def test_task_trim_galore_PE_exceptions(): ## 2 inputs 1 output passed= False try: tg= oxbs_qc_func.task_trim_galore(inFastq= ['test_data/mjb042_oxBS_R1.fastq.gz', 'test_data/mjb042_oxBS_R2.fastq.gz'], outFastq= ['fq1.fq.gz'], tmpdir= 'test_out', opts= '', path= '') except oxbs_qc_func.TrimGaloreException: passed= True assert passed ## 1 inputs 2 output passed= False try: tg= oxbs_qc_func.task_trim_galore(inFastq= ['test_data/mjb042_oxBS_R1.fastq.gz'], outFastq= ['fq1.fq.gz', 'fq2.fq.gz'], tmpdir= 'test_out', opts= '', path= '') except oxbs_qc_func.TrimGaloreException: passed= True assert passed ## same input twice passed= False try: tg= oxbs_qc_func.task_trim_galore(inFastq= ['test_data/mjb042_oxBS_R1.fastq.gz', 'test_data/mjb042_oxBS_R1.fastq.gz'], outFastq= ['fq1.fq.gz', 'fq2.fq.gz'], tmpdir= 'test_out', opts= '', path= '') except oxbs_qc_func.TrimGaloreException: passed= True assert passed ## same Output twice passed= False try: tg= oxbs_qc_func.task_trim_galore(inFastq= ['test_data/mjb042_oxBS_R1.fastq.gz', 'test_data/mjb042_oxBS_R2.fastq.gz'], outFastq= ['fq1.fq.gz', 'fq1.fq.gz'], tmpdir= 'test_out', opts= '', path= '') except oxbs_qc_func.TrimGaloreException: passed= True assert passed
def test_task_trim_galore_PE_exceptions(): ## 2 inputs 1 output passed = False try: tg = oxbs_qc_func.task_trim_galore(inFastq=[ 'test_data/mjb042_oxBS_R1.fastq.gz', 'test_data/mjb042_oxBS_R2.fastq.gz' ], outFastq=['fq1.fq.gz'], tmpdir='test_out', opts='', path='') except oxbs_qc_func.TrimGaloreException: passed = True assert passed ## 1 inputs 2 output passed = False try: tg = oxbs_qc_func.task_trim_galore( inFastq=['test_data/mjb042_oxBS_R1.fastq.gz'], outFastq=['fq1.fq.gz', 'fq2.fq.gz'], tmpdir='test_out', opts='', path='') except oxbs_qc_func.TrimGaloreException: passed = True assert passed ## same input twice passed = False try: tg = oxbs_qc_func.task_trim_galore(inFastq=[ 'test_data/mjb042_oxBS_R1.fastq.gz', 'test_data/mjb042_oxBS_R1.fastq.gz' ], outFastq=['fq1.fq.gz', 'fq2.fq.gz'], tmpdir='test_out', opts='', path='') except oxbs_qc_func.TrimGaloreException: passed = True assert passed ## same Output twice passed = False try: tg = oxbs_qc_func.task_trim_galore(inFastq=[ 'test_data/mjb042_oxBS_R1.fastq.gz', 'test_data/mjb042_oxBS_R2.fastq.gz' ], outFastq=['fq1.fq.gz', 'fq1.fq.gz'], tmpdir='test_out', opts='', path='') except oxbs_qc_func.TrimGaloreException: passed = True assert passed
def test_task_trim_galore_PE_1(): tg= oxbs_qc_func.task_trim_galore(inFastq= ['test_data/mjb042_oxBS_R1.fastq.gz', 'test_data/mjb042_oxBS_R2.fastq.gz'], outFastq= ['fq1.fq.gz', 'fq2.fq.gz'], tmpdir= 'test_out', opts= '-o test_out/trim_galore_pe1', path= '') print(tg) assert tg['fastq'][0] == 'test_out/trim_galore_pe1/fq1.fq.gz' ## Files are named as you expect assert tg['fastq'][1] == 'test_out/trim_galore_pe1/fq2.fq.gz' assert os.path.exists(tg['fastq'][0]) ## Files do exist assert os.path.exists(tg['fastq'][1])
def test_task_trim_galore_SE(): passed= False try: tg= oxbs_qc_func.task_trim_galore(inFastq= ['test_data/mjb042_oxBS_R1.fastq.gz'], outFastq= ['bla/fq1.fq.gz'], tmpdir= 'test_out', opts= '-o test_out/trim_galore', path= '') except oxbs_qc_func.TrimGaloreException: "outFastq has path attached" passed= True assert passed
def test_task_trim_galore_SE_4(): tg = oxbs_qc_func.task_trim_galore( inFastq=['test_data/mjb042_oxBS_R1.txt.gz'], outFastq=['fq1.txt'], tmpdir='test_out', opts='-o test_out/trim_galore_4 --dont_gzip', path='') print(tg) assert tg['fastq'][0] == 'test_out/trim_galore_4/fq1.txt' assert os.path.exists(tg['fastq'][0])
def test_task_trim_galore_PE_3(): tg= oxbs_qc_func.task_trim_galore(inFastq= ['test_data/mjb042_oxBS_R1.txt', 'test_data/mjb042_oxBS_R2.txt'], outFastq= ['fq1.txt', 'fq2.txt'], tmpdir= 'test_out', opts= '-o test_out/trim_galore_pe3', path= '') print(tg) assert tg['fastq'][0] == 'test_out/trim_galore_pe3/fq1.txt' ## Files are named as you expect assert tg['fastq'][1] == 'test_out/trim_galore_pe3/fq2.txt' for x in tg['fastq']: assert os.path.exists(x) ## files do exist for x in tg['report']: assert os.path.exists(x) ## Reports do exist assert len(os.listdir('test_out/trim_galore_pe3/')) == 4
def test_task_trim_galore_SE_1(): tg = oxbs_qc_func.task_trim_galore( inFastq=['test_data/mjb042_oxBS_R1.fastq.gz'], outFastq=['fq1.fq.gz'], tmpdir='test_out', opts='-o test_out/trim_galore_1', path='') print(tg) assert tg['fastq'][0] == 'test_out/trim_galore_1/fq1.fq.gz' assert os.path.exists(tg['fastq'][0]) assert os.path.exists( 'test_out/trim_galore_1/mjb042_oxBS_R1.fastq.gz_trimming_report.txt')
def test_task_trim_galore_SE(): passed = False try: tg = oxbs_qc_func.task_trim_galore( inFastq=['test_data/mjb042_oxBS_R1.fastq.gz'], outFastq=['bla/fq1.fq.gz'], tmpdir='test_out', opts='-o test_out/trim_galore', path='') except oxbs_qc_func.TrimGaloreException: "outFastq has path attached" passed = True assert passed
def test_task_trim_galore_PE_1(): tg = oxbs_qc_func.task_trim_galore(inFastq=[ 'test_data/mjb042_oxBS_R1.fastq.gz', 'test_data/mjb042_oxBS_R2.fastq.gz' ], outFastq=['fq1.fq.gz', 'fq2.fq.gz'], tmpdir='test_out', opts='-o test_out/trim_galore_pe1', path='') print(tg) assert tg['fastq'][ 0] == 'test_out/trim_galore_pe1/fq1.fq.gz' ## Files are named as you expect assert tg['fastq'][1] == 'test_out/trim_galore_pe1/fq2.fq.gz' assert os.path.exists(tg['fastq'][0]) ## Files do exist assert os.path.exists(tg['fastq'][1])
def test_task_trim_galore_PE_3(): tg = oxbs_qc_func.task_trim_galore(inFastq=[ 'test_data/mjb042_oxBS_R1.txt', 'test_data/mjb042_oxBS_R2.txt' ], outFastq=['fq1.txt', 'fq2.txt'], tmpdir='test_out', opts='-o test_out/trim_galore_pe3', path='') print(tg) assert tg['fastq'][ 0] == 'test_out/trim_galore_pe3/fq1.txt' ## Files are named as you expect assert tg['fastq'][1] == 'test_out/trim_galore_pe3/fq2.txt' for x in tg['fastq']: assert os.path.exists(x) ## files do exist for x in tg['report']: assert os.path.exists(x) ## Reports do exist assert len(os.listdir('test_out/trim_galore_pe3/')) == 4
def test_task_trim_galore_SE_4(): tg= oxbs_qc_func.task_trim_galore(inFastq= ['test_data/mjb042_oxBS_R1.txt.gz'], outFastq= ['fq1.txt'], tmpdir= 'test_out', opts= '-o test_out/trim_galore_4 --dont_gzip', path= '') print(tg) assert tg['fastq'][0] == 'test_out/trim_galore_4/fq1.txt' assert os.path.exists(tg['fastq'][0])
def test_task_trim_galore_SE_1(): tg= oxbs_qc_func.task_trim_galore(inFastq= ['test_data/mjb042_oxBS_R1.fastq.gz'], outFastq= ['fq1.fq.gz'], tmpdir= 'test_out', opts= '-o test_out/trim_galore_1', path= '') print(tg) assert tg['fastq'][0] == 'test_out/trim_galore_1/fq1.fq.gz' assert os.path.exists(tg['fastq'][0]) assert os.path.exists('test_out/trim_galore_1/mjb042_oxBS_R1.fastq.gz_trimming_report.txt')