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()