def test_lastal_task_multithreaded(tmpdir, datadir):
with tmpdir.as_cwd():
for n_threads in (3,4,5):
prot = datadir('test-protein.fa')
tr = datadir('pom.50.fa')
out_single = tmpdir.join('out-single').strpath
out_multi = tmpdir.join('out-multi').strpath
db_task = lastdb_task(prot, prot)
aln_task_single = lastal_task(tr, prot, out_single,
translate=True,
cutoff=None)
aln_task_multi = lastal_task(tr, prot, out_multi,
translate=True,
cutoff=None,
n_threads=n_threads)
run_tasks([db_task, aln_task_multi, aln_task_single],
['run'])
alns_single = MafParser(out_single).read()
alns_multi = MafParser(out_multi).read()
assert all(alns_single['E'].sort_values() == \
alns_multi['E'].sort_values())
def test_lastal_task_large(datadir, lastdb_dir, tmpdir_factory, benchmark, n_threads):
with tmpdir_factory.mktemp('THREADS_{0}'.format(n_threads)).as_cwd():
query = datadir('sacPom.cdna.fa')
database = str(lastdb_dir.join('sacPom.pep.fa'))
output = 'out'
aln_task = lastal_task(query, database, output,
translate=True,
cutoff=None,
n_threads=n_threads)
result = benchmark.pedantic(run_tasks,
args=([aln_task], ['run']),
iterations=1,
rounds=1)
assert result == 0
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'
def test_lastal_task_prot_x_prot(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_tasks([db_task, aln_task], ['run'])
aln = ''.join(open(out).readlines())
print(aln, file=sys.stderr)
assert aln.count('SPAC212_RecQ_type_DNA_helicase_PROTEIN') == 2
assert 'EG2=0' in aln
assert 'E=0' in aln
assert 'lambda' in aln, 'lambda missing, wrong LAST version?'
def task(self, *args, **kwargs):
exc = self.deps()
return last.lastal_task(*args, **kwargs)