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, 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, 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 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")
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 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)