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)
