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)