def test_lastdb_task_existing(tmpdir, datadir):
with tmpdir.as_cwd():
tf = datadir('test-protein.fa')
for ext in LASTDB_EXTENSIONS:
touch(tf + ext)
task = lastdb_task(tf, tf, prot=True)
run_tasks([task], ['run'])
print(task, file=sys.stderr)
status = check_status(task)
assert status.status == 'up-to-date'
def test_lastdb_task_prot(tmpdir, datadir):
with tmpdir.as_cwd():
tf = datadir('test-protein.fa')
task = lastdb_task(tf, tf, prot=True)
run_tasks([task], ['run'])
status = check_status(task)
for ext in LASTDB_EXTENSIONS:
assert os.path.isfile(tf + ext)
assert status.status == 'up-to-date'
def test_lastdb_task_nucl(tmpdir, datadir):
with tmpdir.as_cwd():
tf = datadir('test-transcript.fa')
task = lastdb_task(tf, tf, prot=False)
run_tasks([task], ['run'])
status = check_status(task)
print('PATH:', os.environ['PATH'], file=sys.stderr)
for ext in LASTDB_EXTENSIONS:
assert os.path.isfile(tf + ext)
assert status.status == 'up-to-date'
def test_lastal_task_uptodate(tmpdir, datadir):
with tmpdir.as_cwd():
prot = datadir('test-protein.fa')
out = tmpdir.join('test-out').strpath
db_task = lastdb_task(prot, prot)
aln_task = lastal_task(prot, prot, out,
translate=False,
cutoff=None)
# Run it once
run_tasks([db_task, aln_task], ['run'])
# Now run again and check the status
#run_tasks(aln_tasks, ['run'])
print(aln_task)
status = check_status(aln_task, tasks=[aln_task, db_task])
assert status.status == 'up-to-date'