def test_check_prereqs(self):
"Test fullhmmer.check_prereqs()"
expected = []
returned = cluster_hmmer.check_prereqs(self.config)
self.assertListEqual(expected, returned)
assert_same_trace(self.tracer, self.expected_trace)
def test_check_prereqs_missing_exe(self):
"Test fullhmmer.check_prereqs() with a missing executable"
self.config.executables.__dict__.pop("hmmscan")
expected = ["Failed to locate executable: 'hmmscan'"]
returned = cluster_hmmer.check_prereqs(self.config)
self.assertListEqual(expected, returned)
assert_same_trace(self.tracer, self.expected_trace)
def test_check_prereqs_missing_exe(self):
"Test fullhmmer.check_prereqs() with a missing executable"
path.locate_executable.mock_returns = None
expected = ["Failed to locate executable: 'hmmscan'"]
returned = cluster_hmmer.check_prereqs()
self.assertListEqual(expected, returned)
assert_same_trace(self.tracer, self.expected_trace)
def test_check_prereqs_missing_file(self, patched_locate, _patched_run):
patched_locate.side_effect = [None] + EXPECTED_FILES[1:]
expected = [
"Failed to locate file: 'Pfam-A.hmm' in %s/pfam/%s" %
(self.config.database_dir, self.latest_pfam)
]
returned = cluster_hmmer.check_prereqs(self.config)
self.assertListEqual(expected, returned)
def test_check_prereqs_missing_file(self):
"Test fullhmmer.check_prereqs() with a missing file"
self.file_list[0] = None
path.locate_file.mock_returns_iter = self.file_list
expected = [
"Failed to locate file: 'Pfam-A.hmm' in %s/pfam/%s" %
(self.config.database_dir, self.latest_pfam)
]
returned = cluster_hmmer.check_prereqs(self.config)
self.assertListEqual(expected, returned)
assert_same_trace(self.tracer, self.expected_trace)
def test_check_prereqs_missing_exe(self, _patched_locate, _patched_run):
self.config.executables.__dict__.pop("hmmscan")
expected = ["Failed to locate executable: 'hmmscan'"]
returned = cluster_hmmer.check_prereqs(self.config)
self.assertListEqual(expected, returned)
def test_check_prereqs(self, _patched_locate, _patched_run):
expected = []
returned = cluster_hmmer.check_prereqs(self.config)
self.assertListEqual(expected, returned)