def test_help_options(self):
for option in ["--list-plugins"]:
options = build_config([option],
isolated=False,
modules=self.all_modules)
ret_val = main.run_antismash("", options)
assert ret_val == 0
def test_nisin_minimal(self):
# make sure the output directory isn't filled
out_dir = self.default_options.output_dir
assert not list(glob.glob(os.path.join(out_dir, "*")))
# die with neither inputs provided
with self.assertRaisesRegex(
ValueError, "No sequence file or prior results to read"):
run_antismash(None, self.default_options)
# make sure no files created
assert not list(glob.glob(os.path.join(out_dir, "*")))
# do a normal run
run_antismash(get_path_to_nisin_genbank(), self.default_options)
self.check_output_files()
# remove html file and make sure it's recreated
os.unlink(os.path.join(self.default_options.output_dir, "index.html"))
update_config({
"reuse_results":
os.path.join(self.default_options.output_dir, "nisin.json")
})
run_antismash(None, self.default_options)
self.check_output_files()
def test_nisin_minimal(self):
run_antismash(get_path_to_nisin_genbank(), self.default_options)
self.check_output_files()
def test_nisin_minimal(self):
run_antismash(get_path_to_nisin_genbank(), self.config)
self.check_output_files()
def test_check_prereqs(self):
options = build_config(["--check-prereqs"], isolated=False, modules=get_all_modules())
assert run_antismash("", options) == 0
def test_nisin_minimal(self):
path = os.path.abspath(
os.path.join(os.path.dirname(__file__), "data", "nisin.gbk"))
run_antismash(path, self.default_options)
self.check_output_files()
