3 K HERO female"
]
self.assertSamplesFile("_test/s.sample", expected)
shutil.rmtree("_test")
def testPersonConstructor(self):
p = Person("a", "b", "c", "d")
self.assertPerson(p)
def testLoadFilteredPeople(self):
# Shouldn't work when wrong delimiter is specified
thrown = False
try:
person = Person.loadFilteredPeople("tests/_td/dosage_set_1/set.sample", delim=",")
except:
thrown = True
self.assertEqual(thrown, True)
# default load
people = Person.loadFilteredPeople("tests/_td/dosage_set_1/set.sample")
self.assertIsNotNone(people)
self.assertEqual(len(people), 0)
people = Person.loadFilteredPeople("tests/_td/dosage_set_1/set.sample", group_filters=["HERO"])
self.assertIsNotNone(people)
self.assertEqual(len(people), 4)
self.assertPerson(people[0], "ID1", "K", "HERO", "male")
self.assertPerson(people[1], "ID2", "K", "HERO", "female")
self.assertPerson(people[2], "DI5", "K", "HERO", "male")
self.assertPerson(people[3], "ID3", "K", "HERO", "female")
people = Person.loadFilteredPeople("tests/_td/dosage_set_1/set.sample", group_filters=["HERO", "T"])
self.assertIsNotNone(people)
self.assertEqual(len(people), 5)
self.assertPerson(people[0], "ID1", "K", "HERO", "male")
self.assertPerson(people[1], "ID2", "K", "HERO", "female")
self.assertPerson(people[2], "DI5", "K", "HERO", "male")
self.assertPerson(people[3], "ID3", "K", "HERO", "female")
self.assertPerson(people[4], "B1", "L", "T", "female")
people = Person.loadFilteredPeople("tests/_td/dosage_set_1/set.sample", group_filters=["T"])
self.assertIsNotNone(people)
self.assertEqual(len(people), 1)
self.assertPerson(people[0], "B1", "L", "T", "female")
people = Person.loadFilteredPeople(
"tests/_td/dosage_set_1/set.sample", group_filters=["HERO"], individual_filters=[re.compile("ID")]
)
self.assertIsNotNone(people)
self.assertEqual(len(people), 3)
self.assertPerson(people[0], "ID1", "K", "HERO", "male")
self.assertPerson(people[1], "ID2", "K", "HERO", "female")
self.assertPerson(people[2], "ID3", "K", "HERO", "female")
people = Person.loadFilteredPeople(
"tests/_td/dosage_set_1/set.sample",
group_filters=["HERO"],
individual_filters=[re.compile("ID"), re.compile("DI")],
)
self.assertIsNotNone(people)
self.assertEqual(len(people), 4)
self.assertPerson(people[0], "ID1", "K", "HERO", "male")
self.assertPerson(people[1], "ID2", "K", "HERO", "female")
self.assertPerson(people[2], "DI5", "K", "HERO", "male")
self.assertPerson(people[3], "ID3", "K", "HERO", "female")
people = Person.loadFilteredPeople(
"tests/_td/dosage_set_1/set.sample", group_filters=["HERO"], individual_filters=[re.compile("DI")]
)
self.assertIsNotNone(people)
self.assertEqual(len(people), 1)
self.assertPerson(people[0], "DI5", "K", "HERO", "male")
def testPersonLoadFromRow(self):
row = ["a", "b", "c", "d"]
p = Person.loadPersonFromSampleRow(row)
self.assertPerson(p)
def testPersonToLine(self):
p = Person("a", "b", "c", "d")
l = p.toTextLine()
self.assertEqual("a b c d", l)
def testBuildFilteredSamples(self):
if os.path.exists("_test"):
shutil.rmtree("_test")
os.makedirs("_test")
Person.buildFilteredSamples("tests/_td/dosage_set_1/set.sample", "_test/s.sample")
expected = ["ID POP GROUP SEX"]
self.assertSamplesFile("_test/s.sample", expected)
Person.buildFilteredSamples("tests/_td/dosage_set_1/set.sample", "_test/s.sample", group_filters=["HERO"])
expected = ["ID POP GROUP SEX", "ID1 K HERO male", "ID2 K HERO female", "DI5 K HERO male", "ID3 K HERO female"]
self.assertSamplesFile("_test/s.sample", expected)
Person.buildFilteredSamples("tests/_td/dosage_set_1/set.sample", "_test/s.sample", group_filters=["HERO", "T"])
expected = [
"ID POP GROUP SEX",
"ID1 K HERO male",
"ID2 K HERO female",
"DI5 K HERO male",
"ID3 K HERO female",
"B1 L T female",
]
self.assertSamplesFile("_test/s.sample", expected)
Person.buildFilteredSamples("tests/_td/dosage_set_1/set.sample", "_test/s.sample", group_filters=["T"])
expected = ["ID POP GROUP SEX", "B1 L T female"]
self.assertSamplesFile("_test/s.sample", expected)
Person.buildFilteredSamples(
"tests/_td/dosage_set_1/set.sample",
"_test/s.sample",
group_filters=["HERO"],
individual_filters=[re.compile("ID")],
)
expected = ["ID POP GROUP SEX", "ID1 K HERO male", "ID2 K HERO female", "ID3 K HERO female"]
self.assertSamplesFile("_test/s.sample", expected)
Person.buildFilteredSamples(
"tests/_td/dosage_set_1/set.sample",
"_test/s.sample",
group_filters=["HERO"],
individual_filters=[re.compile("DI")],
)
expected = ["ID POP GROUP SEX", "DI5 K HERO male"]
self.assertSamplesFile("_test/s.sample", expected)
Person.buildFilteredSamples(
"tests/_td/dosage_set_1/set.sample",
"_test/s.sample",
group_filters=["HERO"],
individual_filters=[re.compile("DI"), re.compile("ID")],
)
expected = ["ID POP GROUP SEX", "ID1 K HERO male", "ID2 K HERO female", "DI5 K HERO male", "ID3 K HERO female"]
self.assertSamplesFile("_test/s.sample", expected)
shutil.rmtree("_test")
