def MapperPreRun(): if len(worker.fastQFileList) > 2: fastQPairs = len(worker.fastQFileList) - 1 i = 0 while i < fastQPairs: mapper = ReadAligner.Bowtie2(worker.fastQFileList[i], worker.fastQFileList[i + 1], worker.refGenomeList[0], options.output_filepath) worker.mapperClass.append(mapper) mapper.start() i += 2 else: mapper = ReadAligner.Bowtie2(worker.fastQFileList[0], worker.fastQFileList[1], worker.refGenomeList[0], options.output_filepath) worker.mapperClass.append(mapper) mapper.start() for mapper in worker.mapperClass: mapper.join() for mapper in worker.mapperClass: bamWorker = ReadAligner.BamTools(mapper.samFile, mapper.referenceDB) bamWorker.start() worker.bamClass.append(bamWorker) for bamWorker in worker.bamClass: bamWorker.join() for bamWorker in worker.bamClass: visualisationTool = VisualisationTools(bamWorker.samFile) visualisationTool.start() worker.visualisationClass.append(visualisationTool) for visualisationTool in worker.visualisationClass: visualisationTool.join() mapperPrimer = PrimerDesign.PrimerDesignByMapping() for visualisationTool in worker.visualisationClass: mapperPrimer.generateCoords(visualisationTool.depthPerPos) return PrimerDesign.PrimerDesign.runIntersect(mapperPrimer.coordsFile, "/MapperPoI.gff")
def test_readBedToLocal(self): visualisationTools = VisualisationTools("test_data/test", "test_data/") visualisationTools.readBedToLocal() self.assertEqual(len(visualisationTools.depthPerPos), 6)
def test_getCoveragePercentage(self): visualisationTools = VisualisationTools("test_data/test", "test_data/") visualisationTools.readCovBedtoLocal() self.assertAlmostEqual(visualisationTools.getCoveragePercentage(5), 0.65295766, 4)
def test_readCovBedtoLocal(self): visualisationTools = VisualisationTools("test_data/test", "test_data/") visualisationTools.readCovBedtoLocal() self.assertEqual(len(visualisationTools.depthOccurance), 6651)