Python filter_missing_indels Examples

Example #1

File: test_missing_indels.py Project: jeremymcrae/denovoFilter

 def test_filter_missing_indels_child_proportion(self):
     ''' test that filter_missing_indels() screens low child proportion
     '''
     
     self.variants['dp4_child'] = ['20,15,30,25', '30,30,7,7']
     status = filter_missing_indels(self.variants)
     self.assertTrue(all(status == Series([True, False])))

Example #2

File: test_missing_indels.py Project: jeremymcrae/denovoFilter

 def test_filter_missing_indels_parental_depth(self):
     ''' test that filter_missing_indels() screens low parental depth
     '''
     
     self.variants['dp4_mother'] = ['20,20,0,1', '3,3,0,0']
     status = filter_missing_indels(self.variants)
     self.assertTrue(all(status == Series([True, False])))

Example #3

File: test_missing_indels.py Project: jeremymcrae/denovoFilter

 def test_filter_missing_indels_parental_proportion(self):
     ''' test that filter_missing_indels() screens high parental proportion
     '''
     
     self.variants['dp4_mother'] = ['20,20,0,1', '4,4,0,1']
     status = filter_missing_indels(self.variants)
     self.assertTrue(all(status == Series([True, False])))

Example #4

File: test_missing_indels.py Project: jeremymcrae/denovoFilter

 def test_filter_missing_indels_child_depth(self):
     ''' test that filter_missing_indels() screens low child alt depth
     '''
     
     self.variants['dp4_child'] = ['20,15,30,25', '2,2,1,1']
     status = filter_missing_indels(self.variants)
     self.assertTrue(all(status == Series([True, False])))

Example #5

    def test_filter_missing_indels_child_proportion(self):
        ''' test that filter_missing_indels() screens low child proportion
        '''

        self.variants['dp4_child'] = ['20,15,30,25', '30,30,7,7']
        status = filter_missing_indels(self.variants)
        self.assertTrue(all(status == Series([True, False])))

Example #6

    def test_filter_missing_indels_parental_proportion(self):
        ''' test that filter_missing_indels() screens high parental proportion
        '''

        self.variants['dp4_mother'] = ['20,20,0,1', '4,4,0,1']
        status = filter_missing_indels(self.variants)
        self.assertTrue(all(status == Series([True, False])))

Example #7

    def test_filter_missing_indels_parental_depth(self):
        ''' test that filter_missing_indels() screens low parental depth
        '''

        self.variants['dp4_mother'] = ['20,20,0,1', '3,3,0,0']
        status = filter_missing_indels(self.variants)
        self.assertTrue(all(status == Series([True, False])))

Example #8

    def test_filter_missing_indels_child_depth(self):
        ''' test that filter_missing_indels() screens low child alt depth
        '''

        self.variants['dp4_child'] = ['20,15,30,25', '2,2,1,1']
        status = filter_missing_indels(self.variants)
        self.assertTrue(all(status == Series([True, False])))

Example #9

File: test_missing_indels.py Project: jeremymcrae/denovoFilter

 def test_filter_missing_indels_parental_alt(self):
     ''' test that filter_missing_indels() screens high parental alts
     '''
     
     self.variants['dp4_mother'] = ['20,20,0,1', '20,20,0,2']
     self.variants['dp4_father'] = ['30,30,0,1', '30,30,0,2']
     status = filter_missing_indels(self.variants)
     self.assertTrue(all(status == Series([True, False])))

Example #10

    def test_filter_missing_indels_parental_alt(self):
        ''' test that filter_missing_indels() screens high parental alts
        '''

        self.variants['dp4_mother'] = ['20,20,0,1', '20,20,0,2']
        self.variants['dp4_father'] = ['30,30,0,1', '30,30,0,2']
        status = filter_missing_indels(self.variants)
        self.assertTrue(all(status == Series([True, False])))

Example #11

File: test_missing_indels.py Project: jeremymcrae/denovoFilter

 def test_filter_missing_indels(self):
     ''' test that filter_missing_indels() passes the default variants
     '''
     
     status = filter_missing_indels(self.variants)
     self.assertTrue(all(status == Series([True, True])))

Example #12

    def test_filter_missing_indels(self):
        ''' test that filter_missing_indels() passes the default variants
        '''

        status = filter_missing_indels(self.variants)
        self.assertTrue(all(status == Series([True, True])))