Example #1
0
 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
Example #2
0
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, 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()
Example #4
0
 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")
Example #5
0
 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 testCactus_Random(self, matchingAlgorithm):
    configFile = getConfigFile(matchingAlgorithm)
    runWorkflow_multipleExamples(getCactusInputs_random, 
                                 testNumber=TestStatus.getTestSetup(), 
                                 buildReference=True,
                                 configFile=configFile)
    os.remove(configFile)
Example #7
0
 def setUp(self):
     unittest.TestCase.setUp(self)
     self.encodeRegion = "ENm001"
     self.encodePath = os.path.join(TestStatus.getPathToDataSets(), "MAY-2005")
     self.regionPath = os.path.join(self.encodePath, self.encodeRegion)
     self.tempDir = getTempDirectory(os.getcwd())
     self.tempOutputFile = os.path.join(self.tempDir, "results1.txt")
 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")))   
Example #9
0
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  
Example #10
0
 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 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 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)
Example #13
0
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 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)
Example #15
0
 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 run(self):
     simDir = os.path.join(TestStatus.getPathToDataSets(), "blanchettesSimulation", "00.job")
     sequences = os.path.join(simDir, "HUMAN"), os.path.join(simDir, "MOUSE"), os.path.join(simDir, "DOG")
     #, newickTreeString = getInputs(simDir, ("HUMAN", "MOUSE"))
     newickTreeString = "((HUMAN:0.144018,MOUSE:0.356483):0.0238,DOG:0.197);"
     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, "true.maf"), self.params)
Example #17
0
 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_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 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)
Example #20
0
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
Example #21
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 def testENm001(self):
     if TestStatus.getTestStatus() == TestStatus.TEST_VERY_LONG:
         encodePath = TestStatus.getPathToDataSets() + "/MAY-2005/ENm001"
         outputPath = TestStatus.getPathToDataSets() + "/ortheus/encodeTest"
         # 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);'
         treeString = "((((human:0.006969,chimp:0.009727):0.025291,baboon:0.044568):0.108727,(rat:0.081244,mouse:0.072818):0.260327):0.02326,(cow:0.164728,(cat:0.109852,dog:0.107805):0.049576):0.048788):0.749525;"
         seqFiles = [
             "human.ENm001.fa",
             "chimp.ENm001.fa",
             "baboon.ENm001.fa",
             "rat.ENm001.fa",
             "mouse.ENm001.fa",
             "cow.ENm001.fa",
             "cat.ENm001.fa",
             "dog.ENm001.fa",
         ]
         seqFiles = [encodePath + "/" + i for i in seqFiles]
         outputFile = outputPath + "/outputENm001.mfa"
         command = "Ortheus.py -e %s -d '%s' -f %s -j -a -b" % (" ".join(seqFiles), treeString, outputFile)
         print "running command", command
         system(command)
 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 = ""
Example #23
0
def getCactusInputs_blanchette(regionNumber=0, tempDir=None):
    """Gets the inputs for running cactus_workflow using a blanchette simulated region
    (0 <= regionNumber < 50).
    
    Requires setting SON_TRACE_DATASETS variable and having access to datasets.
    """
    assert regionNumber >= 0
    assert regionNumber < 50
    blanchettePath = os.path.join(TestStatus.getPathToDataSets(), "blanchettesSimulation")
    sequences = [os.path.join(blanchettePath, ("%.2i.job" % regionNumber), species) \
                 for species in ("HUMAN", "CHIMP", "BABOON", "MOUSE", "RAT", "DOG", "CAT", "PIG", "COW")] #Same order as tree
    newickTreeString = parseNewickTreeFile(os.path.join(blanchettePath, "tree.newick"))
    return sequences, newickTreeString
Example #24
0
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,
                                 configFile=None, buildJobTreeStats=False, 
                                 useConstraints=False,
                                 cactusWorkflowFunction=runCactusWorkflow,
                                 buildHal=False,
                                 buildFasta=False,
                                 progressive=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())
            if useConstraints:
                sequences, newickTreeString, constraints = inputGenFunction(regionNumber=test, tempDir=tempDir)
            else:
                sequences, newickTreeString = inputGenFunction(regionNumber=test, tempDir=tempDir)
                constraints = None
            experiment = runWorkflow_TestScript(sequences, newickTreeString,
                                                outputDir=tempDir,
                                                batchSystem=batchSystem,
                                                buildAvgs=buildAvgs, buildReference=buildReference, 
                                                buildHal=buildHal,
                                                buildFasta=buildFasta,
                                                configFile=configFile,
                                                buildJobTreeStats=buildJobTreeStats,
                                                constraints=constraints,
                                                progressive=progressive,
                                                cactusWorkflowFunction=cactusWorkflowFunction)
            experiment.cleanupDb()
            system("rm -rf %s" % tempDir)
            logger.info("Finished random test %i" % test)
Example #25
0
def getCactusInputs_encode(regionNumber=0, tempDir=None):
    """Gets the inputs for running cactus_workflow using an Encode pilot project region.
     (0 <= regionNumber < 15).
    
    Requires setting SON_TRACE_DATASETS variable and having access to datasets.
    """
    assert regionNumber >= 0
    assert regionNumber < 14
    encodeRegionString = "ENm%03i" % (regionNumber+1)
    encodeDatasetPath = os.path.join(TestStatus.getPathToDataSets(), "MAY-2005")
    sequences = [ os.path.join(encodeDatasetPath, encodeRegionString, ("%s.%s.fa" % (species, encodeRegionString))) for\
                species in ("human", "chimp", "baboon", "mouse", "rat", "dog", "cow") ]
    newickTreeString = parseNewickTreeFile(os.path.join(encodeDatasetPath, "reducedTree.newick"))
    return sequences, newickTreeString
Example #26
0
def seqFilePairGenerator():
     ##Get sequences
    encodePath = os.path.join(TestStatus.getPathToDataSets(), "MAY-2005")
    encodeRegions = [ "ENm00" + str(i) for i in xrange(1,2) ] #, 2) ] #Could go to six
    species = ("human", "mouse") #, "dog")#, "chimp") 
    #Other species to try "rat", "monodelphis", "macaque", "chimp"
    for encodeRegion in encodeRegions:
        regionPath = os.path.join(encodePath, encodeRegion)
        for i in xrange(len(species)):
            species1 = species[i]
            for species2 in species[i+1:]:
                seqFile1 = os.path.join(regionPath, "%s.%s.fa" % (species1, encodeRegion))
                seqFile2 = os.path.join(regionPath, "%s.%s.fa" % (species2, encodeRegion))
                yield seqFile1, seqFile2
Example #27
0
 def setUp(self):
     self.testNo = TestStatus.getTestSetup()
     self.tempFiles = []
     unittest.TestCase.setUp(self)
Example #28
0
 def testCactusNormalisation_Random(self):
     runWorkflow_multipleExamples(getCactusInputs_random,
                                  testNumber=TestStatus.getTestSetup())
Example #29
0
 def setUp(self):
     self.testNo = TestStatus.getTestSetup()
     unittest.TestCase.setUp(self)
Example #30
0
 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())
Example #32
0
 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):
     """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)
Example #34
0
 def testCactusCore_Random(self):
     for test in xrange(TestStatus.getTestSetup()):
         randomConfigFile = getRandomConfigFile()
         runWorkflow_multipleExamples(getCactusInputs_random,
                                      configFile=randomConfigFile)
         os.remove(randomConfigFile)
Example #35
0
 def setUp(self):
     self.testNo = TestStatus.getTestSetup()
     unittest.TestCase.setUp(self)
     self.tempDir = getTempDirectory(os.getcwd())
     self.tempFiles = []
Example #36
0
 def setUp(self):
     unittest.TestCase.setUp(self)
     self.testNo = TestStatus.getTestSetup(1, 2, 10, 10)
Example #37
0
 def testCactus_Random(self):
     runWorkflow_multipleExamples(getCactusInputs_random,
                                  testNumber=TestStatus.getTestSetup(),
                                  buildAvgs=True)
Example #38
0
 def testCactusCore_Random(self):
     for test in xrange(TestStatus.getTestSetup()):
         randomConfigFile=getRandomConfigFile()
         runWorkflow_multipleExamples(getCactusInputs_random, 
                                      configFile=randomConfigFile)
         os.remove(randomConfigFile)
Example #39
0
 def testCactusRecursiveHalGenerator_Random(self):
     runWorkflow_multipleExamples(getCactusInputs_random,
                                  testNumber=TestStatus.getTestSetup(),
                                  buildReference=True,
                                  buildHal=True,
                                  buildFasta=True)
Example #40
0
 def setUp(self):
     self.testNo = TestStatus.getTestSetup()
     self.tempFiles = []
     unittest.TestCase.setUp(self)
Example #41
0
 def setUp(self):
     self.testNo = TestStatus.getTestSetup()
     unittest.TestCase.setUp(self)
     self.trees = randomTreeSet()