def test_override_input():
sys.argv = ['rabix', '-i', 'rabix/tests/test-cmdline/inputs.json', '-d',
'test_override_input', 'rabix/tests/test-expr/bwa-mem.json', '--',
'--reference', 'rabix/tests/test-files/chr20.fa']
main()
assert os.path.exists(os.path.abspath('./test_override_input') + '/aligned.sam')
shutil.rmtree(os.path.abspath('./test_override_input'))
def test_params_from_input_file():
sys.argv = ['rabix', '-i', 'rabix/tests/test-cmdline/inputs.json',
'rabix/tests/test-expr/bwa-mem.json',
'-d', 'test_from_input_file']
main()
assert os.path.exists(os.path.abspath('./test_from_input_file') + '/aligned.sam')
shutil.rmtree(os.path.abspath('./test_from_input_file'))
def test_fetch_remote_files():
sys.argv = ['rabix', '--dir', 'test_fetch_remote',
'./rabix/tests/test-expr/bwa-mem.json', '--',
'--reads',
'https://s3.amazonaws.com/rabix/rabix-test/'
'example_human_Illumina.pe_1.fastq', '--reads',
'https://s3.amazonaws.com/rabix/rabix-test/'
'example_human_Illumina.pe_2.fastq', '--reference',
'./rabix/tests/test-files/chr20.fa']
main()
assert os.path.exists(os.path.abspath('./test_fetch_remote') + '/aligned.sam')
shutil.rmtree(os.path.abspath('./test_fetch_remote'))
def test_expr_and_meta():
sys.argv = ['rabix', './rabix/tests/test-expr/bwa-mem.json',
'-i', './rabix/tests/test-cmdline/inputs.json',
'--dir', 'test1', '--']
main()
with open(os.path.abspath('./test1') + '/aligned.sam.rbx.json') as m:
meta = json.load(m)
assert meta['metadata']['expr_test'] == 'successful'
shutil.rmtree(os.path.abspath('./test1'))
sys.argv = ['rabix', '-i', './rabix/tests/test-cmdline/inputs.json',
'./rabix/tests/test-expr/bwa-mem.json',
'--dir', 'test2']
main()
with open(os.path.abspath('./test2') + '/aligned.sam.rbx.json') as m:
meta = json.load(m)
assert meta['metadata']['expr_test'] == 'successful'
shutil.rmtree(os.path.abspath('./test2'))
def test_parallelization():
'''
Testing implicit parallelization in workflows
'''
cwd = os.getcwd()
try:
os.mkdir('test_parralelization')
sys.argv = ['rabix', '../rabix/tests/test_workflows/parallelization_workflow.json',
'--', '--input', '../rabix/tests/test-files/chr20.fa']
os.chdir('./test_parralelization')
main()
dir = filter(lambda x: os.path.isdir(x) and 'index_file' in x, os.walk('.').next()[1])
for d in dir:
check_result(d, result_parallel_workflow)
finally:
os.chdir(cwd)
shutil.rmtree(os.path.abspath('./test_parralelization'))
def test_nested_workflow():
'''
Testing nested workflows, inputs type directory and
tools which creates index files
'''
cwd = os.getcwd()
try:
os.mkdir('test_workflow')
sys.argv = ['rabix', '../rabix/tests/test_workflows/nested_workflow.json',
'--', '--input', '../rabix/tests/test-files/chr20.fa']
os.chdir('./test_workflow')
main()
dir = filter(lambda x: os.path.isdir(x) and 'index_file' in x,
os.walk('.').next()[1])
for d in dir:
check_result(d, result_nested_workflow)
finally:
os.chdir(cwd)
shutil.rmtree(os.path.abspath('./test_workflow'))
