def snpsA(seed, iid_count, sid_count, use_distributed):
import numpy as np
from pysnptools.snpreader import Bed
from pysnptools.snpreader import DistributedBed
from pysnptools.snpreader import SnpGen
chrom_count = 10
global top_cache
if use_distributed:
test_snp_path = (
cache_top /
f"snpsA_{seed}_{chrom_count}_{iid_count}_{sid_count}_db")
else:
test_snp_path = (
cache_top /
f"snpsA_{seed}_{chrom_count}_{iid_count}_{sid_count}.bed")
count_A1 = False
if not test_snp_path.exists():
snpgen = SnpGen(
seed=seed,
iid_count=iid_count,
sid_count=sid_count,
chrom_count=chrom_count,
block_size=1000,
)
if use_distributed:
test_snps = DistributedBed.write(str(test_snp_path), snpgen)
else:
test_snps = Bed.write(str(test_snp_path),
snpgen.read(dtype="float32"),
count_A1=count_A1)
else:
if use_distributed:
test_snps = DistributedBed(str(test_snp_path))
else:
test_snps = Bed(str(test_snp_path), count_A1=count_A1)
from pysnptools.snpreader import SnpData
np.random.seed(seed)
pheno = SnpData(
iid=test_snps.iid,
sid=["pheno"],
val=np.random.randn(test_snps.iid_count, 1) * 3 + 2,
)
covar = SnpData(
iid=test_snps.iid,
sid=["covar1", "covar2"],
val=np.random.randn(test_snps.iid_count, 2) * 2 - 3,
)
return test_snps, pheno, covar
pstutil.create_directory_if_necessary(local, isfile=True)
if __name__ == "__main__":
logging.basicConfig(level=logging.INFO)
if False:
from pysnptools.util.filecache import PeerToPeer, ip_address
def id_and_path_function():
ip = ip_address()
return ip, 'peertopeer1/{0}'.format(ip)
file_cache = PeerToPeer(common_directory='peertopeer1/common',
id_and_path_function=id_and_path_function)
file_cache
#PeerToPeer('peertopeer1/common',id_and_path_function=...')
file_cache.rmtree()
from pysnptools.snpreader import SnpGen, Dense
snp_gen = SnpGen(seed=123, iid_count=1000, sid_count=5000)
with file_cache.open_write(
'r123.1000x5000.dense.txt') as local_filename:
Dense.write(local_filename, snp_gen.read())
list(file_cache.walk())
#['r123.1000x5000.dense.txt']
import doctest
doctest.testmod(optionflags=doctest.ELLIPSIS)
# There is also a unit test case in 'pysnptools\test.py' that calls this doc test