def test_predict_genes_wrong_input(self):
for fp in self.negative_fps:
with self.assertRaisesRegex(
ApplicationError,
r'Sequence read failed \(file must be Fasta, '
'Genbank, or EMBL format\).'):
predict_genes(fp, self.temp_dir, 'foo')
def test_predict_genes(self):
for fp, params, prefix, suffix in zip(self.positive_fps,
self.positive_params,
self.positive_prefices,
self.positive_suffices):
res = predict_genes(fp, self.temp_dir, prefix, params)
self.assertEqual(res['ExitStatus'], 0)
for i in ['-o', '-d', '-a']:
fp = self.get_prodigal_path('.'.join([prefix, suffix[i]]))
with open(fp) as f:
self.assertEqual(f.read(), res[i].read())
res[i].close()
res['StdOut'].close()
res['StdErr'].close()
