def test_task_bismark_aln_2(): x = oxbs_qc_func.task_bismark_aln(inFastq=[ 'test_data/mjb042_oxBS_R1.txt.gz', 'test_data/mjb042_oxBS_R2.txt.gz' ], ref='control_reference/bsseq_synthetic4', tmpdir='test_out', outSam='mjb042.sam', opts='-o test_out') print(x) assert x['sam'] == 'test_out/mjb042.sam' ## Outut sam is what you expect assert os.path.exists(x['sam']) ## Sam exists assert len(x['all_out']) > 1 ## There are more files in output dir
def test_task_bismark_exceptions(): passed = False try: oxbs_qc_func.task_bismark_aln(inFastq=['NA'], ref='control_reference/bsseq_synthetic4', outSam='mjb042_oxBS_R1.sam', opts='') ## No input fastq except oxbs_qc_func.BismarkException: passed = True assert passed passed = False try: oxbs_qc_func.task_bismark_aln( inFastq=['test_data/mjb042_oxBS_R1.txt.gz'], ref='control_reference/bsseq_synthetic4', outSam='mjb042_oxBS_R1', opts='') ## No exts on sam except oxbs_qc_func.BismarkException: passed = True assert passed passed = False try: oxbs_qc_func.task_bismark_aln( inFastq=['test_data/mjb042_oxBS_R1.txt.gz'], ref='control_reference/bsseq_synthetic4/', outSam='mjb042_oxBS_R1.sam', opts='') ## No ref except oxbs_qc_func.BismarkException: passed = True assert passed
def test_task_bismark_exceptions(): passed= False try: oxbs_qc_func.task_bismark_aln(inFastq= ['NA'], ref= 'control_reference/bsseq_synthetic4', outSam= 'mjb042_oxBS_R1.sam', opts= '') ## No input fastq except oxbs_qc_func.BismarkException: passed= True assert passed passed= False try: oxbs_qc_func.task_bismark_aln(inFastq= ['test_data/mjb042_oxBS_R1.txt.gz'], ref= 'control_reference/bsseq_synthetic4', outSam= 'mjb042_oxBS_R1', opts= '') ## No exts on sam except oxbs_qc_func.BismarkException: passed= True assert passed passed= False try: oxbs_qc_func.task_bismark_aln(inFastq= ['test_data/mjb042_oxBS_R1.txt.gz'], ref= 'control_reference/bsseq_synthetic4/', outSam= 'mjb042_oxBS_R1.sam', opts= '') ## No ref except oxbs_qc_func.BismarkException: passed= True assert passed
def test_task_bismark_aln_2(): x= oxbs_qc_func.task_bismark_aln(inFastq= ['test_data/mjb042_oxBS_R1.txt.gz', 'test_data/mjb042_oxBS_R2.txt.gz'], ref= 'control_reference/bsseq_synthetic4', tmpdir= 'test_out', outSam= 'mjb042.sam', opts= '-o test_out') print(x) assert x['sam'] == 'test_out/mjb042.sam' ## Outut sam is what you expect assert os.path.exists(x['sam']) ## Sam exists assert len(x['all_out']) > 1 ## There are more files in output dir