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import sys, os, shutil, glob, gzip
os.chdir(os.path.split(os.path.realpath(__file__))[0])
suffix = " > /dev/null 2>&1"
dir = "__results__"
def clear():
if os.path.exists("temp_output"):
shutil.rmtree("temp_output")
if os.path.exists("__results__"):
shutil.rmtree("__results__")
os.mkdir(dir)
def decompress_simka_results(dir):
result_filenames = glob.glob(os.path.join(dir, '*.csv.gz'))
for filename_gz in result_filenames:
#filename_gz = result_dir + "/" + filename
with gzip.open(filename_gz, 'rb') as f:
outFile = open(filename_gz[:-3], "wb")
outFile.write(f.read())
outFile.close()
os.remove(filename_gz)
def __test_matrices(simka_vs_truth, result_dir, truth_dir):
ok = True
decompress_simka_results(result_dir)
result_filenames = glob.glob(os.path.join(result_dir, '*.csv'))
if len(result_filenames) == 0:
print("Error: no results")
exit(1)
if simka_vs_truth:
truth_filenames = glob.glob(os.path.join(truth_dir, '*.csv'))
else: #simka vs simka
#if result_dir+"/mat_abundance_jaccard.csv" in truth_filenames: #comparing simka results vs simka results
#truth_filenames.remove(result_dir+"/mat_abundance_jaccard.csv") #This distance is computed from Bray Curtis distance
decompress_simka_results(truth_dir)
truth_filenames = glob.glob(os.path.join(truth_dir, '*.csv'))
truth_filenames.sort()
result_filenames.sort()
for result_filename in result_filenames:
distanceName = os.path.split(result_filename)[1]
for truth_filename in truth_filenames:
distanceName2 = os.path.split(truth_filename)[1]
if distanceName != distanceName2: continue
res_file = open(result_filename, "r")
truth_file = open(truth_filename, "r")
#print res_file, truth_file
res_str = res_file.read()
truth_str = truth_file.read()
res_file.close()
truth_file.close()
if(res_str != truth_str):
print("\t- TEST ERROR: " + distanceName)
ok = False
return ok
def test_dists(dir):
if(__test_matrices(True, "__results__/" + dir, "truth/" + dir)):
print("\tOK")
else:
print("\tFAILED")
sys.exit(1)
def test_parallelization():
if(__test_matrices(False, "__results__/results_resources1", "__results__/results_resources2")):
print("\tOK")
else:
print("\tFAILED")
sys.exit(1)
#----------------------------------------------------------------
#----------------------------------------------------------------
#----------------------------------------------------------------
#test k=31 t=0
clear()
print("TESTING k=31 t=0", flush=True)
command = "simka -in simka_input.txt -out ./__results__/results_k31_t0 -out-tmp ./temp_output -simple-dist -complex-dist -kmer-size 31 -abundance-min 0 -verbose 0 -nb-cores 1"
print(command, flush=True)
os.system(command + suffix)
test_dists("results_k31_t0")
#test k=21 t=0
clear()
print("TESTING k=21 t=0", flush=True)
command = "simka -in simka_input.txt -out ./__results__/results_k21_t0 -out-tmp ./temp_output -simple-dist -complex-dist -kmer-size 21 -abundance-min 0 -verbose 0 -nb-cores 1"
print(command, flush=True)
os.system(command + suffix)
test_dists("results_k21_t0")
#test k=31 t=2
clear()
print("TESTING k=31 t=2", flush=True)
command = "simka -in simka_input.txt -out ./__results__/results_k31_t2 -out-tmp ./temp_output -simple-dist -complex-dist -kmer-size 31 -abundance-min 2 -verbose 0 -nb-cores 1"
print(command, flush=True)
os.system(command + suffix)
test_dists("results_k31_t2")
#test k=21 t=2
clear()
print("TESTING k=21 t=2", flush=True)
command = "simka -in simka_input.txt -out ./__results__/results_k21_t2 -out-tmp ./temp_output -simple-dist -complex-dist -kmer-size 21 -abundance-min 2 -verbose 0 -nb-cores 1"
print(command, flush=True)
os.system(command + suffix)
test_dists("results_k21_t2")
#test resources 1
clear()
print("TESTING parallelization", flush=True)
command = "simka -in simka_input.txt -out ./__results__/results_resources1 -out-tmp ./temp_output -simple-dist -complex-dist -kmer-size 21 -abundance-min 0 -nb-cores 20 -max-memory 4000 -verbose 0"
os.system(command + suffix)
command = "simka -in simka_input.txt -out ./__results__/results_resources2 -out-tmp ./temp_output -simple-dist -complex-dist -kmer-size 21 -abundance-min 0 -nb-cores 2 -max-memory 2000 -verbose 0"
os.system(command + suffix)
test_parallelization()
#----------------------------------------------------------------
#----------------------------------------------------------------
#----------------------------------------------------------------
clear()
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