def testCactusSetup(self):
"""Creates a bunch of random inputs and then passes them to cactus setup.
"""
for test in xrange(self.testNo):
tempDir = os.path.relpath(getTempDirectory(os.getcwd()))
sequenceNumber = random.choice(xrange(100))
sequences, newickTreeString = getCactusInputs_random(
tempDir=tempDir, sequenceNumber=sequenceNumber)
#Setup the flower disk.
experiment = getCactusWorkflowExperimentForTest(
sequences, newickTreeString,
os.path.join('/data', os.path.relpath(tempDir)))
cactusDiskDatabaseString = experiment.getDiskDatabaseString()
cactusSequencesPath = os.path.join(experiment.getDbDir(),
"cactusSequences")
runCactusSetup(cactusDiskDatabaseString=cactusDiskDatabaseString,
cactusSequencesPath=cactusSequencesPath,
sequences=sequences,
newickTreeString=newickTreeString)
runCactusSetup(cactusDiskDatabaseString=cactusDiskDatabaseString,
cactusSequencesPath=cactusSequencesPath,
sequences=sequences,
newickTreeString=newickTreeString)
experiment.cleanupDb()
system("rm -rf %s" % tempDir)
logger.info("Finished test %i of cactus_setup.py", test)
def testCactus_Random_UseSubtreeRoot(self):
"""Tests that cactus doesn't crash when aligning a subtree of a larger
species tree."""
getBigSpeciesTree = lambda regionNumber=0,tempDir=None: getCactusInputs_random(regionNumber, tempDir, treeLeafNumber=5)
runWorkflow_multipleExamples(getBigSpeciesTree,
testNumber=1,
batchSystem=self.batchSystem, buildToilStats=True,
progressive=True,
configFile=self.configFile,
cactusWorkflowFunction=self.progressiveWithSubtreeRootFunction)
def testCactusSetup(self):
"""Creates a bunch of random inputs and then passes them to cactus setup.
"""
for test in xrange(self.testNo):
tempDir = getTempDirectory(os.getcwd())
sequenceNumber = random.choice(xrange(100))
sequences, newickTreeString = getCactusInputs_random(tempDir=tempDir, sequenceNumber=sequenceNumber)
#Setup the flower disk.
experiment = getCactusWorkflowExperimentForTest(sequences, newickTreeString, tempDir)
cactusDiskDatabaseString = experiment.getDiskDatabaseString()
runCactusSetup(cactusDiskDatabaseString, sequences, newickTreeString)
runCactusSetup(cactusDiskDatabaseString, sequences, newickTreeString)
experiment.cleanupDb()
system("rm -rf %s" % tempDir)
logger.info("Finished test %i of cactus_setup.py", test)
def testCactus_Random_UseSubtreeRoot(self):
# TODO: this doesn't actually need the test data, but this is
# being used as a signal that the tester doesn't want to run
# the long tests. The tests should be refactored soon.
if "SON_TRACE_DATASETS" not in os.environ:
return
"""Tests that cactus doesn't crash when aligning a subtree of a larger
species tree."""
getBigSpeciesTree = lambda regionNumber=0, tempDir=None: getCactusInputs_random(
regionNumber, tempDir, treeLeafNumber=5)
runWorkflow_multipleExamples(
getBigSpeciesTree,
testNumber=1,
testRestrictions=(TestStatus.TEST_SHORT, ),
batchSystem=self.batchSystem,
buildToilStats=True,
progressive=True,
configFile=self.configFile,
cactusWorkflowFunction=self.progressiveWithSubtreeRootFunction)
def testCactus_Random_fixedAncestor(self):
"""Tests that cactus doesn't crash when aligning to a fixed ancestral sequence."""
sequences, _ = getCactusInputs_random(treeLeafNumber=3)
rootSeq = sequences.pop()
# Create a star tree
tree = '(%s)root;' % ",".join([str(x) + ":1.0" for x in range(len(sequences))])
outputDir = getTempDirectory()
experiment = getCactusWorkflowExperimentForTest(sequences, tree,
outputDir,
progressive=True)
experiment.setSequenceID("root", rootSeq)
experiment.setRootReconstructed(False)
experimentFile = os.path.join(outputDir, "experiment.xml")
experiment.writeXML(experimentFile)
jobTreeDir = os.path.join(outputDir, "jobTree")
self.progressiveFunction(experimentFile, jobTreeDir, 'singleMachine',
False, True, True, False)