def setUp(self):
unittest.TestCase.setUp(self)
self.testNo = TestStatus.getTestSetup(1, 1, 2, 2)
self.depth = TestStatus.getTestSetup(1, 2, 3, 5)
self.jobTreeDir = os.path.join(os.getcwd(), "jobTree") #A directory for the job tree to be created in
self.tempFileTreeDir = os.path.join(os.getcwd(), "tempFileTree") #Ensures that file tree is visible
self.tempFileTree = TempFileTree(self.tempFileTreeDir) #A place to get temp files from
def setUp(self):
unittest.TestCase.setUp(self)
self.testNo = TestStatus.getTestSetup(1, 1, 5, 5)
self.depth = TestStatus.getTestSetup(1, 2, 2, 3)
self.jobTreeDir = os.getcwd() + "/jobTree" #A directory for the job tree to be created in
self.tempFileTreeDir = os.path.join(os.getcwd(), "tempFileTree")
self.tempFileTree = TempFileTree(self.tempFileTreeDir) #A place to get temp files from
parasolRestart()
def testCactus_Random(self, matchingAlgorithm):
configFile = getConfigFile(matchingAlgorithm)
runWorkflow_multipleExamples(getCactusInputs_random,
testNumber=TestStatus.getTestSetup(),
buildReference=True,
configFile=configFile)
os.remove(configFile)
def setUp(self):
unittest.TestCase.setUp(self)
self.testNo = TestStatus.getTestSetup(1, 2, 10, 10)
self.tempDir = getTempDirectory(os.getcwd())
self.jobTreeDir = os.path.join(
self.tempDir,
"testJobTree") #A directory for the job tree to be created in
def runCactus_Random(self, matchingAlgorithm):
configFile = getConfigFile(matchingAlgorithm)
runWorkflow_multipleExamples(self.id(),
getCactusInputs_random,
testNumber=TestStatus.getTestSetup(),
configFile=configFile)
os.remove(configFile)
def testCactus_Random(self, matchingAlgorithm):
configFile = getConfigFile(matchingAlgorithm)
runWorkflow_multipleExamples(getCactusInputs_random,
testNumber=TestStatus.getTestSetup(),
buildReference=True,
configFile=configFile)
os.remove(configFile)
def setUp(self):
#This is the number of random problems to solve, handed to the test code
self.testNo = TestStatus.getTestSetup(shortTestNo=1, mediumTestNo=5,
longTestNo=10, veryLongTestNo=100)
self.tempFiles = []
self.tempDir = getTempDirectory(os.getcwd())
self.tempBlossomDirectory = self.tempDir + "/tempBlossom"
unittest.TestCase.setUp(self)
def setUp(self):
#This is the number of random problems to solve, handed to the test code
self.testNo = TestStatus.getTestSetup(shortTestNo=1, mediumTestNo=5,
longTestNo=10, veryLongTestNo=100)
self.tempFiles = []
self.tempDir = getTempDirectory(os.getcwd())
self.tempMatchGraphDirectory = self.tempDir + "/tempMatchGraph"
unittest.TestCase.setUp(self)
def testCactus_RandomAlignmentsOnly(self):
"""Build mafs from cactusDisks containing no trees, faces or reference.
"""
runWorkflow_multipleExamples(
getCactusInputs_random, #Just for the alignments.
testNumber=TestStatus.getTestSetup(),
makeMAFs=True,
buildAvgs=False,
buildReference=False)
def setUp(self):
self.testNo = TestStatus.getTestSetup(1, 5, 10, 100)
self.tempDir = getTempDirectory(os.getcwd())
self.tempFiles = []
unittest.TestCase.setUp(self)
self.tempOutputFile = os.path.join(self.tempDir, "results1.txt")
self.tempFiles.append(self.tempOutputFile)
self.tempOutputFile2 = os.path.join(self.tempDir, "results2.txt")
self.tempFiles.append(self.tempOutputFile2)
self.encodePath = os.path.join(TestStatus.getPathToDataSets(), "MAY-2005")
def setUp(self):
self.testNo = TestStatus.getTestSetup(1, 5, 10, 100)
self.tempDir = getTempDirectory(os.getcwd())
self.tempFiles = []
unittest.TestCase.setUp(self)
self.tempOutputFile = os.path.join(self.tempDir, "results1.txt")
self.tempFiles.append(self.tempOutputFile)
self.tempOutputFile2 = os.path.join(self.tempDir, "results2.txt")
self.tempFiles.append(self.tempOutputFile2)
self.encodePath = os.path.join(TestStatus.getPathToDataSets(), "MAY-2005")
def setUp(self):
self.testNo = TestStatus.getTestSetup()
unittest.TestCase.setUp(self)
self.tempDir = getTempDirectory(os.getcwd())
self.tempFiles = []
def setUp(self):
self.testNo = TestStatus.getTestSetup()
unittest.TestCase.setUp(self)
def setUp(self):
self.testNo = TestStatus.getTestSetup()
unittest.TestCase.setUp(self)
self.tempDir = getTempDirectory(os.getcwd())
self.tempFiles = []
def setUp(self):
self.testNo = TestStatus.getTestSetup(3, 10, 0, 0)
self.batchSystem = "parasol"
unittest.TestCase.setUp(self)
def setUp(self):
unittest.TestCase.setUp(self)
self.testNo = TestStatus.getTestSetup(1, 2, 10, 10)
self.tempDir = getTempDirectory(os.getcwd())
self.jobTreeDir = os.path.join(self.tempDir, "jobTree") #A directory for the job tree to be created in
def testCactus_Random(self):
runWorkflow_multipleExamples(getCactusInputs_random,
testNumber=TestStatus.getTestSetup(),
buildCactusPDF=True,
buildAdjacencyPDF=True)
def testCactus_RandomAlignmentsOnly(self):
"""Build mafs from cactusDisks containing no trees, faces or reference.
"""
runWorkflow_multipleExamples(getCactusInputs_random, #Just for the alignments.
testNumber=TestStatus.getTestSetup(),
makeMAFs=True,buildAvgs=False, buildReference=False)
def setUp(self):
unittest.TestCase.setUp(self)
self.testNo = TestStatus.getTestSetup(1, 2, 10, 10)
def setUp(self):
self.testNo = TestStatus.getTestSetup()
unittest.TestCase.setUp(self)
def testCactus_Random(self):
"""Build mafs from cactusDisks containing trees, face and an reference (the output will include the MAFS ordered by reference)
"""
runWorkflow_multipleExamples(getCactusInputs_random,
testNumber=TestStatus.getTestSetup(),
makeMAFs=True)
def setUp(self):
self.testNo = TestStatus.getTestSetup()
unittest.TestCase.setUp(self)
self.trees = randomTreeSet()
def testCactus_Random(self):
runWorkflow_multipleExamples(getCactusInputs_random,
testNumber=TestStatus.getTestSetup(),
buildAvgs=True)
def setUp(self):
self.testNo = TestStatus.getTestSetup(3, 10, 0, 0)
self.batchSystem = "parasol"
unittest.TestCase.setUp(self)
def testCactusNormalisation_Random(self):
runWorkflow_multipleExamples(self.id(),
getCactusInputs_random,
testNumber=TestStatus.getTestSetup())
def testCactus_Random(self):
runWorkflow_multipleExamples(self.id(),
getCactusInputs_random,
testNumber=TestStatus.getTestSetup(),
buildAvgs=True)
def testCactusRecursiveHalGenerator_Random(self):
runWorkflow_multipleExamples(getCactusInputs_random,
testNumber=TestStatus.getTestSetup(),
buildReference=True, buildHal=True, buildFasta=True)
def setUp(self):
unittest.TestCase.setUp(self)
self.testNo = TestStatus.getTestSetup(1, 2, 10, 10)
def setUp(self):
self.testNo = TestStatus.getTestSetup()
self.tempFiles = []
unittest.TestCase.setUp(self)
def testCactusNormalisation_Random(self):
runWorkflow_multipleExamples(getCactusInputs_random,
testNumber=TestStatus.getTestSetup())
def setUp(self):
self.testNo = TestStatus.getTestSetup()
unittest.TestCase.setUp(self)
self.trees = randomTreeSet()
def testCactusCore_Random(self):
for test in xrange(TestStatus.getTestSetup()):
randomConfigFile=getRandomConfigFile()
runWorkflow_multipleExamples(getCactusInputs_random,
configFile=randomConfigFile)
os.remove(randomConfigFile)
def testCactusCore_Random(self):
for test in xrange(TestStatus.getTestSetup()):
randomConfigFile = getRandomConfigFile()
runWorkflow_multipleExamples(getCactusInputs_random,
configFile=randomConfigFile)
os.remove(randomConfigFile)
def setUp(self):
self.testNo = TestStatus.getTestSetup()
self.tempFiles = []
unittest.TestCase.setUp(self)
def testCactus_Random(self):
"""Build mafs from cactusDisks containing trees, face and an reference (the output will include the MAFS ordered by reference)
"""
runWorkflow_multipleExamples(getCactusInputs_random,
testNumber=TestStatus.getTestSetup(),
makeMAFs=True)
def testCactus_Random(self):
runWorkflow_multipleExamples(getCactusInputs_random,
testNumber=TestStatus.getTestSetup(),
makeCactusTreeStats=True)
def testCactusRecursiveHalGenerator_Random(self):
runWorkflow_multipleExamples(getCactusInputs_random,
testNumber=TestStatus.getTestSetup(),
buildReference=True,
buildHal=True,
buildFasta=True)
