def test_lastal_task_nucl_x_prot(self):
with TemporaryDirectory() as td:
with Move(td):
with TestData('test-protein.fa', td) as prot, \
TestData('test-transcript.fa', td) as tr, \
TemporaryFile(td) as out:
print(os.listdir(td), file=sys.stderr)
db_task = tasks.get_lastdb_task(prot, prot,
self.lastdb_cfg)
aln_task = tasks.get_lastal_task(tr,
prot,
out,
self.lastal_cfg,
translate=True,
cutoff=None)
run_tasks([db_task, aln_task], ['run'])
aln = ''.join(open(out).readlines())
print(aln, file=sys.stderr)
self.assertIn('SPAC212_RecQ_type_DNA_helicase_PROTEIN',
aln)
self.assertIn('SPAC212_RecQ_type_DNA_helicase_TRANSCRIPT',
aln)
self.assertIn('lambda',
aln,
msg='lambda missing, wrong LAST version?')
def test_lastal_task_multithreaded(self):
with TemporaryDirectory() as td:
with Move(td):
with TestData('test-protein.fa', td) as prot, \
TestData('pom.50.fa', td) as tr, \
TemporaryFile(td) as out_single,\
TemporaryFile(td) as out_multi:
for n_threads in (3,4,5):
print(os.listdir(td), file=sys.stderr)
db_task = tasks.get_lastdb_task(prot, prot, self.lastdb_cfg)
aln_task_single = tasks.get_lastal_task(tr, prot, out_single,
self.lastal_cfg,
translate=True,
cutoff=None)
aln_task_multi = tasks.get_lastal_task(tr, prot, out_multi,
self.lastal_cfg,
translate=True,
cutoff=None,
n_threads=n_threads)
run_tasks([db_task, aln_task_single, aln_task_multi],
['run'])
alns_single = MafParser(out_single).read()
alns_multi = MafParser(out_multi).read()
self.assertTrue(all(alns_single['E'].sort_values() == \
alns_multi['E'].sort_values()))
def test_lastdb_task_prot(self):
with TemporaryDirectory() as td:
with Move(td):
with TestData('test-protein.fa', td) as tf:
task = tasks.get_lastdb_task(tf, tf, self.lastdb_cfg,
prot=True)
run_tasks([task], ['run'])
status = check_status(task)
print(os.listdir(td), file=sys.stderr)
for ext in self.extensions:
self.assertTrue(os.path.isfile(tf + ext))
self.assertEquals(status.status, 'up-to-date')
def test_lastal_task_uptodate(self):
with TemporaryDirectory() as td:
with Move(td):
with TestData('test-protein.fa', td) as prot, \
TemporaryFile(td) as out:
print(os.listdir(td), file=sys.stderr)
db_task = tasks.get_lastdb_task(prot, prot, self.lastdb_cfg)
aln_task = tasks.get_lastal_task(prot, prot, out, False,
None, 1, self.lastal_cfg)
# Run it once
run_tasks([db_task, aln_task], ['run'])
# Now run again and check the status
run_tasks([aln_task], ['run'])
status = check_status(aln_task)
self.assertEquals(status.status, 'up-to-date')
def test_lastal_task_nucl_x_prot(self):
with TemporaryDirectory() as td:
with Move(td):
with TestData('test-protein.fa', td) as prot, \
TestData('test-transcript.fa', td) as tr, \
TemporaryFile(td) as out:
print(os.listdir(td), file=sys.stderr)
db_task = tasks.get_lastdb_task(prot, prot, self.lastdb_cfg)
aln_task = tasks.get_lastal_task(tr, prot, out, True, None, 1,
self.lastal_cfg)
run_tasks([db_task, aln_task], ['run'])
aln = ''.join(open(out).readlines())
print(aln, file=sys.stderr)
self.assertIn('SPAC212_RecQ_type_DNA_helicase_PROTEIN',
aln)
self.assertIn('SPAC212_RecQ_type_DNA_helicase_TRANSCRIPT',
aln)
self.assertIn('lambda', aln,
msg='lambda missing, wrong LAST version?')
def test_lastal_task_prot_x_prot(self):
with TemporaryDirectory() as td:
with Move(td):
with TestData('test-protein.fa', td) as prot, \
TemporaryFile(td) as out:
print(os.listdir(td), file=sys.stderr)
db_task = tasks.get_lastdb_task(prot, prot, self.lastdb_cfg)
aln_task = tasks.get_lastal_task(prot, prot, out, False,
None, 1, self.lastal_cfg)
run_tasks([db_task, aln_task], ['run'])
aln = ''.join(open(out).readlines())
print(aln, file=sys.stderr)
self.assertEquals(
aln.count('SPAC212_RecQ_type_DNA_helicase_PROTEIN'),
2)
self.assertIn('EG2=0', aln)
self.assertIn('E=0', aln)
self.assertIn('lambda', aln,
msg='lambda missing, wrong LAST version?')
def test_lastal_task_multithreaded(self):
with TemporaryDirectory() as td:
with Move(td):
with TestData('test-protein.fa', td) as prot, \
TestData('pom.50.fa', td) as tr, \
TemporaryFile(td) as out_single,\
TemporaryFile(td) as out_multi:
for n_threads in (3, 4, 5):
print(os.listdir(td), file=sys.stderr)
db_task = tasks.get_lastdb_task(
prot, prot, self.lastdb_cfg)
aln_task_single = tasks.get_lastal_task(
tr,
prot,
out_single,
self.lastal_cfg,
translate=True,
cutoff=None)
aln_task_multi = tasks.get_lastal_task(
tr,
prot,
out_multi,
self.lastal_cfg,
translate=True,
cutoff=None,
n_threads=n_threads)
run_tasks([db_task, aln_task_single, aln_task_multi],
['run'])
alns_single = MafParser(out_single).read()
alns_multi = MafParser(out_multi).read()
self.assertTrue(all(alns_single['E'].sort_values() == \
alns_multi['E'].sort_values()))
def test_lastal_task_prot_x_prot(self):
with TemporaryDirectory() as td:
with Move(td):
with TestData('test-protein.fa', td) as prot, \
TemporaryFile(td) as out:
print(os.listdir(td), file=sys.stderr)
db_task = tasks.get_lastdb_task(prot, prot, self.lastdb_cfg)
aln_task = tasks.get_lastal_task(prot, prot, out,
self.lastal_cfg,
translate=False,
cutoff=None)
run_tasks([db_task, aln_task], ['run'])
aln = ''.join(open(out).readlines())
print(aln, file=sys.stderr)
self.assertEquals(
aln.count('SPAC212_RecQ_type_DNA_helicase_PROTEIN'),
2)
self.assertIn('EG2=0', aln)
self.assertIn('E=0', aln)
self.assertIn('lambda', aln,
msg='lambda missing, wrong LAST version?')
