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)
