def testEvolver_Mammals_Large(self):
inputDir = os.path.join(TestStatus.getPathToDataSets(), "evolver", "mammals", "large")
mammalSequences = ("simCow.masked.fa", "simDog.masked.fa", "simHuman.masked.fa", "simMouse.masked.fa", "simRat.masked.fa")
runWorkflow_multipleExamples(self.id(),
lambda regionNumber=0, tempDir=None : getInputs(inputDir, mammalSequences),
batchSystem=self.batchSystem,
buildToilStats=True)
def run(self):
simDir = os.path.join(TestStatus.getPathToDataSets(), "evolver", "mammals", "loci1")
sequences, newickTreeString = getInputs(simDir, ("simHuman.chr6", "simMouse.chr6", "simRat.chr6", "simCow.chr6", "simDog.chr6"))
outputDir = os.path.join(self.options.outputDir, "%s%s" % (self.name, self.params))
self.addChildTarget(MakeAlignment(self.options, sequences, newickTreeString, outputDir,
self.params))
self.setupStats(outputDir, os.path.join(simDir, "all.burnin.maf"), self.params)
def testEvolver_Primates_Large(self):
inputDir = os.path.join(TestStatus.getPathToDataSets(), "evolver", "primates", "large")
primateSequences = ("simChimp.masked.fa", "simGorilla.masked.fa", "simHuman.masked.fa", "simOrang.masked.fa")
runWorkflow_multipleExamples(self.id(),
lambda regionNumber=0, tempDir=None : getInputs(inputDir, primateSequences),
batchSystem=self.batchSystem,
buildToilStats=True)
def run(self):
simDir = os.path.join(TestStatus.getPathToDataSets(), "evolver", "mammals", "large")
sequences, newickTreeString = getInputs(simDir, ("simHuman.masked.fa", "simMouse.masked.fa"))
newickTreeString = "(simHuman:0.144018,simMouse:0.356483);"
outputDir = os.path.join(self.options.outputDir, "%s%s" % (self.name, self.params))
self.addChildTarget(MakeAlignment(self.options, sequences, newickTreeString, outputDir,
self.params))
self.setupStats(outputDir, os.path.join(simDir, "all.burnin.maf"), self.params)
def testEvolver_Mammals_Large(self):
if "SON_TRACE_DATASETS" not in os.environ:
return
inputDir = os.path.join(TestStatus.getPathToDataSets(), "evolver", "mammals", "large")
mammalSequences = ("simCow.masked.fa", "simDog.masked.fa", "simHuman.masked.fa", "simMouse.masked.fa", "simRat.masked.fa")
runWorkflow_multipleExamples(lambda regionNumber=0, tempDir=None : getInputs(inputDir, mammalSequences),
testRestrictions=(TestStatus.TEST_VERY_LONG,),
batchSystem=self.batchSystem,
buildJobTreeStats=True)
def testEvolver_Primates_Large(self):
if "SON_TRACE_DATASETS" not in os.environ:
return
inputDir = os.path.join(TestStatus.getPathToDataSets(), "evolver", "primates", "large")
primateSequences = ("simChimp.masked.fa", "simGorilla.masked.fa", "simHuman.masked.fa", "simOrang.masked.fa")
runWorkflow_multipleExamples(lambda regionNumber=0, tempDir=None : getInputs(inputDir, primateSequences),
testRestrictions=(TestStatus.TEST_VERY_LONG,),
batchSystem=self.batchSystem,
buildJobTreeStats=True)
def testEvolver_Mammals_Large(self):
if "SON_TRACE_DATASETS" not in os.environ:
return
inputDir = os.path.join(TestStatus.getPathToDataSets(), "evolver", "mammals", "large")
mammalSequences = ("simCow.masked.fa", "simDog.masked.fa", "simHuman.masked.fa", "simMouse.masked.fa", "simRat.masked.fa")
runWorkflow_multipleExamples(lambda regionNumber=0, tempDir=None : getInputs(inputDir, mammalSequences),
testRestrictions=(TestStatus.TEST_VERY_LONG,),
batchSystem=self.batchSystem,
buildToilStats=True)
def testEvolver_Primates_Large(self):
if "SON_TRACE_DATASETS" not in os.environ:
return
inputDir = os.path.join(TestStatus.getPathToDataSets(), "evolver", "primates", "large")
primateSequences = ("simChimp.masked.fa", "simGorilla.masked.fa", "simHuman.masked.fa", "simOrang.masked.fa")
runWorkflow_multipleExamples(lambda regionNumber=0, tempDir=None : getInputs(inputDir, primateSequences),
testRestrictions=(TestStatus.TEST_VERY_LONG,),
batchSystem=self.batchSystem,
buildToilStats=True)
def testEvolver_Mammals_Loci1(self):
if "SON_TRACE_DATASETS" not in os.environ:
return
inputDir = os.path.join(TestStatus.getPathToDataSets(), "evolver", "mammals", "loci1")
mammalSequences = ("simCow.chr6", "simDog.chr6", "simHuman.chr6", "simMouse.chr6", "simRat.chr6")
runWorkflow_multipleExamples(lambda regionNumber=0, tempDir=None : getInputs(inputDir, mammalSequences),
testRestrictions=(TestStatus.TEST_MEDIUM,),
batchSystem=self.batchSystem,
buildToilStats=True)
def testEvolver_Primates_Loci1(self):
if "SON_TRACE_DATASETS" not in os.environ:
return
inputDir = os.path.join(TestStatus.getPathToDataSets(), "evolver", "primates", "loci1")
primateSequences = ("simChimp.chr6", "simGorilla.chr6", "simHuman.chr6", "simOrang.chr6")
runWorkflow_multipleExamples(lambda regionNumber=0, tempDir=None : getInputs(inputDir, primateSequences),
testRestrictions=(TestStatus.TEST_SHORT,),
batchSystem=self.batchSystem,
buildToilStats=True)