def setUp(self):
# Create and populate a SolidPrimaryData instance
self.solid_primary_data = SolidPrimaryData()
self.solid_primary_data.add_file(utils.MockArchiveFile('test1_F3.csfasta'))
self.solid_primary_data.add_file(utils.MockArchiveFile('test1_F3_QV.qual'))
self.solid_primary_data.add_file(utils.MockArchiveFile('test1_F5-BC.csfasta'))
self.solid_primary_data.add_file(utils.MockArchiveFile('test1_F5-BC_QV.qual'))
def test_paired_end(self):
# F3 file pair
self.assertFalse(SolidPrimaryData(
utils.MockArchiveFile('test1_F3.csfasta'),
utils.MockArchiveFile('test1_F3_QV.qual')).paired_end)
# F5 file pair
self.assertTrue(SolidPrimaryData(
utils.MockArchiveFile('test1_F5-BC.csfasta'),
utils.MockArchiveFile('test1_F5-BC_QV.qual')).paired_end)
# Not a file pair
self.assertFalse(SolidPrimaryData(
utils.MockArchiveFile('test1_F5-BC.csfasta')).paired_end)
def test_timestamps(self):
# No timestamps for 'empty' library
lib = SolidLibrary('PB','PJB_01')
self.assertEqual(lib.timestamps,[])
# Add dummy fileset
lib.add_file_set('9876543210',SolidPrimaryData())
self.assertEqual(lib.timestamps,['9876543210'])
def test_get_file_sets(self):
# Add and retrieve fileset to/from a library
lib = SolidLibrary('PB','PJB_01')
fs1 = SolidPrimaryData()
lib.add_file_set('9876543210',fs1)
# Retrieve from specific timestamp
self.assertEqual(lib.get_file_sets('9876543210'),[fs1])
# Retrieve all file sets
self.assertEqual(lib.get_file_sets(),[fs1])
def test_is_valid(self):
# F3 file pair
self.assertTrue(SolidPrimaryData(
utils.MockArchiveFile('test1_F3.csfasta'),
utils.MockArchiveFile('test1_F3_QV.qual')).is_valid)
# F5 file pair
self.assertTrue(SolidPrimaryData(
utils.MockArchiveFile('test1_F5-BC.csfasta'),
utils.MockArchiveFile('test1_F5-BC_QV.qual')).is_valid)
# Not a file pair
self.assertFalse(SolidPrimaryData(
utils.MockArchiveFile('test1_F3.csfasta')).is_valid)
self.assertFalse(SolidPrimaryData(
utils.MockArchiveFile('test1_F5-BC_QV.qual')).is_valid)
# Too many files
self.assertFalse(SolidPrimaryData(
utils.MockArchiveFile('test1_F3.csfasta'),
utils.MockArchiveFile('test1_F3_QV.qual'),
utils.MockArchiveFile('test2_F3_QV.qual')).is_valid)
def test_add_file_set(self):
# Add a fileset to a library
# !!!This isn't really a test!!!
lib = SolidLibrary('PB','PJB_01')
lib.add_file_set('9876543210',SolidPrimaryData())
class TestSolidPrimaryData(unittest.TestCase):
def setUp(self):
# Create and populate a SolidPrimaryData instance
self.solid_primary_data = SolidPrimaryData()
self.solid_primary_data.add_file(utils.MockArchiveFile('test1_F3.csfasta'))
self.solid_primary_data.add_file(utils.MockArchiveFile('test1_F3_QV.qual'))
self.solid_primary_data.add_file(utils.MockArchiveFile('test1_F5-BC.csfasta'))
self.solid_primary_data.add_file(utils.MockArchiveFile('test1_F5-BC_QV.qual'))
def test_add_file(self):
# Add files
# !!!This isn't really a test!!!
raise unittest.SkipTest("SolidPrimaryData.add_file not testable?")
def test_f3(self):
# Retrieve F3 files
self.assertEqual(len(self.solid_primary_data.f3),2)
files = [f.path for f in self.solid_primary_data.f3]
self.assertTrue(os.path.abspath('test1_F3.csfasta') in files)
self.assertTrue(os.path.abspath('test1_F3_QV.qual') in files)
def test_f5(self):
# Retrieve F5 files
self.assertEqual(len(self.solid_primary_data.f5),2)
files = [f.path for f in self.solid_primary_data.f5]
self.assertTrue(os.path.abspath('test1_F5-BC.csfasta') in files)
self.assertTrue(os.path.abspath('test1_F5-BC_QV.qual') in files)
def test_files(self):
# Retrieve all files
self.assertEqual(len(self.solid_primary_data.files),4)
files = [f.path for f in self.solid_primary_data.files]
self.assertTrue(os.path.abspath('test1_F3.csfasta') in files)
self.assertTrue(os.path.abspath('test1_F3_QV.qual') in files)
self.assertTrue(os.path.abspath('test1_F5-BC.csfasta') in files)
self.assertTrue(os.path.abspath('test1_F5-BC_QV.qual') in files)
def test_is_valid(self):
# F3 file pair
self.assertTrue(SolidPrimaryData(
utils.MockArchiveFile('test1_F3.csfasta'),
utils.MockArchiveFile('test1_F3_QV.qual')).is_valid)
# F5 file pair
self.assertTrue(SolidPrimaryData(
utils.MockArchiveFile('test1_F5-BC.csfasta'),
utils.MockArchiveFile('test1_F5-BC_QV.qual')).is_valid)
# Not a file pair
self.assertFalse(SolidPrimaryData(
utils.MockArchiveFile('test1_F3.csfasta')).is_valid)
self.assertFalse(SolidPrimaryData(
utils.MockArchiveFile('test1_F5-BC_QV.qual')).is_valid)
# Too many files
self.assertFalse(SolidPrimaryData(
utils.MockArchiveFile('test1_F3.csfasta'),
utils.MockArchiveFile('test1_F3_QV.qual'),
utils.MockArchiveFile('test2_F3_QV.qual')).is_valid)
def test_paired_end(self):
# F3 file pair
self.assertFalse(SolidPrimaryData(
utils.MockArchiveFile('test1_F3.csfasta'),
utils.MockArchiveFile('test1_F3_QV.qual')).paired_end)
# F5 file pair
self.assertTrue(SolidPrimaryData(
utils.MockArchiveFile('test1_F5-BC.csfasta'),
utils.MockArchiveFile('test1_F5-BC_QV.qual')).paired_end)
# Not a file pair
self.assertFalse(SolidPrimaryData(
utils.MockArchiveFile('test1_F5-BC.csfasta')).paired_end)