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)
