def __plink_to_npz(self, p, file_name):
'''Convert p from plink to npz format using the file set specified by file_name.'''
npz = file_name+'.npz'
# Save test problem in plink format
io.write_plink(p, prefix=file_name)
# Convert plink -> npz
io.plink_to_npz(file_name, npz)
# Load npz and check that the problem object didn't change
p2 = io.read_npz(npz)
return p2
def __main(options):
'''
--------------------------------------------------
Main program - accepts an options struct.
--------------------------------------------------
'''
if options.target == 'npz':
haplotype = options.prefix + '.hap.tped'
haplotype = haplotype if os.path.isfile(haplotype) else None
return io.plink_to_npz(options.prefix, options.npz, options.pedigree, haplotype=haplotype,
info=None,verbose=options.debug,
pedigree_genotyped=options.pedigree_genotyped)
else:
return io.npz_to_plink(options.npz, options.prefix, verbose=options.debug)
def __main(options):
'''
--------------------------------------------------
Main program - accepts an options struct.
--------------------------------------------------
'''
if options.target == 'npz':
haplotype = options.prefix + '.hap.tped'
haplotype = haplotype if os.path.isfile(haplotype) else None
return io.plink_to_npz(options.prefix,
options.npz,
options.pedigree,
haplotype=haplotype,
info=None,
verbose=options.debug,
pedigree_genotyped=options.pedigree_genotyped)
else:
return io.npz_to_plink(options.npz,
options.prefix,
verbose=options.debug)