def test_longorfs_task(self): with TemporaryDirectory() as td: with Move(td): with TestData('test-transcript.fa', td) as transcript, \ TestData('test-transcript-orf.pep', td) as exp_orf: task = tasks.get_transdecoder_orf_task(transcript, self.longorfs_cfg) run_tasks([task], ['run']) output_dir = transcript + '.transdecoder_dir' exp_pep = open(exp_orf).read() pep_fn = os.path.join(output_dir, 'longest_orfs.pep') self.assertTrue(os.path.isfile(pep_fn)) pep = open(pep_fn).read() self.assertIn(exp_pep, pep)
def test_predict_task(self): with TemporaryDirectory() as td: with Move(td): with TestData('test-transcript.fa', td) as transcript, \ TestData('test-protein-x-pfam-a.tbl', td) as pfam: orf_task = tasks.get_transdecoder_orf_task(transcript, self.longorfs_cfg) pred_task = tasks.get_transdecoder_predict_task(transcript, pfam, self.predict_cfg) run_tasks([orf_task, pred_task], ['run']) for ext in self.extensions: fn = os.path.join(td, transcript+'.transdecoder'+ext) self.assertTrue(os.path.isfile(fn)) contents = open(fn).read() if ext == '.gff3': self.assertIn('mRNA', contents) self.assertIn('gene', contents) self.assertIn('CDS', contents) self.assertIn('three_prime_UTR', contents) self.assertIn('exon', contents)