def setUp(self):
unittest.TestCase.setUp(self)
self.g = DNAHistoryGraph()
self.s1 = self.g.newSegment()
self.s2 = self.g.newSegment("A")
self.s3 = self.g.newSegment("T")
self.s4 = self.g.newSegment("A")
self.g.createBranch(self.s1, self.s2)
self.g.createBranch(self.s1, self.s3)
self.g.createBranch(self.s1, self.s4)
def setUp(self):
unittest.TestCase.setUp(self)
self.g = DNAHistoryGraph()
self.s1 = self.g.newSegment()
self.s2 = self.g.newSegment("A")
self.s3 = self.g.newSegment("T")
self.s4 = self.g.newSegment("A")
self.g.createBranch(self.s1, self.s2)
self.g.createBranch(self.s1, self.s3)
self.g.createBranch(self.s1, self.s4)
class DNAHistoryGraphTest(unittest.TestCase):
"""Tests the DNA history graph functions, particularly the acyclicity functions
"""
def setUp(self):
unittest.TestCase.setUp(self)
self.g = DNAHistoryGraph()
self.s1 = self.g.newSegment("A")
self.s2 = self.g.newSegment("T")
self.s3 = self.g.newSegment("T")
self.s4 = self.g.newSegment("A")
self.s5 = self.g.newSegment("A")
self.g.createBranch(self.s1, self.s2)
self.g.createBranch(self.s1, self.s3)
self.g.createBranch(self.s3, self.s4)
self.g.createBranch(self.s3, self.s5)
self.s1b = self.g.newSegment("A")
self.s2b = self.g.newSegment("A")
self.s3b = self.g.newSegment()
self.s4b = self.g.newSegment("T")
self.s5b = self.g.newSegment("T")
self.g.createBranch(self.s1b, self.s2b)
self.g.createBranch(self.s1b, self.s3b)
self.g.createBranch(self.s3b, self.s4b)
self.g.createBranch(self.s3b, self.s5b)
def tearDown(self):
unittest.TestCase.tearDown(self)
def testInterpolateSegment(self):
#Test case where segment is root
self.assertEqual(self.s1.parent, None)
s6 = self.g.interpolateSegment(self.s1)
self.assertEqual(self.s1.parent, s6)
self.assertEqual(s6.children, set([ self.s1 ]))
#Test case where segment is not root
self.assertEqual(self.s2.parent, self.s1)
self.assertEqual(self.s1.children, set([ self.s2, self.s3 ]))
s6 = self.g.interpolateSegment(self.s2)
self.assertEqual(self.s2.parent, s6)
self.assertEqual(s6.children, set([ self.s2 ]))
self.assertEqual(self.s1.children, set([ s6, self.s3 ]))
def testPullDown(self):
s6 = self.g.pullDown(self.s1, [ self.s2, self.s3 ])
self.assertEqual(s6.parent, self.s1)
self.assertEqual(self.s1.children, set([ s6 ]))
self.assertEqual(s6.children, set([self.s2, self.s3 ]))
self.assertEqual(s6, self.s2.parent)
self.assertEqual(s6, self.s3.parent)
def testCreateBond(self):
self.g.createBond(self.s1.left, self.s1b.left)
self.assertEquals(self.s1.left.bond, self.s1b.left)
self.assertEquals(self.s1b.left.bond, self.s1.left)
self.g.createBond(self.s3.left, self.s4b.left)
self.assertEquals(self.s3.left.bond, self.s4b.left)
self.assertEquals(self.s4b.left.bond, self.s3.left)
try: #Try to make bond that violates acyclicity
self.g.createBond(self.s4.left, self.s3b.left)
self.assertTrue(False)
except RuntimeError:
pass
def testDeleteBond(self):
self.g.createBond(self.s1.left, self.s1b.left)
self.g.createBond(self.s2.left, self.s2b.left)
self.g.createBond(self.s3.left, self.s3b.left)
self.g.createBond(self.s4.left, self.s4b.left)
self.g.createBond(self.s5.left, self.s5b.left)
self.assertEquals(self.s3.left.bond, self.s3b.left)
self.assertEquals(self.s3b.left.bond, self.s3.left)
self.g.deleteBond(self.s3.left)
self.assertEquals(self.s3.left.bond, None)
self.assertEquals(self.s3b.left.bond, None)
self.g.deleteBond(self.s4.left)
self.g.deleteBond(self.s5.left)
self.g.createBond(self.s4.left, self.s3b.left)
self.assertEquals(self.s4.left.bond, self.s3b.left)
self.assertEquals(self.s3b.left.bond, self.s4.left)
self.g.deleteBond(self.s4.left)
self.g.createBond(self.s3.left, self.s4b.left)
self.assertEquals(self.s3.left.bond, self.s4b.left)
self.assertEquals(self.s4b.left.bond, self.s3.left)
def testAreSiblings(self):
pass
def testSubstitutionAmbiguity(self):
self.assertEquals(self.g.substitutionAmbiguity(), 3)
def testRearrangementAmbiguity(self):
pass
def testAmbiguity(self):
pass
def testLowerBoundSubstitutionCost(self):
self.assertEquals(self.g.lowerBoundSubstitutionCost(), 3)
def testUpperBoundSubstitutionCost(self):
self.assertEquals(self.g.upperBoundSubstitutionCost(), 6)
class ExtensionMovesTest(unittest.TestCase):
def setUp(self):
unittest.TestCase.setUp(self)
self.g = DNAHistoryGraph()
self.s1 = self.g.newSegment()
self.s2 = self.g.newSegment("A")
self.s3 = self.g.newSegment("T")
self.s4 = self.g.newSegment("A")
self.g.createBranch(self.s1, self.s2)
self.g.createBranch(self.s1, self.s3)
self.g.createBranch(self.s1, self.s4)
def tearDown(self):
unittest.TestCase.tearDown(self)
def testCase1(self):
print "Graph has substitution ambiguity", self.g.substitutionAmbiguity(
)
while self.g.substitutionAmbiguity():
chosenExtension = random.choice(listCase1(self.g))
chosenExtension.function(chosenExtension.args)
print "Graph now has substitution ambiguity", self.g.substitutionAmbiguity(
)
self.assertEquals(self.g.substitutionAmbiguity(), 0)
def testCases_random(self):
experimentNumber = 10
iterationNumber = 10
last = time.time()
experiment = 0
while experiment < experimentNumber:
print 'EXPERIMENT', experiment, time.time() - last
last = time.time()
#Create a random history
history = RandomHistory(3, 3)
avg = history.avg()
#Undo stuff in the first graph
baseGraph = deAVG(avg)
if baseGraph.substitutionAmbiguity(
) == 0 or baseGraph.rearrangementAmbiguity() == 0:
continue
def reportGraph(graph, graphName, iteration, step):
graph = copy.copy(graph)
graph.addFreeRoots()
print "\t".join([
"graphName", graphName, "experiment",
str(experiment), "iteration",
str(iteration), "step",
str(step), "ambiguity",
str(graph.ambiguity()), "u_s",
str(graph.substitutionAmbiguity()), "u_r",
str(graph.rearrangementAmbiguity()), "lbsc",
str(graph.lowerBoundSubstitutionCost()), "lbrc",
str(graph.lowerBoundRearrangementCost()), "ubsc",
str(graph.upperBoundSubstitutionCost()), "ubrc",
str(graph.upperBoundRearrangementCost())
])
#Report the starting point
reportGraph(avg, "H", "n/a", "n/a")
assert avg.validate()
#Write stuff about G
reportGraph(baseGraph, "G", "n/a", "n/a")
assert baseGraph.validate()
for iteration in range(iterationNumber):
print "Starting iteration", iteration
graph = copy.copy(baseGraph)
#Undo the ambiguity
lBSC = graph.lowerBoundSubstitutionCost()
lBRC = graph.lowerBoundRearrangementCost()
step = 1
while graph.ambiguity():
reportGraph(graph, "G'", iteration, step)
c1EL = listCase1(graph)
c2EL = listCase2(graph)
#print "There are %s labeling extensions and %s bond extensions" % (len(c1EL), len(c2EL))
chosenExtension = random.choice(c1EL + c2EL)
chosenExtension.function(chosenExtension.args)
assert graph.validate()
assert lBSC <= graph.lowerBoundSubstitutionCost()
assert lBRC <= graph.lowerBoundRearrangementCost()
lBSC = graph.lowerBoundSubstitutionCost()
lBRC = graph.lowerBoundRearrangementCost()
step += 1
#Report final AVG
reportGraph(graph, "G'", iteration, step)
assert graph.validate()
assert graph.lowerBoundSubstitutionCost(
) == graph.upperBoundSubstitutionCost()
assert graph.lowerBoundRearrangementCost(
) == graph.upperBoundRearrangementCost()
for m in graph.modules():
assert m.isSimple()
experiment += 1
class ExtensionMovesTest(unittest.TestCase):
def setUp(self):
unittest.TestCase.setUp(self)
self.g = DNAHistoryGraph()
self.s1 = self.g.newSegment()
self.s2 = self.g.newSegment("A")
self.s3 = self.g.newSegment("T")
self.s4 = self.g.newSegment("A")
self.g.createBranch(self.s1, self.s2)
self.g.createBranch(self.s1, self.s3)
self.g.createBranch(self.s1, self.s4)
def tearDown(self):
unittest.TestCase.tearDown(self)
def testCase1(self):
print "Graph has substitution ambiguity", self.g.substitutionAmbiguity()
while self.g.substitutionAmbiguity():
chosenExtension = random.choice(listCase1(self.g))
chosenExtension.function(chosenExtension.args)
print "Graph now has substitution ambiguity", self.g.substitutionAmbiguity()
self.assertEquals(self.g.substitutionAmbiguity(), 0)
def testCases_random(self):
experimentNumber = 10
iterationNumber = 10
last = time.time()
experiment = 0
while experiment < experimentNumber:
print 'EXPERIMENT', experiment, time.time() - last
last = time.time()
#Create a random history
history = RandomHistory(3, 3)
avg = history.avg()
#Undo stuff in the first graph
baseGraph = deAVG(avg)
if baseGraph.substitutionAmbiguity() == 0 or baseGraph.rearrangementAmbiguity() == 0:
continue
def reportGraph(graph, graphName, iteration, step):
graph = copy.copy(graph)
graph.addFreeRoots()
print "\t".join([ "graphName", graphName,
"experiment", str(experiment),
"iteration", str(iteration),
"step", str(step),
"ambiguity", str(graph.ambiguity()),
"u_s", str(graph.substitutionAmbiguity()),
"u_r", str(graph.rearrangementAmbiguity()),
"lbsc", str(graph.lowerBoundSubstitutionCost()),
"lbrc", str(graph.lowerBoundRearrangementCost()),
"ubsc", str(graph.upperBoundSubstitutionCost()),
"ubrc", str(graph.upperBoundRearrangementCost()) ])
#Report the starting point
reportGraph(avg, "H", "n/a", "n/a")
assert avg.validate()
#Write stuff about G
reportGraph(baseGraph, "G", "n/a", "n/a")
assert baseGraph.validate()
for iteration in range(iterationNumber):
print "Starting iteration", iteration
graph = copy.copy(baseGraph)
#Undo the ambiguity
lBSC = graph.lowerBoundSubstitutionCost()
lBRC = graph.lowerBoundRearrangementCost()
step = 1
while graph.ambiguity():
reportGraph(graph, "G'", iteration, step)
c1EL = listCase1(graph)
c2EL = listCase2(graph)
#print "There are %s labeling extensions and %s bond extensions" % (len(c1EL), len(c2EL))
chosenExtension = random.choice(c1EL + c2EL)
chosenExtension.function(chosenExtension.args)
assert graph.validate()
assert lBSC <= graph.lowerBoundSubstitutionCost()
assert lBRC <= graph.lowerBoundRearrangementCost()
lBSC = graph.lowerBoundSubstitutionCost()
lBRC = graph.lowerBoundRearrangementCost()
step += 1
#Report final AVG
reportGraph(graph, "G'", iteration, step)
assert graph.validate()
assert graph.lowerBoundSubstitutionCost() == graph.upperBoundSubstitutionCost()
assert graph.lowerBoundRearrangementCost() == graph.upperBoundRearrangementCost()
for m in graph.modules():
assert m.isSimple()
experiment += 1