def test_setInOutFiles(self):
"""Test PBAlignFiles.SetInOutFiles()."""
p = PBAlignFiles()
self.assertIsNone(p.inputFileName)
self.assertIsNone(p.outputFileName)
self.assertIsNone(p.referencePath)
p.SetInOutFiles(self.inputFileName, self.referenceFile,
self.outputFileName, None)
self.assertTrue(filecmp.cmp(p.inputFileName, self.inputFileName))
self.assertTrue(filecmp.cmp(p.referencePath, self.referenceFile))
self.assertTrue(filecmp.cmp(p.targetFileName, self.referenceFile))
self.assertTrue(filecmp.cmp(p.outputFileName, self.outputFileName))
self.assertIsNone(p.regionTable)
class Test_ForQuiverService(unittest.TestCase):
"""Test pbalign.forquiverservice.forquiver."""
def setUp(self):
self.inCmpFile = path.join(DATA_DIR, "testforquiver.cmp.h5")
self.outCmpFile = mkstemp(suffix=".cmp.h5")[1]
copyfile(self.inCmpFile, self.outCmpFile)
self.basFile = path.join(DATA_DIR, "lambda_bax.fofn")
refpath = "/pbi/dept/secondary/siv/references/lambda/"
self.fileNames = PBAlignFiles()
self.fileNames.SetInOutFiles(self.basFile, refpath, self.outCmpFile,
None, None)
self.options = Opt()
self.obj = ForQuiverService(self.fileNames, self.options)
def tearDown(self):
remove(self.outCmpFile)
def test_run(self):
"""Test ForQuiverService.__init__()."""
self.obj.run()