def test_non_acgt(self): with TemporaryDirectory() as td: with Move(td): with TestData('non-actg-transcripts.fa', td) as transcript: output_fn = os.path.join(td, 'test') tsk = tasks.get_transcriptome_stats_task( transcript, output_fn) stat = run_task(tsk) self.assertEquals(stat, 2)
def test_non_acgt(self): with TemporaryDirectory() as td: with Move(td): with TestData('non-actg-transcripts.fa', td) as transcript: output_fn = os.path.join(td, 'test') tsk = tasks.get_transcriptome_stats_task(transcript, output_fn) stat = run_task(tsk) self.assertEquals(stat, 2)
def test_output(self): with TemporaryDirectory() as td: with Move(td): with TestData('test-transcript.fa', td) as transcript: output_fn = os.path.join(td, 'test') tsk = tasks.get_transcriptome_stats_task( transcript, output_fn) run_tasks([tsk], ['run']) with open(output_fn) as fp: results = json.load(fp) self.assertIn('n_ambiguous', results) self.assertEquals(results['n_ambiguous'], 0) self.assertIn('N', results) self.assertEquals(results['N'], 1)
def test_output(self): with TemporaryDirectory() as td: with Move(td): with TestData('test-transcript.fa', td) as transcript: output_fn = os.path.join(td, 'test') tsk = tasks.get_transcriptome_stats_task(transcript, output_fn) run_tasks([tsk], ['run']) with open(output_fn) as fp: results = json.load(fp) self.assertIn('n_ambiguous', results) self.assertEquals(results['n_ambiguous'], 0) self.assertIn('N', results) self.assertEquals(results['N'], 1)
def test_ambiguous_transcript(self): with TemporaryDirectory() as td: with Move(td): with TestData('test-transcript-N.fa', td) as transcript: output_fn = os.path.join(td, 'test') tsk = tasks.get_transcriptome_stats_task( transcript, output_fn) stat = run_task(tsk) self.assertEquals(stat, 0) print(os.listdir(td)) with open(output_fn) as fp: results = json.load(fp) self.assertIn('n_ambiguous', results) self.assertEquals(results['n_ambiguous'], 1) self.assertIn('N', results) self.assertEquals(results['N'], 1) print(results)
def test_ambiguous_transcript(self): with TemporaryDirectory() as td: with Move(td): with TestData('test-transcript-N.fa', td) as transcript: output_fn = os.path.join(td, 'test') tsk = tasks.get_transcriptome_stats_task(transcript, output_fn) stat = run_task(tsk) self.assertEquals(stat, 0) print(os.listdir(td)) with open(output_fn) as fp: results = json.load(fp) self.assertIn('n_ambiguous', results) self.assertEquals(results['n_ambiguous'], 1) self.assertIn('N', results) self.assertEquals(results['N'], 1) print(results)