Python bioio.TestStatus类代码示例

def runWorkflow_multipleExamples(inputGenFunction,
                                 testNumber=1, 
                                 testRestrictions=(TestStatus.TEST_SHORT, TestStatus.TEST_MEDIUM, \
                                                   TestStatus.TEST_LONG, TestStatus.TEST_VERY_LONG,),
                               inverseTestRestrictions=False,
                               batchSystem="single_machine",
                               buildAvgs=False, buildReference=False,
                               buildReferenceSequence=False,
                               buildCactusPDF=False, buildAdjacencyPDF=False,
                               buildReferencePDF=False,
                               makeCactusTreeStats=False, makeMAFs=False,
                               configFile=None, buildJobTreeStats=False):
    """A wrapper to run a number of examples.
    """
    if (inverseTestRestrictions and TestStatus.getTestStatus() not in testRestrictions) or \
        (not inverseTestRestrictions and TestStatus.getTestStatus() in testRestrictions):
        for test in xrange(testNumber): 
            tempDir = getTempDirectory(os.getcwd())
            sequences, newickTreeString = inputGenFunction(regionNumber=test, tempDir=tempDir)
            runWorkflow_TestScript(sequences, newickTreeString,
                                   batchSystem=batchSystem,
                                   buildAvgs=buildAvgs, buildReference=buildReference, 
                                   buildCactusPDF=buildCactusPDF, buildAdjacencyPDF=buildAdjacencyPDF,
                                   makeCactusTreeStats=makeCactusTreeStats, makeMAFs=makeMAFs, configFile=configFile,
                                   buildJobTreeStats=buildJobTreeStats)
            system("rm -rf %s" % tempDir)
            logger.info("Finished random test %i" % test)

 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 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 testSimulation(self):
     if TestStatus.getTestStatus() == TestStatus.TEST_LONG:
         blanchettePath = TestStatus.getPathToDataSets() + "/blanchettesSimulation/00.job"
         outputPath = TestStatus.getPathToDataSets() + "/ortheus/blanchettesSimulationTest"
         treeString = "(((((((((((((human:0.006969,chimp:0.009727):0.025291,((baboon:0.008968):0.011019):0.024581):0.023649):0.066673):0.018405,((rat:0.081244,mouse:0.072818):0.238435):0.021892):0.02326,(((cow:0.164728,(cat:0.109852,dog:0.107805):0.049576):0.004663):0.010883):0.033242):0.028346):0.016015):0.226853):0.063898):0.126639):0.119814):0.16696);"
         seqFiles = ["HUMAN", "CHIMP", "BABOON", "RAT", "MOUSE", "COW", "CAT", "DOG"]
         seqFiles = [blanchettePath + "/" + i for i in seqFiles]
         outputFile = outputPath + "/outputJob1.mfa"
         command = "Ortheus.py -e %s -d '%s' -f %s -j -a -b" % (" ".join(seqFiles), treeString, outputFile)
         print "running command", command
         system(command)

 def run(self):
     previousOutputFile = None
     previousOutputFile2 = None
     blanchettePath = os.path.join(TestStatus.getPathToDataSets(), "blanchettesSimulation")
     for i in xrange(self.options.blanchetteRepeats):
         trueAlignmentMFA = os.path.join(os.path.join(blanchettePath, "%.2i.job" % i), "true.mfa")
         trueAlignmentMAF = os.path.join(self.getLocalTempDir(), "temp.maf")
         treeFile = os.path.join(blanchettePath, "tree.newick")
         system("mfaToMaf --mfaFile %s --outputFile %s --treeFile %s" % (trueAlignmentMFA, trueAlignmentMAF, treeFile))
         
         
         trueRenamedMAF = trueAlignmentMAF + ".renamed"
         expPath = os.path.join(self.outputDir, str(i), "experiment.xml")
         applyNamingToMaf(expPath, trueAlignmentMAF, trueRenamedMAF)
         trueAlignmentMAF = trueRenamedMAF
         if self.params.vanilla == False:            
             predictedAlignmentMaf = os.path.join(self.outputDir, str(i), "progressiveCactusAlignment", "Anc0", "Anc0.maf")
         else:
             predictedAlignmentMaf = os.path.join(self.outputDir, str(i), "cactusVanilla.maf")
         
         outputFile = os.path.join(self.getLocalTempDir(), "temp%i" % i)
         system("mafComparator --mafFile1 %s --mafFile2 %s --outputFile %s" % (trueAlignmentMAF, predictedAlignmentMaf, outputFile))
         system("cp %s %s" % (outputFile, os.path.join(self.outputDir, str(i), "mafComparison.xml")))
         if previousOutputFile != None:
             system("mergeMafComparatorResults.py --results1 %s --results2 %s --outputFile %s" % (outputFile, previousOutputFile, outputFile))
         previousOutputFile = outputFile
         
     system("mv %s %s" % (previousOutputFile, os.path.join(self.outputDir, "mafComparison.xml")))   

def testCactus_Random(self, matchingAlgorithm):
    configFile = getConfigFile(matchingAlgorithm)
    runWorkflow_multipleExamples(getCactusInputs_random, 
                                 testNumber=TestStatus.getTestSetup(), 
                                 buildReference=True,
                                 configFile=configFile)
    os.remove(configFile)

def getInputs(path, sequenceNames):
    """Requires setting SON_TRACE_DATASETS variable and having access to datasets.
    """
    seqPath = os.path.join(TestStatus.getPathToDataSets(), path)
    sequences = [ os.path.join(seqPath, sequence) for sequence in sequenceNames ] #Same order as tree
    newickTreeString = parseNewickTreeFile(os.path.join(path, "tree.newick"))
    return sequences, newickTreeString  

 def testAndyYatesFirstExample(self):
     if TestStatus.getTestStatus() == TestStatus.TEST_LONG:
         filePath = TestStatus.getPathToDataSets() + "/ortheus/andyYatesExample1"
         seqs = "seq1.fa seq2.fa seq3.fa seq4.fa seq5.fa seq6.fa seq7.fa seq8.fa seq9.fa seq10.fa seq11.fa \
         seq12.fa seq13.fa seq14.fa seq15.fa seq16.fa seq17.fa seq18.fa seq19.fa seq20.fa seq21.fa seq22.fa seq23.fa seq24.fa seq25.fa seq26.fa \
         seq27.fa seq28.fa seq29.fa seq30.fa seq31.fa seq32.fa seq33.fa seq34.fa seq35.fa seq36.fa"
         seqs = " ".join(["%s/%s" % (filePath, i) for i in seqs.split()])
         command = (
             'Ortheus.py -l "#-j 0 -e" -e %s -z \
         "(((1012:0.0112,1051:0.0119):0.0026,(1055:0.0015,1052:0.0018):0.0370):0.0022,1054:0.0108,1053:0.0116);" \
         -A 1054 1051 1054 1054 1053 1012 1054 1054 1053 1054 1051 1054 1051 1051 1053 1051 1051 1012 1051 1054 1012 1054 1053 1051 1053 \
         1054 1054 1051 1012 1012 1054 1053 1053 1012 1054 1051 -f %s/output.16163.mfa -g %s/output.16163.tree-a -k "# -A" -m "java -Xmx1800m -Xms1800m" -a -b'
             % (seqs, filePath, filePath)
         )
         print "running command", command
         system(command)

 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 getCactusInputs_evolverPrimates():
    """Gets the inputs for running cactus_workflow using some simulated, half megabase primate chromosomes.
    
    Requires setting SON_TRACE_DATASETS variable and having access to datasets.
    """
    evolverPath = os.path.join(TestStatus.getPathToDataSets(), "evolver", "primates", "loci1")
    sequences = [ os.path.join(evolverPath, seqFile) for seqFile in ("simHuman.chr6", "simChimp.chr6", "simGorilla.chr6" , "simOrang.chr6") ]
    newickTreeString = parseNewickTreeFile(os.path.join(evolverPath, "tree.newick"))
    return sequences, newickTreeString

 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)

def getCactusInputs_chromosomeX(regionNumber=0, tempDir=None):
    """Gets the inputs for running cactus_workflow using an some mammlian chromosome
    X's.
    
    Requires setting SON_TRACE_DATASETS variable and having access to datasets.
    """
    chrXPath = os.path.join(TestStatus.getPathToDataSets(), "chr_x")
    sequences = [ os.path.join(chrXPath, seqFile) for seqFile in ("cow.fa", "dog.fa", "human.fa", "mouse.fa", "rat.fa") ]
    newickTreeString = parseNewickTreeFile(os.path.join(chrXPath, "newickTree.txt"))
    return sequences, newickTreeString

 def setUp(self):
     unittest.TestCase.setUp(self)
     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")
     self.defaultLastzArguments = "--ambiguous=iupac"
     self.defaultRealignArguments = ""