Python PED Examples

Example #1

 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)

Example #2

File: ped_tests.py Project: jeffhsu3/genda

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

Example #3

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

Example #4

File: ped_tests.py Project: jeffhsu3/genda

 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)