def test_analyseCountFileFail(self):
countFile = pathlib.Path(__file__).parent / "falseStructure.tsv"
sig = Signature.loadSignaturesFromFile(type="SBS")
try:
weights = sig.analyseCountsFile(countFile)
except Exception as e:
self.assertEqual(str(e), f"File {countFile} could not be parsed")
def test_decompQP_complex(self):
sig = Signature.loadSignaturesFromFile(type="SBS")
# building artificial counts
mix = np.zeros(67)
mix[0] = 0.25
mix[2] = 0.05
mix[4] = 0.46
mix[6] = 0.1
mix[23] = 0.03
mix[25] = 0.01
mix[35] = 0.08
mix[61] = 0.02
# get the counts how they look like
counts = sig.data.dot(mix) * 100000
# QP actually wants a matrix
counts = counts.reshape((1, 96))
# deconstruct
weights = sig.whichSignaturesQP(counts)
weights = weights.flatten()
# compare true weights with deconstructed weights
error = calculateError(weights, mix)
# error should be very small
self.assertTrue(error < 0.0001)
def test_analyseCountFile(self):
countFile = pathlib.Path(__file__).parent / "SBScounts.tsv"
sig = Signature.loadSignaturesFromFile(type="SBS")
weights = sig.analyseCountsFile(countFile).values.flatten()
# building the truth
mix = np.zeros(67)
mix[0] = mix[2] = mix[5] = mix[9] = 0.25
# compare true weights with deconstructed weights
error = calculateError(weights, mix)
# error should be very small
self.assertTrue(error < 0.0001)
def test_decompILM(self):
sig = Signature.loadSignaturesFromFile(type="SBS")
# building artificial counts
mix = np.zeros(67)
mix[0] = mix[2] = mix[5] = mix[9] = 0.25
# get the counts how they look like
counts = sig.data.dot(mix) * 100000
weights = sig.whichSignaturesILM(counts)
# compare true weights with deconstructed weights
error = calculateError(weights, mix)
# error should be very small
self.assertTrue(error < 0.0001)
def test_decompILM_complex(self):
sig = Signature.loadSignaturesFromFile(type="SBS")
# building artificial counts
mix = np.zeros(67)
mix[0] = 0.25
mix[2] = 0.05
mix[4] = 0.46
mix[6] = 0.1
mix[23] = 0.03
mix[25] = 0.01
mix[35] = 0.08
mix[61] = 0.02
# get the counts how they look like
counts = sig.data.dot(mix) * 100000
# deconstruct
weights = sig.whichSignaturesILM(counts)
# compare true weights with deconstructed weights
error = calculateError(weights, mix)
# error should be very small, but ILM really f***s this, sooooo
self.assertTrue(error < 0.1)
def test_loadDefaultDBSSignature(self):
self.assertIsInstance(Signature.loadSignaturesFromFile(type="DBS"),
Signature)