def test_write_normal_output(self):
self.proteins = self.spi.readInputFile(
self.runner.pcssConfig['fasta_file'])
modelColumns = pcssModels.PcssModelTableColumns(
self.runner.internalConfig['model_table_column_file'])
self.modelTable = pcssModels.PcssModelTable(self.runner, modelColumns)
pcssProtein = self.getProtein(
"76c3a409540532138c6b44bde9e4d248MDDRDENQ", self.proteins)
disopredFileHandler = pcssFeatureHandlers.DisopredFileHandler(
self.pcssConfig, self.runner.pdh)
disopredReader = pcssFeatureHandlers.DisopredReader(
disopredFileHandler)
disopredRunner = pcssFeatureHandlers.SequenceFeatureRunner(
disopredFileHandler)
pcssProtein.processDisopred(disopredReader, disopredRunner)
psipredFileHandler = pcssFeatureHandlers.PsipredFileHandler(
self.pcssConfig, self.runner.pdh)
psipredReader = pcssFeatureHandlers.PsipredReader(psipredFileHandler)
psipredRunner = pcssFeatureHandlers.SequenceFeatureRunner(
psipredFileHandler)
pcssProtein.processPsipred(psipredReader, psipredRunner)
pcssProtein.addModels(self.modelTable)
pcssProtein.processDssp()
rankedModels = pcssProtein.getRankedModels()
afw = pcssIO.AnnotationFileWriter(self.runner)
afw.writeAllOutput(self.proteins)
annotationFileName = self.runner.pdh.getFullOutputFile(
"annotationOutput.txt")
reader = pcssIO.AnnotationFileReader(self.runner)
reader.readAnnotationFile(annotationFileName)
newProteins = reader.getProteins()
for newProtein in newProteins:
oldProtein = self.getProtein(newProtein.modbaseSequenceId,
self.proteins)
self.assertTrue(oldProtein.isEqual(newProtein))
def setupSpecificTest(self):
self.readProteins()
self.seqData = DisopredData()
self.fileHandler = pcssFeatureHandlers.DisopredFileHandler(
self.pcssConfig, self.runner.pdh)
self.sequenceFeatureReader = pcssFeatureHandlers.DisopredReader(
self.fileHandler)
self.sequenceFeatureRunner = pcssFeatureHandlers.SequenceFeatureRunner(
self.fileHandler)
self.errorDirName = "disopredErrors"
self.name = "disopred"
def runDisopred(self):
disopredFileHandler = pcssFeatureHandlers.DisopredFileHandler(
self.pcssConfig, self.pdh)
disopredReader = pcssFeatureHandlers.DisopredReader(
disopredFileHandler)
disopredRunner = pcssFeatureHandlers.SequenceFeatureRunner(
disopredFileHandler)
for protein in self.proteins:
protein.processDisopred(disopredReader, disopredRunner)
def addPeptideFeatures(self):
modelColumns = pcssModels.PcssModelTableColumns(
self.internalConfig['model_table_column_file'])
modelTable = pcssModels.PcssModelTable(self, modelColumns)
disopredFileHandler = pcssFeatureHandlers.DisopredFileHandler(
self.pcssConfig, self.pdh)
disopredReader = pcssFeatureHandlers.DisopredReader(
disopredFileHandler)
disopredRunner = pcssFeatureHandlers.SequenceFeatureRunner(
disopredFileHandler)
psipredFileHandler = pcssFeatureHandlers.PsipredFileHandler(
self.pcssConfig, self.pdh)
psipredReader = pcssFeatureHandlers.PsipredReader(psipredFileHandler)
psipredRunner = pcssFeatureHandlers.SequenceFeatureRunner(
psipredFileHandler)
for protein in self.proteins:
protein.processDisopred(disopredReader, disopredRunner)
protein.processPsipred(psipredReader, psipredRunner)
protein.addModels(modelTable)
protein.processDssp()