def test_pred_run(self):
for fp, params, outdir in zip(self.positive_fps, self.positive_params,
self.positive_outdir):
exp_d = _get_named_data_path(outdir)
obs_d = join(self.tmp_dir, outdir)
pred = FeaturePred(None, obs_d)
res = pred.run(fp, params)
self.assertEqual(res['ExitStatus'], 0)
for f in listdir(exp_d):
self.assertTrue(
cmp(join(obs_d, f), join(exp_d, f), shallow=False))
res['StdOut'].close()
res['StdErr'].close()
def test_pred_run(self):
for fp, params, outdir in zip(self.positive_fps,
self.positive_params,
self.positive_outdir):
exp_d = _get_named_data_path(outdir)
obs_d = join(self.tmp_dir, outdir)
pred = FeaturePred(None, obs_d)
res = pred.run(fp, params)
self.assertEqual(res['ExitStatus'], 0)
for f in listdir(exp_d):
self.assertTrue(
cmp(join(obs_d, f), join(exp_d, f), shallow=False))
res['StdOut'].close()
res['StdErr'].close()
def test_pred_wrong_input_fp(self):
pred = FeaturePred(None, self.tmp_dir)
for fp in self.negative_fps:
with self.assertRaisesRegex(
ApplicationError,
r'(Sequence read failed)|(no input sequences to analyze)'):
pred(fp)
def test_pred_parse_faa(self):
pred = FeaturePred(None, self.tmp_dir)
obs = pred._parse_faa(self.parse_fp)
for e, o in zip(self.parse_exp, obs):
self.assertEqual(e, o)
def test_pred_parse_faa(self):
pred = FeaturePred(None, self.tmp_dir)
obs = pred._parse_faa(self.parse_fp)
for e, o in zip(self.parse_exp, obs):
self.assertEqual(e, o)
