def run_locally(options):
"""
Run triplexator locally by iterating over the given parameter ranges and submits a job to the cluster for each
parameter combination.
:param options:
:return:
"""
# create path if non-existing
if not os.path.isdir(options.dataOutDir):
os.mkdir(options.dataOutDir)
# set input files according to mode
if options.mode == "br" or options.mode == "bp":
input_file_options = '-ss ' + options.inputTFO + " -ds " + options.inputTTS + " "
else:
input_file_options = '-as ' + options.inputAB + " "
for l in range(int(options.minLengthLow), int(options.minLengthHigh) + 1, 5):
for e in range(int(options.errLow), int(options.errHigh) + 1, 5):
for c in range(int(options.consLow), int(options.consHigh) + 1, 1):
out_file_tpx = utils.get_output_filename_from_parameters(options.dataPrefix, options.maxLength, l, e, c)
utils.lib_triplexator.runTriplexator(input_file_options + get_triplexator_option(options.mode) +
" -e " + str(e) + " -c " + str(c) + " -l " + str(l) + " -L " +
str(options.maxLength) + " " + " -od " + options.dataOutDir +
" -o " + out_file_tpx + options.tpxOptions)
def run_bit_parallel_unit_test(test_id=""):
"""
:param test_id:
:return:
"""
dirs = [test_id] if test_id != "" else [dn for dp, dn, fn in os.walk(utils.PATH_UNIT_TESTS)][0]
for _dir in dirs:
# make sure path exists
if not os.path.isdir(utils.PATH_UNIT_TESTS + _dir):
print(OSError("Test directory '" + _dir + "' doesn't exist."))
continue
test_id = _dir # get test number / id
ref_file_name = next((x for x in os.listdir(utils.PATH_UNIT_TESTS + _dir) if x.endswith(".tpx")), None)
rna_data = utils.PATH_UNIT_TESTS + _dir + "/rna.data"
dna_data = utils.PATH_UNIT_TESTS + _dir + "/dna.data"
print ("\n\n##################################################################")
print ("Running test " + test_id)
if ref_file_name is None:
print (IOError("No reference file found in directory for test " + test_id))
continue
# get parameters
L_param = 30
e_pattern = re.compile("e([0-9]+)")
e_param = re.search(e_pattern, ref_file_name).group(1)
c_pattern = re.compile("c([0-9]+)")
c_param = re.search(c_pattern, ref_file_name).group(1)
l_pattern = re.compile("l([0-9]+)")
l_param = re.search(l_pattern, ref_file_name).group(1)
result_file_name = utils.get_output_filename_from_parameters("bp", l_param, 30, e_param, c_param)
utils.lib_triplexator.runTriplexator('-ss ' + rna_data + " -ds " + dna_data +
" --bit-parallel -e " + str(e_param) + " -c " + str(c_param) +
" -l " + str(l_param) + " -L " + str(L_param) + " " + " -od " +
utils.PATH_UNIT_TESTS + _dir + " -o " + result_file_name)
os.remove(utils.PATH_UNIT_TESTS + _dir + "/" + result_file_name + ".log")
os.remove(utils.PATH_UNIT_TESTS + _dir + "/" + result_file_name + ".summary")
# evaluate result
ref_file = utils.PATH_UNIT_TESTS + _dir + "/" + ref_file_name
result_file = utils.PATH_UNIT_TESTS + _dir + "/" + result_file_name
print "\n"
print "Test passed." if compare_result(ref_file, result_file) else "Test failed."
