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")
def test_empty_rules_file(self):
self.pcssConfig["rules_file"] = self.getErrorInputFile(
"emptyPeptideRulesFile")
spi = pcssIO.ScanPeptideImporter(self.runner)
proteins = spi.readInputFile(self.runner.pcssConfig['fasta_file'])
firstProtein = proteins[0]
self.assertEquals(248, len(firstProtein.peptides.values()))
def readProteins(self):
peptideImporterType = self.pcssConfig["peptide_importer_type"]
peptideImporter = None
if (peptideImporterType == "scan"):
peptideImporter = pcssIO.ScanPeptideImporter(self)
elif (peptideImporterType == "defined"):
peptideImporter = pcssIO.DefinedPeptideImporter(self)
else:
peptideImporter = pcssIO.FullProteinImporter(self)
self.proteins = peptideImporter.readInputFile(
self.pcssConfig['fasta_file'])
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'])
def setupSpecificTest(self):
self.runner = pcssTools.AnnotationRunner(self.pcssConfig)
self.spi = pcssIO.ScanPeptideImporter(self.runner)
self.errorDirName = "ioErrors"
self.testName = "io"