def test_cmscan_task_multithreaded(self, tmpdir, datadir):
with tmpdir.as_cwd():
transcript = datadir('rnaseP-bsu.fa')
cm = datadir('rnaseP-eubact.c.cm')
out_single = str(tmpdir.join('single'))
out_multi = str(tmpdir.join('multi'))
for n_threads in (2, 3, 4, 5):
db_task = CMPressTask().task(cm, params=self.cmpress_cfg)
aln_tasks_single = CMScanTask().task(transcript,
out_single,
cm,
cutoff=1.0,
n_threads=1)
aln_tasks_multi = CMScanTask().task(transcript,
out_multi,
cm,
cutoff=1.0,
n_threads=n_threads)
run_tasks([db_task, aln_tasks_single], ['run'])
run_task(aln_tasks_multi)
alns_single = pd.concat(InfernalParser(out_single))
alns_multi = pd.concat(InfernalParser(out_multi))
assert all(alns_single['e_value'].sort_values() == \
alns_multi['e_value'].sort_values())
def test_cmpress_task(self, tmpdir, datadir):
with tmpdir.as_cwd():
tf = datadir('test-covariance-model.cm')
task = CMPressTask().task(tf, params=self.cmpress_cfg)
run_tasks([task], ['run'])
status = check_status(task)
print(os.listdir(), file=sys.stderr)
for ext in self.extensions:
assert os.path.isfile(tf + ext)
assert status.status == 'up-to-date'
def register_rfam_tasks(handler, params, databases):
rfam = databases['Rfam']
archive_fn = '{0}.{1}'.format(rfam['filename'], rfam['fileformat'])
target_fn = path.join(handler.directory, rfam['filename'])
dl_task = get_download_task(rfam['url'], archive_fn, md5=rfam['md5'])
gz_task = get_gunzip_task(archive_fn, target_fn)
handler.register_task('download:Rfam',
dl_task,
files={'Rfam-gz': archive_fn})
handler.register_task('gunzip:Rfam', gz_task, files={'Rfam': target_fn})
handler.register_task('cmpress:Rfam',
CMPressTask().task(target_fn, params=params))
return handler
def test_cmscan_task(self, tmpdir, datadir):
with tmpdir.as_cwd():
transcript = datadir('test-transcript.fa')
cm = datadir('test-covariance-model.cm')
out = str(tmpdir.join('test.out'))
db_task = CMPressTask().task(cm, params=self.cmpress_cfg)
aln_task = CMScanTask().task(transcript,
out,
cm,
cutoff=1.0,
n_threads=1)
run_tasks([db_task, aln_task], ['run'])
print(os.listdir(), file=sys.stderr)
aln = ''.join(open(out).readlines())
print(aln, file=sys.stderr)
# TODO: better correctness check
assert aln.count('accession') == 2
assert 'E-value' in aln