def test2(self): old_dir = os.getcwd() os.chdir(os.path.dirname(os.path.realpath(__file__))) logging.info("in TestBgen test2") bgen = Bgen("../examples/bits1.bgen") bgen.read() bgen2 = bgen[:2, ::3] bgen2.read() os.chdir(old_dir)
def test1(self): old_dir = os.getcwd() os.chdir(os.path.dirname(os.path.realpath(__file__))) logging.info("in TestBgen test1") bgen = Bgen('../examples/example.bgen') distdata = bgen.read() bgen2 = bgen[:2, ::3] distdata2 = bgen2.read() os.chdir(old_dir)
def test2(self): from pysnptools.distreader import Bgen old_dir = os.getcwd() os.chdir(os.path.dirname(os.path.realpath(__file__))) bgen = Bgen('../examples/example.bgen') distmemmap = DistMemMap.write("tempdir/bgentomemmap.dist.memamp", bgen) assert DistData.allclose(bgen.read(), distmemmap.read(), equal_nan=True) os.chdir(old_dir)
def test_bgen_reader_without_metadata(self): with example_filepath("example.32bits.bgen") as filepath: bgen = Bgen(filepath) bgen.read() samples = bgen.iid assert samples[-1, 1] == "sample_500"
dist_gen, bits=8, compression="zlib", cleanup_temp_files=False) # print(os.path.getsize(filename)) # if False: #!!!c,l # from pysnptools.distreader import Bgen # bgen = Bgen(r'D:\OneDrive\programs\hide\bgen-reader-py\bgen_reader\_example\complex.23bits.no.samples.bgen',allow_complex=True) # print(bgen.sid_count) if False: from pysnptools.distreader import Bgen bgen = Bgen(r"M:\deldir\2500x100.bgen") bgen.read() print(bgen.shape) print("") if False: from pysnptools.distreader import Bgen bgen = Bgen(r"M:\deldir\1x1000000.bgen", verbose=True) print(bgen.shape) print("") if False: from pysnptools.distreader import Bgen bgen2 = Bgen(r"M:\deldir\10x5000000.bgen", verbose=True) print(bgen2.shape)
# Download a sample file from pysnptools.util import example_file bgen_file = example_file("pysnptools/examples/example.bgen") # Read from the file from pysnptools.distreader import Bgen bgen = Bgen(bgen_file) # Create a reader probs0 = bgen[:, 0].read().val # Read 1st SNP print(probs0.shape) # Shape of the NumPy array assert probs0.shape == (500, 1, 3) probs_all = bgen.read().val # Read all variants print(probs_all.shape) # Shape of the NumPy array assert probs_all.shape == (500, 199, 3)