def test_loadGTF(self):
bh = BetterHits(log=self.log)
regions = []
data = bh.loadGTF(os.path.join(self.testPath, "test_2S_rRNA.gtf"),
regions)
self.assertEqual(3, len(data))
self.assertEqual(("rDNA", 16526, 16555), data[0])
self.assertEqual(("chrX", 23291700, 23291729), data[1])
def test_overlap_wrongCoords(self):
bh = BetterHits(log=self.log)
with bh.openFile(os.path.join(self.testPath,
"test_genomic_mm2.sam")) as fd:
data = fd.fetch(until_eof=True)
data.__next__()
data.__next__()
rec = data.__next__()
self.assertFalse(bh.overlaps(rec, [("chr2L", 6000, 8000)]))
def test_loadHits_unwanted(self):
bh = BetterHits(log=self.log)
data = bh.loadHits(os.path.join(self.testPath,
"test_unwanted_dm6.sam"))
self.assertEqual(3, len(data))
self.assertEqual(27, data["K00252:335:HWMMGBBXX:2:1101:25966:1437"])
self.assertEqual(24, data["K00252:335:HWMMGBBXX:2:1101:2372:1455"])
self.assertTrue(
self.hdlr.matches("loaded 4 reference sequences \(3 primary\)$"))
def test_compare(self):
bh = BetterHits(log=self.log)
ref = os.path.join(self.testPath, "test_unwanted_dm6.sam")
alt = os.path.join(self.testPath, "test_genomic_mm2.sam")
found = bh.compare(ref, alt, None)
results = bh.getResults()
self.assertEqual(2, found)
self.assertEqual("K00252:335:HWMMGBBXX:2:1101:25966:1437",
results[1][0])
self.assertEqual(28, results[1][1])
self.assertEqual(27, results[1][2])
def test_loadHits_genomic(self):
bh = BetterHits(log=self.log)
data = bh.loadHits(os.path.join(self.testPath, "test_genomic_mm2.sam"))
self.assertEqual(8,
len(data)) # filters out non-primary hits, so 8 kept
def test_sanity(self):
bh = BetterHits(log=self.log)
bh.log.debug("This is a test: %s", os.getcwd())
bh.log.debug("Who am I? %s", __file__)
self.assertTrue(self.hdlr.matches("Who am I\? .*betterHits_test.py$"))
self.assertTrue(self.hdlr.matches("This is a test: .*samUtilities$"))