def test_model_len(self):
cf = config.Config(self.args)
with self.assertRaises(RuntimeError) as ctx:
with self.catch_log():
cf.model_len
self.assertEqual(str(ctx.exception), "'model_attc' is not define.")
self.args.attc_model = 'foo'
cf = config.Config(self.args)
with self.assertRaises(IOError) as ctx:
with self.catch_log():
cf.model_len
self.assertEqual(
str(ctx.exception),
"Path to model_attc '{}' does not exists".format(
cf.model_attc_path))
model_path = os.path.join(os.path.dirname(__file__), 'data',
'Replicons', 'acba.007.p01.13.fst')
self.args.attc_model = model_path
cf = config.Config(self.args)
with self.assertRaises(RuntimeError) as ctx:
with self.catch_log():
cf.model_len
self.assertEqual(
str(ctx.exception),
"CLEN not found in '{}', maybe it's not infernal model file".
format(model_path))
self.args.attc_model = 'attc_4.cm'
cf = config.Config(self.args)
cf._prefix_data = os.path.join(os.path.dirname(__file__), 'data')
self.assertEqual(cf.model_len, 47)
# test the model_len cache
self.assertEqual(cf.model_len, 47)
def test_model_attc_name(self):
cf = config.Config(self.args)
with self.assertRaises(RuntimeError) as ctx:
cf.model_attc_name
self.assertEqual(str(ctx.exception), "'model_attc' is not define.")
self.args.attc_model = 'bar'
cf = config.Config(self.args)
cf._prefix_data = 'foo'
self.assertEqual(cf.model_attc_name, 'bar')
self.args.attc_model = 'bar/baz'
self.assertEqual(cf.model_attc_name, 'baz')
def test_default_topology(self):
self.args.circular = True
self.args.linear = False
cf = config.Config(self.args)
self.assertEqual(cf.default_topology, 'circ')
self.args.circular = False
self.args.linear = True
cf = config.Config(self.args)
self.assertEqual(cf.default_topology, 'lin')
self.args.circular = False
self.args.linear = False
cf = config.Config(self.args)
self.assertIsNone(cf.default_topology)
self.args = argparse.Namespace()
cf = config.Config(self.args)
self.assertIsNone(cf.default_topology)
def test_log_level(self):
for v, q, l in [(0, 0, 20), (0, 2, 40), (0, 5, 50), (1, 0, 10),
(3, 0, 10), (2, 2, 20)]:
self.args.verbose = v
self.args.quiet = q
cf = config.Config(self.args)
self.assertEqual(cf.log_level, l)
def test_getattr(self):
self.args.replicon = 'foo'
self.args.bar = 'baz'
cf = config.Config(self.args)
self.assertEqual(cf.input_seq_path, os.path.abspath('foo'))
self.assertEqual(cf.bar, 'baz')
with self.assertRaises(AttributeError) as ctx:
self.assertEqual(cf.foobar, 'foobar')
self.assertEqual(str(ctx.exception),
"config object has no attribute 'foobar'")
def test_result_dir(self):
replicon = '../foo.fasta'
outdir = 'outdir'
self.args.replicon = replicon
self.args.outdir = outdir
cf = config.Config(self.args)
exp_result_dir = os.path.abspath(
os.path.join(
outdir, "Results_Integron_Finder_" +
os.path.splitext(os.path.split(replicon)[1])[0]))
self.assertEqual(cf.result_dir, exp_result_dir)
def test_tmp_dir(self):
replicon_id = 'foo'
replicon_path = '../{}.fasta'.format(replicon_id)
outdir = 'outdir'
self.args.replicon = replicon_path
self.args.outdir = outdir
cf = config.Config(self.args)
exp_result_tmp_dir = os.path.abspath(
os.path.join(outdir,
"Results_Integron_Finder_{}".format(replicon_id),
"tmp_{}".format(replicon_id)))
self.assertEqual(cf.tmp_dir(replicon_id), exp_result_tmp_dir)
def test_resultdir_not_writable(self):
replicon_filename = 'acba.007.p01.13'
args = argparse.Namespace()
args.replicon = self.find_data(os.path.join('Replicons', '{}.fst'.format(replicon_filename)))
args.outdir = self.out_dir
cf = config.Config(args)
os.mkdir(cf.result_dir, mode=0o500)
command = "integron_finder --outdir {out_dir} {replicon}".format(out_dir=self.out_dir,
replicon=self.find_data(
os.path.join('Replicons',
'{}.fst'.format(replicon_filename))
)
)
with self.assertRaises(PermissionError) as ctx:
with self.catch_io(out=True):
# in case the error is not raised
# anyway do not want to mess up the test output
# I cannot catch log because loggers are reinitialized in main
# I need to catch stdout as log are write on
main(command.split()[1:])
err_msg = "result dir '{}' already exists and is not writable".format(self.out_dir)
self.assertEqual(err_msg, str(ctx.exception))
def test_input_dir(self):
self.args.replicon = '../foo.fasta'
cf = config.Config(self.args)
self.assertEqual(cf.input_dir,
os.path.split(os.path.abspath('../foo'))[0])
def test_replicon_path(self):
self.args.replicon = '../foo'
cf = config.Config(self.args)
self.assertEqual(cf.input_seq_path, os.path.abspath('../foo'))
def test_func_annot_path(self):
cf = config.Config(self.args)
cf._prefix_data = 'foo'
self.assertEqual(cf.func_annot_path,
os.path.join('foo', 'Functional_annotation'))
def test_model_phage_int(self):
cf = config.Config(self.args)
cf._prefix_data = 'foo'
self.assertEqual(cf.model_phage_int,
os.path.join('foo', 'Models', 'phage-int.hmm'))
def test_model_integrase(self):
cf = config.Config(self.args)
cf._prefix_data = 'foo'
self.assertEqual(
cf.model_integrase,
os.path.join('foo', 'Models', 'integron_integrase.hmm'))
def test_model_dir(self):
cf = config.Config(self.args)
cf._prefix_data = 'foo'
self.assertEqual(cf.model_dir, os.path.join('foo', 'Models'))
