def test_trim_fastq_exception(): passed = False try: oxbs_qc_func.trim_fastq('test_data/mjb042_oxBS_R1.txt', -1, 'mjb042_oxBS_R1.fq') ### Invalid -1 except oxbs_qc_func.TrimFastqException: passed = True assert passed passed = False try: x = oxbs_qc_func.trim_fastq( 'test_data/mjb042_oxBS_R1.txt.gz', 1, 'test_data/mjb042_oxBS_R1.txt.gz') ## input == output except oxbs_qc_func.TrimFastqException: passed = True assert passed passed = False try: x = oxbs_qc_func.trim_fastq( 'test_data/mjb042_oxBS_R1.txt.gz', 1, '/nonsense/mjb042_oxBS_R1.txt.gz') ## output dir does not exists except oxbs_qc_func.TrimFastqException: passed = True assert passed
def test_trim_fastq_exception(): passed= False try: oxbs_qc_func.trim_fastq('test_data/mjb042_oxBS_R1.txt', -1, 'mjb042_oxBS_R1.fq') ### Invalid -1 except oxbs_qc_func.TrimFastqException: passed= True assert passed passed= False try: x= oxbs_qc_func.trim_fastq('test_data/mjb042_oxBS_R1.txt.gz', 1, 'test_data/mjb042_oxBS_R1.txt.gz') ## input == output except oxbs_qc_func.TrimFastqException: passed= True assert passed passed= False try: x= oxbs_qc_func.trim_fastq('test_data/mjb042_oxBS_R1.txt.gz', 1, '/nonsense/mjb042_oxBS_R1.txt.gz') ## output dir does not exists except oxbs_qc_func.TrimFastqException: passed= True assert passed
def test_trim_fastq_1(): try: os.makedirs('test_out') except OSError: pass xout= oxbs_qc_func.trim_fastq('test_data/mjb042_oxBS_R1.txt.gz', 20, 'test_out/mjb042_oxBS_R1.fq') assert xout assert os.path.exists('test_out/mjb042_oxBS_R1.fq.gz') ## Note .gz included! ## Same number of lines in input and output tfq= gzip.open('test_out/mjb042_oxBS_R1.fq.gz').readlines() fq= gzip.open('test_data/mjb042_oxBS_R1.txt.gz').readlines() assert len(tfq) == len(fq) ## Lenght of read AND quality == 20 read_quality_qlen= [len(tfq[x].strip()) for x in range(1, 100, 2)] assert set(read_quality_qlen) == set([20])
def test_trim_fastq_1(): try: os.makedirs('test_out') except OSError: pass xout = oxbs_qc_func.trim_fastq('test_data/mjb042_oxBS_R1.txt.gz', 20, 'test_out/mjb042_oxBS_R1.fq') assert xout assert os.path.exists( 'test_out/mjb042_oxBS_R1.fq.gz') ## Note .gz included! ## Same number of lines in input and output tfq = gzip.open('test_out/mjb042_oxBS_R1.fq.gz').readlines() fq = gzip.open('test_data/mjb042_oxBS_R1.txt.gz').readlines() assert len(tfq) == len(fq) ## Lenght of read AND quality == 20 read_quality_qlen = [len(tfq[x].strip()) for x in range(1, 100, 2)] assert set(read_quality_qlen) == set([20])