def setUp(self):
self.h = Haplotypes()
self.h.read_ms_file("test/test.msms")
class TestMsmsData(unittest.TestCase):
"""
my first try at an unittest. Loads a simple msms data set and
runs some standard tests
"""
def setUp(self):
self.h = Haplotypes()
self.h.read_ms_file("test/test.msms")
def test_coords(self):
d = Coords(np.arange(0,1,.01))
self.assertTrue(np.all(d.f == sorted(d.f)))
for k,v in d.r.d.items():
self.assertEqual(k,d[v])
#setting
d[4] = 0.84
self.assertEqual(d.f, sorted(d.f))
#inserting
d.insert(34,.345)
self.assertTrue(np.all(d.f == sorted(d.f)))
for k,v in d.r.d.items():
self.assertEqual(k,d[v])
#append
d.append(1.01)
self.assertTrue(np.all(d.f == sorted(d.f)))
for k,v in d.r.d.items():
self.assertEqual(k,d[v])
def test_subsetters(self):
"""
test if the selectors work properly
"""
subset = self.h[10:20,3:7]._data
self.assertTrue(subset.shape == (4,10))
subset = self.h[10:20]._data
self.assertTrue(subset.shape == (self.h.n_hap,10))
subset = self.h[:,4:19]._data
self.assertTrue(subset.shape == (15,self.h.n_snp))
subset = self.h[:,[4,5,13]]._data
self.assertTrue(subset.shape == (3,self.h.n_snp))
subset = self.h[:,23]._data
self.assertTrue(subset.shape == (1,37))
subset = self.h[10]._data
self.assertTrue(subset.shape == (self.h.n_hap,1))
subset = self.h[10,:]._data
self.assertTrue(subset.shape == (self.h.n_hap,1))
subset = self.h[10,:10]._data
self.assertTrue(subset.shape == (10,1))
def test_subsetters_pos(self):
""" tests if subsetters work using genetic positions"""
self.h.default_coordinate_system='pos'
subset = self.h[:,[23,43]]._data
self.assertTrue(subset.shape == (2,37))
subset = self.h[:.3,43]._data
self.assertEqual(subset.shape[1],sum(self.h.coords['pos'].f<0.3))
subset = self.h[.2:,23]._data
self.assertEqual(subset.shape[1],sum(self.h.coords['pos'].f>=0.2))
subset = self.h[0.01809]._data
self.assertEqual(subset.shape,(100,1))
subset = self.h[[0.04667,0.70350]]._data
self.assertEqual(subset.shape,(100,2))
def test_sfs_freqt(self):
"""
test the creation of the SFS and freqtable
"""
sfs,freqt = self.h.make_SFS()
self.assertEqual(len(freqt),sum(sfs.sfs))
for i,snp in enumerate(self.h._data.transpose()):
self.assertEqual(freqt[i],sum(snp))
for i, freq in enumerate(sfs.sfs):
self.assertEqual(freq, sum(freqt._data == i))
self.h.default_coordinate_system = "id"
print self.h.default_coordinate_system
def test_EHH_IHS(self):
self.assertEqual(len(self.h._unique_haplotypes()),21)
self.assertNotEqual(self.h.EHH((3,6),id=11,coords='id'),7)
self.assertNotEqual(self.h.EHH((.3,.6),id=11,coords='bp'),7)