def write(filename, snpdata):
"""Writes a :class:`SnpData` to SnpNpz format.
:param filename: the name of the file to create
:type filename: string
:param snpdata: The in-memory data that should be written to disk.
:type snpdata: :class:`SnpData`
>>> from pysnptools.snpreader import SnpNpz, Bed
>>> import pysnptools.util as pstutil
>>> snpdata = Bed('../examples/toydata.bed',count_A1=False)[:,:10].read() # Read first 10 snps from Bed format
>>> pstutil.create_directory_if_necessary("tempdir/toydata10.snp.npz")
>>> SnpNpz.write("tempdir/toydata10.snp.npz",snpdata) # Write data in SnpNpz format
"""
PstNpz.write(filename, snpdata)
def write(filename, snpdata):
"""Writes a :class:`SnpData` to SnpNpz format.
:param filename: the name of the file to create
:type filename: string
:param snpdata: The in-memory data that should be written to disk.
:type snpdata: :class:`SnpData`
>>> from pysnptools.snpreader import SnpNpz, Bed
>>> import pysnptools.util as pstutil
>>> snpdata = Bed('../examples/toydata.bed')[:,:10].read() # Read first 10 snps from Bed format
>>> pstutil.create_directory_if_necessary("tempdir/toydata10.snp.npz")
>>> SnpNpz.write("tempdir/toydata10.snp.npz",snpdata) # Write data in SnpNpz format
"""
PstNpz.write(filename,snpdata)
def write(filename, kerneldata):
"""Writes a :class:`KernelData` to KernelNpz format.
:param filename: the name of the file to create
:type filename: string
:param kerneldata: The in-memory data that should be written to disk.
:type kerneldata: :class:`KernelData`
>>> from pysnptools.snpreader import Bed
>>> from pysnptools.standardizer import Unit
>>> import pysnptools.util as pstutil
>>> kerneldata = Bed('../examples/toydata.bed',count_A1=False).read_kernel(Unit()) # Create a kernel from the data in the Bed file
>>> pstutil.create_directory_if_necessary("tempdir/toydata.kernel.npz")
>>> KernelNpz.write("tempdir/toydata.kernel.npz",kerneldata) # Write data in KernelNpz format
"""
PstNpz.write(filename,kerneldata)
def write(filename, kerneldata):
"""Writes a :class:`KernelData` to KernelNpz format.
:param filename: the name of the file to create
:type filename: string
:param kerneldata: The in-memory data that should be written to disk.
:type kerneldata: :class:`KernelData`
>>> from pysnptools.snpreader import Bed
>>> from pysnptools.standardizer import Unit
>>> import pysnptools.util as pstutil
>>> kerneldata = Bed('pysnptools/examples/toydata.bed',count_A1=False).read_kernel(Unit()) # Create a kernel from the data in the Bed file
>>> pstutil.create_directory_if_necessary("tempdir/toydata.kernel.npz")
>>> KernelNpz.write("tempdir/toydata.kernel.npz",kerneldata) # Write data in KernelNpz format
"""
PstNpz.write(filename, kerneldata)
def test_big_npz(self):
logging.info("in test_big_npz")
n = 1000
pstdata = PstData(row=range(n-1),col=range(n+1),val=np.zeros([n-1,n+1]))
output = "tempdir/pstreader/big.npz"
create_directory_if_necessary(output)
PstNpz.write(output,pstdata)
pstnpz = PstNpz(output)
pstdata1 = pstnpz[::2,::4].read()
pstdata2 = pstnpz.read(order='A')
assert pstdata2.val.flags['C_CONTIGUOUS']
pstdata = PstData(row=range(n-1),col=range(n+1),val=np.zeros([n-1,n+1],order='F'))
PstNpz.write(output,pstdata)
pstnpz = PstNpz(output)
pstdata2 = pstnpz.read(order='A')
pstdata2.val.flags['F_CONTIGUOUS']
print("done")
def test_respect_read_inputs(self):
from pysnptools.pstreader import _MergeRows, _MergeCols
previous_wd = os.getcwd()
os.chdir(os.path.dirname(os.path.realpath(__file__)))
for pstreader in [
PstNpz('../examples/toydata10.snp.npz'),
_MergeRows([
PstHdf5('../examples/toydata.snpmajor.snp.hdf5')
[:5, :].read(),
PstHdf5('../examples/toydata.snpmajor.snp.hdf5')[
5:, :].read()
]),
_MergeCols([
PstHdf5(
'../examples/toydata.snpmajor.snp.hdf5')[:, :5].read(),
PstHdf5('../examples/toydata.snpmajor.snp.hdf5')
[:, 5:].read()
]),
PstHdf5('../examples/toydata.snpmajor.snp.hdf5')[::2, ::2],
PstHdf5('../examples/toydata.snpmajor.dist.hdf5').read(),
PstHdf5('../examples/toydata.kernel.hdf5'),
PstMemMap('../examples/tiny.pst.memmap')
]:
logging.info(str(pstreader))
for order in ['F', 'C', 'A']:
for dtype in [np.float32, np.float64]:
for force_python_only in [True, False]:
for view_ok in [True, False]:
val = pstreader.read(
order=order,
dtype=dtype,
force_python_only=force_python_only,
view_ok=view_ok).val
has_right_order = order == "A" or (
order == "C" and val.flags["C_CONTIGUOUS"]
) or (order == "F" and val.flags["F_CONTIGUOUS"])
if hasattr(pstreader, 'val') and not view_ok:
assert pstreader.val is not val
if (hasattr(pstreader, 'val') and view_ok
and pstreader.val is not val and
(order == 'A' or
(order == 'F'
and pstreader.val.flags['F_CONTIGUOUS']) or
(order == 'C'
and pstreader.val.flags['C_CONTIGUOUS']))
and (dtype is None
or pstreader.val.dtype == dtype)):
logging.info(
"{0} could have read a view, but didn't".
format(pstreader))
assert val.dtype == dtype and has_right_order
os.chdir(previous_wd)
def write(filename, kerneldata):
"""Writes a :class:`KernelData` to KernelNpz format and returns the :class:`.KernelNpz`.
:param filename: the name of the file to create
:type filename: string
:param kerneldata: The in-memory data that should be written to disk.
:type kerneldata: :class:`KernelData`
:rtype: :class:`.KernelNpz`
>>> from pysnptools.snpreader import Bed
>>> from pysnptools.standardizer import Unit
>>> import pysnptools.util as pstutil
>>> from pysnptools.util import example_file # Download and return local file name
>>> bed_file = example_file('pysnptools/examples/toydata.5chrom.*','*.bed')
>>> kerneldata = Bed(bed_file,count_A1=False).read_kernel(Unit()) # Create a kernel from the data in the Bed file
>>> pstutil.create_directory_if_necessary("tempdir/toydata.kernel.npz")
>>> KernelNpz.write("tempdir/toydata.kernel.npz",kerneldata) # Write data in KernelNpz format
KernelNpz('tempdir/toydata.kernel.npz')
"""
PstNpz.write(filename, kerneldata)
return KernelNpz(filename)
def cmktest_big_npz(self):
logging.info("in test_big_npz")
n = 1000
pstdata = PstData(row=range(n-1),col=range(n+1),val=np.zeros([n-1,n+1]))
output = "tempdir/pstreader/big.npz"
create_directory_if_necessary(output)
PstNpz.write(output,pstdata)
pstnpz = PstNpz(output)
pstdata1 = pstnpz[::2,::4].read()
pstdata2 = pstnpz.read(order='A')
assert pstdata2.val.flags['C_CONTIGUOUS']
pstdata = PstData(row=range(n-1),col=range(n+1),val=np.zeros([n-1,n+1],order='F'))
PstNpz.write(output,pstdata)
pstnpz = PstNpz(output)
pstdata2 = pstnpz.read(order='A')
pstdata2.val.flags['F_CONTIGUOUS']
print("done")