def setUp(self):
"""Set up a workflow.
"""
fqqf = FastqQualityFilter(
name="quality_filter", args={"-i": "fastq.fq", "-o": "qfastq.fq", "-Q": "33", "-q": "20", "-p": "90"}
)
fq2a = FastqToFasta(name="fastq_to_fasta", args={"-i": "qfastq.fq", "-o": "qfasta.fa"})
fq2a.add_dependencies(done=[fqqf])
self.wf = WorkFlow([fqqf, fq2a])
self.fqqf = fqqf
self.fq2a = fq2a
def setUp(self):
"""Set up a job initialized with out input parameters.
Job used in class test cases.
"""
self.fq2a_job = FastqToFasta()
def setUp(self):
"""Set up a job initialized with input parameters.
Job used in class test cases.
"""
self.fq2a_job = FastqToFasta(name='myFastq2Fasta',
args={'-i': 'input_file.fq',
'-o': 'output_file.fa'},
dep_str='previous_job',
)
class ModuleEmptyInit(unittest.TestCase):
"""Test initialization of module when key-word input arguments are empty.
"""
def setUp(self):
"""Set up a job initialized with out input parameters.
Job used in class test cases.
"""
self.fq2a_job = FastqToFasta()
def test_job_init_cmd(self):
"""Module should inherit job and initialize cmd.
"""
self.assertEqual(self.fq2a_job.cmd, 'fastq_to_fasta')
def test_job_init_args(self):
"""Module initialized without args, args should be empty dictionary.
"""
self.assertDictEqual(self.fq2a_job.args, {})
def test_job_init_name(self):
"""Module init without name, name should be random string, 8 letters.
"""
self.assertTrue(len(self.fq2a_job.name) == 8)
self.assertIsInstance(self.fq2a_job.name, str)
def test_job_init_dep_str(self):
"""Module dependency string should be empty.
"""
self.assertEqual(self.fq2a_job.dep_str, '')
def test_job_init_dep_at_init(self):
"""Module if dep_string is empty, attribute False.
"""
self.assertFalse(self.fq2a_job.dep_str_at_init)
def test_job_init_dep(self):
"""Dependencies are empty, nested lists in a dictionary.
"""
self.assertIsInstance(self.fq2a_job.dep, dict)
for k in self.fq2a_job.dep.keys():
self.assertIsInstance(self.fq2a_job.dep[k], list)
self.assertEqual(self.fq2a_job.dep[k], [])
def test_job_as_string(self):
"""__str__ method returns a command line execution representation.
"""
self.assertEqual(str(self.fq2a_job), "fastq_to_fasta ")
def test_add_argument(self):
"""Method to add arguments to job.
"""
self.fq2a_job.add_argument('-i', 'inputfile.fq')
self.assertDictEqual(self.fq2a_job.args, {'-i': 'inputfile.fq'})
self.assertEqual(str(self.fq2a_job), 'fastq_to_fasta -i inputfile.fq')
def test_add_jobname(self):
"""Replace 8 char random string with human readable option.
"""
self.fq2a_job.add_jobname("ThisIsMyTestJob")
self.assertEqual(self.fq2a_job.name, "ThisIsMyTestJob")
def test_add_dependency_invalid_arg(self):
"""Test dependency condition passed is a valid LSF option.
"""
# problem here with assertRaises
self.assertRaises(InvalidInput,
self.fq2a_job.add_dependencies,
typo=['somejob',])
def test_add_dependency_no_dep_str(self):
"""Add dependency, create LSF dependency string.
"""
self.fq2a_job.add_dependencies(done=['job1', 'job2'],
exit=['job3'])
self.assertDictEqual(self.fq2a_job.dep,
{'done':['job1','job2'],
'exit':['job3',],
'ended': [],
'external': [],
'post_done': [],
'post_err': [],
'started': []})
self.fq2a_job.add_dependencies(ended=['job4',])
self.assertDictEqual(self.fq2a_job.dep,
{'done':['job1','job2'],
'exit':['job3',],
'ended': ['job4',],
'external': [],
'post_done': [],
'post_err': [],
'started': []})
def test_add_dependency_with_dep_str(self):
"""Add dependency, build LSF dependency string.
"""
self.fq2a_job.add_dependencies(done=['job1', 'job2'],
exit=['job3'])
self.assertDictEqual(self.fq2a_job.dep,
{'done':['job1','job2'],
'exit':['job3',],
'ended': [],
'external': [],
'post_done': [],
'post_err': [],
'started': []})
self.fq2a_job.add_dependencies(ended=['job4',],
dep_str="done||done||ended||exit")
self.assertDictEqual(self.fq2a_job.dep,
{'done':['job1','job2'],
'exit':['job3',],
'ended': ['job4',],
'external': [],
'post_done': [],
'post_err': [],
'started': []})
def test_show_as_list(self):
"""Method returns cmd and arguments as list to submit to shell.
Note: list not in order because arguements are stored as a dictionary.
"""
self.fq2a_job.add_argument('-i', 'input_file.fq')
self.fq2a_job.add_argument('-o', 'output_file.fa')
self.assertListEqual(self.fq2a_job.show_as_list(),
['fastq_to_fasta',
'-o', 'output_file.fa',
'-i', 'input_file.fq'])
def test_get_command(self):
"""Method returns cmd and argument as string to submit to shell.
"""
self.fq2a_job.add_argument('-i', 'input_file.fq')
self.fq2a_job.add_argument('-o', 'output_file.fa')
self.assertEqual(self.fq2a_job.get_command(),
"fastq_to_fasta -o output_file.fa -i input_file.fq")
class ModuleInitWithParamaters(unittest.TestCase):
"""Test initialization of module when key-word input arguments are not empty.
"""
def setUp(self):
"""Set up a job initialized with input parameters.
Job used in class test cases.
"""
self.fq2a_job = FastqToFasta(name='myFastq2Fasta',
args={'-i': 'input_file.fq',
'-o': 'output_file.fa'},
dep_str='previous_job',
)
def test_job_init_cmd(self):
"""Module should inherit job and initialize cmd.
"""
self.assertEqual(self.fq2a_job.cmd, 'fastq_to_fasta')
def test_job_init_args(self):
"""Module initialized with args, args dictionary must match.
"""
self.assertDictEqual(self.fq2a_job.args, {'-i': 'input_file.fq',
'-o': 'output_file.fa'})
def test_job_init_name(self):
"""Module init with name, name is initialized value.
"""
self.assertEqual(self.fq2a_job.name, 'myFastq2Fasta')
self.assertIsInstance(self.fq2a_job.name, str)
def test_job_init_dep_str(self):
"""Module dependency string must match initialized dep_str.
"""
self.assertEqual(self.fq2a_job.dep_str, 'previous_job')
def test_job_init_dep_at_init(self):
"""Module if dep_string is not empty, attribute True.
"""
self.assertTrue(self.fq2a_job.dep_str_at_init)
def test_job_as_string(self):
"""__str__ method returns a command line execution representation.
"""
job_str = "fastq_to_fasta -o output_file.fa -i input_file.fq"
self.assertEqual(str(self.fq2a_job), job_str)
def test_add_argument(self):
"""Method to add arguments to job.
"""
self.fq2a_job.add_argument('-C', '')
self.assertDictEqual(self.fq2a_job.args, {'-i': 'input_file.fq',
'-o': 'output_file.fa',
'-C': ''})
job_str = 'fastq_to_fasta -o output_file.fa -i input_file.fq -C'
self.assertEqual(str(self.fq2a_job), job_str)
