示例#1
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 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)
示例#3
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 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)
示例#5
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 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)
示例#6
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 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)
示例#7
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 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)
示例#8
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 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)
示例#10
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 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)