Python AnnotationRunner Examples

Example #1

File: test_models.py Project: salilab/pcss-python

    def setupSpecificTest(self):
        self.runner = pcssTools.AnnotationRunner(self.pcssConfig)

        spi = pcssIO.ScanPeptideImporter(self.runner)
        self.proteins = spi.readInputFile(self.runner.pcssConfig['fasta_file'])
        currentModelFile = self.runner.pdh.getFullModelFileFromId(
            "741bc8ce184702f143409644b7a6f690")

Example #2

    def readProteins(self):

        self.runner = pcssTools.AnnotationRunner(self.pcssConfig)
        self.internalConfig = self.runner.internalConfig
        spi = pcssIO.ScanPeptideImporter(self.runner)
        self.proteins = spi.readInputFile(self.runner.pcssConfig['fasta_file'])

Example #3

 def dtest_annotation_internal_error(self):
     self.runner = pcssTools.AnnotationRunner(self.pcssConfig)
     self.throwInternalException()
     self.checkErrorThrown("internalError")

Example #4

File: test_read_input.py Project: salilab/pcss-python

    def setupSpecificTest(self):

        self.runner = pcssTools.AnnotationRunner(self.pcssConfig)
        self.spi = pcssIO.ScanPeptideImporter(self.runner)
        self.errorDirName = "ioErrors"
        self.testName = "io"

Example #5

 def dtest_annotation_pcss_error(self):
     self.runner = pcssTools.AnnotationRunner(self.pcssConfig)
     self.throwPcssException()
     self.checkErrorThrown("pcssError")