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])))
