def test_multichange():
# timing for performance test
t0 = time.time()
# sending data to main function
data_path = "../data/result/test2_result"
write_path = " ../data/result/test2_result"
strain_num = 6268
# calling the main function
reader(data_path, write_path, strain_num)
# call(["bgzip","../data/result/test2_result_result.vcf"])
# generatig checksums
crossval_hash = hash("../data/test/test2.vcf.gz")
result_hash = hash("../data/result/test2_result_result.vcf.gz")
#validating checksums
assert crossval_hash == result_hash
# printing time outputs
t1 = time.time()
print " Extra test 1:" + str(t1 - t0)
def test2_test():
# timing for performance test
t0 = time.time()
#sending data to main function
data_path = "../data/test/test2"
write_path = "../data/result/test2"
strain_num = 6268
# calling main fucntion
reader(data_path, write_path, strain_num)
# compressing file to .vcf.gz
call(["bgzip", "../data/result/test2_result.vcf"])
# generating checksums
crossval_hash = hash("../data/cross_validation/test2_crossval.vcf.gz")
result_hash = hash("../data/result/test2_result.vcf.gz")
# validating checksums
assert crossval_hash == result_hash
#printing time results
t1 = time.time()
print "Indel test time: " + str(t1 - t0)
def test_multiChange():
# timing the function for performance
t0 = time.time()
#sending data to main function
data_path = "../data/result/test1_result"
write_path = "../data/result/test1_result"
strain_num = 6268
#calling main function
reader(data_path, write_path, strain_num)
# compressing the results to .vcf.gz
call(["bgzip", "../data/result/test1_result_result.vcf"])
# generating checksum for validation
test_hash = hash("../data/test/test1.vcf.gz")
result_hash = hash("../data/result/test1_result_result.vcf.gz")
# asserting test validation
assert test_hash == result_hash
#printing time results
t1 = time.time()
print "SNP Multichange time:" + str(t1 - t0)
def test1_test():
# timing the function for performance testing
t0 = time.time()
#sending data to main function
data_path = "../data/test/test1"
write_path = "../data/result/test1"
strain_num = 6268
#calling main function
reader(data_path, write_path, strain_num)
#compressing the file
call(["bgzip", "../data/result/test1_result.vcf"])
#asserting the results
crossval_hash = hash("../data/cross_validation/test1_crossval.vcf.gz")
result_hash = hash("../data/result/test1_result.vcf.gz")
assert crossval_hash == result_hash
#printing tie results
t1 = time.time()
print "Time for snp change :" + str(t1 - t0)
def test3_test():
#timing for performance test
t0 = time.time()
data_path = "../data/test/test3"
write_path = " ../data/result/test3"
strain_num = 6268
print reader(data_path, write_path, strain_num)
call(["bgzip","test3_result.vcf"])
crossval_hash = hash("../data/cross_validation/test3_crossval.vcf.gz")
result_hash = hash("../data/result/test3_result.vcf.gz")
assert crossval_hash == result_hash
t1 = time.time()
print "Time for test 3:" + (t1-t0)
def test31_test():
# timing for performance test
t0 = time.time()
data_path = "../data/test/test3_result"
write_path = " ../data/result/test3_cons"
strain_num = 6269
print reader(data_path, write_path, strain_num)
call(["bgzip","test3_cons_result.vcf"])
crossval_hash = hash("../data/cross_validation/test3_cons_crossval.vcf.gz")
result_hash = hash("../data/result/test3_result.vcf.gz")
assert crossval_hash == result_hash
t1 = time.time()
print "time for test 3.1 :" + (t1-t0)
# Cleaning files created
os.remove("../data/result/test3_result.vcf.gz")
os.remove("../data/result/test3_cons_result.vcf.gz")