class TestLoadingSingleColumnData(unittest.TestCase):
""" Testing loading VCF files into pandas
"""
def setUp(self):
self.pedfile = './data/test.ped'
self.mapfile = './data/test.map'
self.encoder = {'snp1':'A/C','snp2':'A/C','snp3':'C/A','snp4':'T/G','snp5':'C/A'}
self.PED = PED(self.pedfile, self.mapfile, encoder = self.encoder)
def testSamples(self):
self.assertEqual(self.PED.geno.shape, (5,4))
self.assertEqual(self.PED.geno.ix[0,0],0)
self.assertEqual(np.isnan(self.PED.geno.ix[0,3]), True)
self.assertEqual(self.PED.hardyweinberg('snp1'), True)
def testInfo(self):
pass
def setUp(self):
self.pedfile = './data/test.ped'
self.mapfile = './data/test.map'
self.encoder = {'snp1':'A/C','snp2':'A/C','snp3':'C/A','snp4':'T/G','snp5':'C/A'}
self.PED = PED(self.pedfile, self.mapfile, encoder = self.encoder)