def test_zstd_compressed(self):
''' check we can parse genotypes from zstd compressed geno probabilities
'''
path = self.folder / 'example.16bits.zstd.bgen'
bfile = BgenFile(str(path))
for var, g in zip(bfile, self.gen_data):
self.assertEqual(g, var)
self.assertTrue(
arrays_equal(g.probabilities, var.probabilities, 16))
def test_load_haplotypes_bgen(self):
''' check we can open a bgen with haplotypes, and parse genotypes correctly
'''
path = self.folder / 'haplotypes.bgen'
bfile = BgenFile(str(path))
bit_depth = 16
for var, g in zip(bfile, self.haps_data):
self.assertEqual(g, var)
self.assertTrue(
arrays_equal(g.probabilities, var.probabilities, bit_depth))
def test_v11(self):
''' check we can open a bgen in v1.1 format, and parse genotypes correctly
'''
path = self.folder / 'example.v11.bgen'
bfile = BgenFile(str(path))
bit_depth = 16
for var, g in zip(bfile, self.gen_data):
self.assertEqual(g, var)
self.assertTrue(
arrays_equal(g.probabilities, var.probabilities, bit_depth))
def test_load_complex_file(self):
''' make sure we can open a complex bgen file
'''
path = self.folder / 'complex.bgen'
bfile = BgenFile(path)
bit_depth = 16
for var, g in zip(bfile, self.vcf_data):
self.assertEqual(g, var)
self.assertTrue(
arrays_equal(g.probabilities, var.probabilities, bit_depth))
self.assertTrue(all(x == y for x, y in zip(g.ploidy, var.ploidy)))
def test_load_example_genotypes_bit_depths(self):
''' check parsing genotypes from the example files with different bit depths
'''
for path in self.folder.glob('example.*bits.bgen'):
bit_depth = int(path.stem.split('.')[1].strip('bits'))
bfile = BgenFile(str(path))
for var, g in zip(bfile, self.gen_data):
self.assertEqual(g, var)
self.assertTrue(
arrays_equal(g.probabilities, var.probabilities,
bit_depth))
def test_load_complex_files(self):
''' make sure we can open the complex bgen files
'''
for path in self.folder.glob('complex.*.bgen'):
bit_depth = int(path.stem.split('.')[1].strip('bits'))
bfile = BgenFile(path)
for var, g in zip(bfile, self.vcf_data):
self.assertEqual(g, var)
self.assertTrue(
arrays_equal(g.probabilities, var.probabilities,
bit_depth))