def storage_closure():
def id_and_path_function():
self.count += 1
return self.count, temp_dir + '/{0}'.format(self.count)
storage = PeerToPeer(common_directory=temp_dir + '/common',
id_and_path_function=id_and_path_function)
return storage
def too_slow_test_peertopeer(self):
logging.info("test_peertopeer")
output_file = self.file_name("peertopeer")
def id_and_path_function():
from pysnptools.util.filecache import ip_address_pid
ip_pid = ip_address_pid()
#Need to put the 'cache_top' here explicitly.
return ip_pid, 'peertopeer/{0}'.format(ip_pid)
storage = PeerToPeer(common_directory='peertopeer/common',
id_and_path_function=id_and_path_function)
test_snps_cache = storage.join('test_snps')
test_snps_cache.rmtree()
test_snps = DistributedBed.write(test_snps_cache,
self.bed,
piece_per_chrom_count=2)
runner = LocalMultiProc(
taskcount=5) #Run on 5 additional Python processes
for clear_cache in (True, False):
if clear_cache:
storage.join('cache').rmtree()
results_df = single_snp_scale(test_snps=test_snps,
pheno=self.phen_fn,
covar=self.cov_fn,
cache=storage.join('cache'),
output_file_name=output_file,
runner=runner)
self.compare_files(results_df, "old")
if os.path.exists(directory_name) and os.path.isfile(directory_name):
os.remove(directory_name)
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