def test_getter_setter(self):
age_calc = RNAAgeCalc(tissue="brain")
with self.assertRaises(AssertionError):
age_calc.exprtype = "unknown"
age_calc.exprtype = "count"
self.assertEqual(age_calc.exprtype, "count")
self.assertEqual(age_calc._exprtype, "count")
with self.assertRaises(AssertionError):
age_calc.idtype = "unknown"
age_calc.idtype = "refseq"
self.assertEqual(age_calc.idtype, "refseq")
self.assertEqual(age_calc._idtype, "refseq")
with self.assertRaises(AssertionError):
age_calc.stype = "unknown"
age_calc.stype = "Caucasian"
self.assertEqual(age_calc.stype, "Caucasian")
self.assertEqual(age_calc._stype, "Caucasian")
age_calc2 = RNAAgeCalc(exprtype="count", idtype="refseq")
self.assertEqual(age_calc2.exprtype, "count")
self.assertEqual(age_calc2._exprtype, "count")
self.assertEqual(age_calc2.idtype, "refseq")
self.assertEqual(age_calc2._idtype, "refseq")
self.assertEqual(age_calc2.stype, "all")
self.assertEqual(age_calc2._stype, "all")
def test_assert_raises5(self):
rawcount1 = rawcount
age_calc = RNAAgeCalc(tissue="brain", idtype="symbol")
with self.assertRaises(AssertionError):
age_calc._count2FPKM(rawcount=rawcount1, genelength=1)
with self.assertRaises(AssertionError):
genelength1 = pd.DataFrame(list(range(rawcount1.shape[0] - 1)))
age_calc._count2FPKM(rawcount=rawcount1, genelength=genelength1)
with self.assertRaises(AssertionError):
genelength1 = pd.DataFrame(["unknown"] * (rawcount1.shape[0] - 1))
age_calc._count2FPKM(rawcount=rawcount1, genelength=genelength1)
with self.assertRaises(AssertionError):
genelength1 = pd.Series(list(range(rawcount1.shape[0] - 1)))
age_calc._count2FPKM(rawcount=rawcount1, genelength=genelength1)
with self.assertRaises(AssertionError):
genelength1 = pd.Series(["unknown"] * (rawcount1.shape[0] - 1))
age_calc._count2FPKM(rawcount=rawcount1, genelength=genelength1)
with self.assertRaises(AssertionError):
genelength1 = list(range(24989))
genelength1[0] = "unknown"
age_calc._count2FPKM(rawcount=rawcount1, genelength=genelength1)
with self.assertRaises(AssertionError):
genelength1 = list(range(24988))
age_calc._count2FPKM(rawcount=rawcount1, genelength=genelength1)
with self.assertRaises(AssertionError):
genelength1 = np.array(["unknown"] * rawcount1.shape[0])
genelength1 = genelength1.reshape(1, rawcount1.shape[0])
age_calc._count2FPKM(rawcount=rawcount1, genelength=genelength1)
with self.assertRaises(AssertionError):
genelength1 = list(range(24989))
genelength1[0] = -1
age_calc._count2FPKM(rawcount=rawcount1, genelength=genelength1)
def test_assert_raises4(self):
chronage1 = pd.DataFrame()
chronage1["sampleid"] = ["SRR2166176", "SRR2167642"]
chronage1["chronage"] = [50, 60]
age_calc = RNAAgeCalc(tissue="brain")
with self.assertRaises(AssertionError):
age_calc.predict_age(exprdata=fpkm, chronage=1)
# with self.assertRaises(AssertionError):
# chronage1["sampleid"] = [50, 60]
# rnaagepy.predict_age(exprdata=fpkm, chronage=chronage1)
with self.assertRaises(AssertionError):
chronage1["chronage"] = ["SRR2166176", "SRR2167642"]
age_calc.predict_age(exprdata=fpkm, chronage=chronage1)
with self.assertRaises(AssertionError):
chronage1["sampleid"] = ["SRR2166176", "SRR2166176"]
age_calc.predict_age(exprdata=fpkm, chronage=chronage1)
with self.assertRaises(AssertionError):
chronage1["sampleid"] = ["SRR2166176", "unknown"]
age_calc.predict_age(exprdata=fpkm, chronage=chronage1)
with self.assertRaises(AssertionError):
chronage1["chronage"] = [-20, 50]
age_calc.predict_age(exprdata=fpkm, chronage=chronage1)
def test_assert_raises3(self):
with self.assertRaises(AssertionError):
RNAAgeCalc(idtype=1)
with self.assertRaises(AssertionError):
RNAAgeCalc(idtype="unknown")
def test_getter_setter2(self):
age_calc = RNAAgeCalc()
self.assertEqual(age_calc._tissue, "all_tissues")
self.assertEqual(age_calc.tissue, "all_tissues")
self.assertEqual(age_calc._signature, "GTExAge")
self.assertEqual(age_calc.signature, "GTExAge")
with self.assertRaises(AssertionError):
RNAAgeCalc(signature="unknown")
age_calc = RNAAgeCalc(signature="DESeq2")
self.assertEqual(age_calc._signature, "Pearson")
self.assertEqual(age_calc.signature, "Pearson")
age_calc = RNAAgeCalc(signature="DESeq")
self.assertEqual(age_calc._signature, "Pearson")
self.assertEqual(age_calc.signature, "Pearson")
with self.assertRaises(AssertionError):
RNAAgeCalc(tissue=1)
age_calc = RNAAgeCalc(tissue="brain")
self.assertEqual(age_calc._tissue, "brain")
self.assertEqual(age_calc.tissue, "brain")
self.assertEqual(age_calc._signature, "DESeq2")
self.assertEqual(age_calc.signature, "DESeq2")
age_calc = RNAAgeCalc(tissue="brain", signature="Peters")
self.assertEqual(age_calc._signature, "Peters")
self.assertEqual(age_calc.signature, "Peters")
age_calc = RNAAgeCalc(tissue="notfound")
self.assertEqual(age_calc._tissue, "all_tissues")
self.assertEqual(age_calc.tissue, "all_tissues")
self.assertEqual(age_calc._signature, "GTExAge")
self.assertEqual(age_calc.signature, "GTExAge")
with self.assertRaises(AssertionError):
age_calc = RNAAgeCalc(tissue="notfound", signature="unknown")
age_calc = RNAAgeCalc(tissue="notfound", signature="DESeq2")
self.assertEqual(age_calc._signature, "Pearson")
self.assertEqual(age_calc.signature, "Pearson")
age_calc = RNAAgeCalc(tissue="notfound", signature="DESeq")
self.assertEqual(age_calc._signature, "Pearson")
self.assertEqual(age_calc.signature, "Pearson")
with self.assertRaises(SetterError):
age_calc = RNAAgeCalc(signature="DESeq2")
age_calc.signature = "Pearson"
with self.assertRaises(SetterError):
age_calc = RNAAgeCalc(signature="DESeq2")
age_calc.tissue = "brain"
age_calc = RNAAgeCalc(signature="DESeq", tissue="brain")
self.assertEqual(age_calc._signature, "DESeq2")
age_calc1 = RNAAgeCalc(signature="DESeq", tissue="brain")
res1 = age_calc1.predict_age(exprdata=fpkm)
age_calc2 = RNAAgeCalc(signature="DESeq2", tissue="brain")
res2 = age_calc2.predict_age(exprdata=fpkm)
self.assertTrue(res1.equals(res2))
def test_assert_raises1(self):
#fpkm1 = fpkm.copy(deep=True)
age_calc = RNAAgeCalc(tissue="brain")
with self.assertRaises(AssertionError):
age_calc.predict_age(exprdata=1)
with self.assertRaises(AssertionError):
fpkm1 = fpkm.copy(deep=True)
fpkm1.iloc[:, 0] = "unknown"
age_calc.predict_age(exprdata=fpkm1)
with self.assertRaises(AssertionError):
fpkm1 = fpkm.copy(deep=True)
fpkm1.index = list(range(fpkm1.shape[0]))
age_calc.predict_age(exprdata=fpkm1)
with self.assertRaises(AssertionError):
fpkm1 = fpkm.copy(deep=True)
fpkm1.columns = list(range(fpkm1.shape[1]))
age_calc.predict_age(exprdata=fpkm1)
with self.assertRaises(AssertionError):
fpkm1 = fpkm.copy(deep=True)
templist = list(fpkm1.index)
templist[1] = templist[0]
fpkm1.index = templist
age_calc.predict_age(exprdata=fpkm1)
with self.assertRaises(AssertionError):
fpkm1 = fpkm.copy(deep=True)
fpkm1.iloc[0, 0] = -1
age_calc.predict_age(exprdata=fpkm1)