def setUp(self): path = os.path.dirname(os.path.abspath(__file__)) self.pedfile = path + '/data/test.ped' self.mapfile = path + '/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)
class TestLoadingSingleColumnData(unittest.TestCase): """ Testing loading VCF files into pandas """ def setUp(self): path = os.path.dirname(os.path.abspath(__file__)) self.pedfile = path + '/data/test.ped' self.mapfile = path + '/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
class TestLoadingSingleColumnData(unittest.TestCase): """ Testing loading VCF files into pandas """ def setUp(self): path = os.path.dirname(os.path.abspath(__file__)) self.pedfile = path + '/data/test.ped' self.mapfile = path + '/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): path = os.path.dirname(os.path.abspath(__file__)) self.pedfile = path + '/data/test.ped' self.mapfile = path + '/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)