def test_filter_denovogear_sites(self): ''' check that filter_denovogear_sites() works correctly ''' initial = [True, True] status = filter_denovogear_sites(self.variants, initial) self.assertTrue(all(status == Series([True, True])))
def test_filter_denovogear_sites(self): ''' check that filter_denovogear_sites() works correctly ''' initial = [True, True] status = filter_denovogear_sites(self.variants, initial) self.assertTrue(all(status == Series([True, True])))
def test_filter_denovogear_sites_strand_bias(self): ''' check that filter_denovogear_sites() identifies strand biased sites ''' initial = [True, True] # define a site with extreme strand bias self.variants['pos'] = [1, 2] self.variants['dp4_child'] = ['40,15,20,25', '20,15,30,25'] self.variants['dp4_mother'] = ['40,15,0,1', '20,20,0,1'] self.variants['dp4_father'] = ['60,30,0,1', '30,30,0,1'] status = filter_denovogear_sites(self.variants, initial) self.assertTrue(all(status == Series([False, True]))) # but indels don't use the same strand bias filter self.variants['ref'] = ['AG', 'A'] status = filter_denovogear_sites(self.variants, initial) self.assertTrue(all(status == Series([True, True])))
def test_filter_denovogear_sites_strand_bias(self): ''' check that filter_denovogear_sites() identifies strand biased sites ''' initial = [True, True] # define a site with extreme strand bias self.variants['pos'] = [1, 2] self.variants['dp4_child'] = ['40,15,20,25', '20,15,30,25'] self.variants['dp4_mother'] = ['40,15,0,1', '20,20,0,1'] self.variants['dp4_father'] = ['60,30,0,1', '30,30,0,1'] status = filter_denovogear_sites(self.variants, initial) self.assertTrue(all(status == Series([False, True]))) # but indels don't use the same strand bias filter self.variants['ref'] = ['AG', 'A'] status = filter_denovogear_sites(self.variants, initial) self.assertTrue(all(status == Series([True, True])))
def test_filter_denovogear_sites_parental_bias(self): ''' check that filter_denovogear_sites() identifies parentally biased sites ''' initial = [True, True] # define a site with extreme parental bias self.variants['pos'] = [1, 2] self.variants['dp4_child'] = ['20,15,20,25', '20,15,30,25'] self.variants['dp4_mother'] = ['10,10,0,2', '20,20,0,1'] self.variants['dp4_father'] = ['10,10,0,1', '30,30,0,0'] status = filter_denovogear_sites(self.variants, initial) self.assertTrue(all(status == Series([False, True]))) # define a site which only fails one of the filtering criteria, an # extreme parental alt bias at a site. self.variants['pos'] = [1, 2] self.variants['dp4_child'] = ['20,15,20,25', '20,15,30,25'] self.variants['dp4_mother'] = ['8,8,0,3', '100,100,0,1'] self.variants['dp4_father'] = ['10,10,0,0', '100,100,0,0'] status = filter_denovogear_sites(self.variants, initial) self.assertTrue(all(status == Series([True, True])))
def test_filter_denovogear_sites_parental_bias(self): ''' check that filter_denovogear_sites() identifies parentally biased sites ''' initial = [True, True] # define a site with extreme parental bias self.variants['pos'] = [1, 2] self.variants['dp4_child'] = ['20,15,20,25', '20,15,30,25'] self.variants['dp4_mother'] = ['10,10,0,2', '20,20,0,1'] self.variants['dp4_father'] = ['10,10,0,1', '30,30,0,0'] status = filter_denovogear_sites(self.variants, initial) self.assertTrue(all(status == Series([False, True]))) # define a site which only fails one of the filtering criteria, an # extreme parental alt bias at a site. self.variants['pos'] = [1, 2] self.variants['dp4_child'] = ['20,15,20,25', '20,15,30,25'] self.variants['dp4_mother'] = ['8,8,0,3', '100,100,0,1'] self.variants['dp4_father'] = ['10,10,0,0', '100,100,0,0'] status = filter_denovogear_sites(self.variants, initial) self.assertTrue(all(status == Series([True, True])))