def test_hmmscan_task_multithreaded(self):
with TemporaryDirectory() as td:
with Move(td):
with TestData('20aa-alitest.fa', td) as prot, \
TestData('20aa.hmm', td) as hmm, \
TemporaryFile(td) as out_single,\
TemporaryFile(td) as out_multi:
for n_threads in (2,3,4,5):
db_task = tasks.get_hmmpress_task(hmm, self.hmmpress_cfg)
aln_task_single = tasks.get_hmmscan_task(prot, out_single,
hmm, 1.0, 1,
self.hmmscan_cfg)
aln_task_multi = tasks.get_hmmscan_task(prot, out_multi,
hmm, 1.0, n_threads,
self.hmmscan_cfg)
run_tasks([db_task, aln_task_single], ['run'])
run_task(aln_task_multi)
print(os.listdir(td), file=sys.stderr)
print(open(out_single).read())
alns_single = pd.concat(hmmscan_to_df_iter(out_single))
alns_multi = pd.concat(hmmscan_to_df_iter(out_multi))
self.assertTrue(all(alns_single['domain_i_evalue'].sort_values() == \
alns_multi['domain_i_evalue'].sort_values()))
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_cmscan_task_multithreaded(self):
with TemporaryDirectory() as td:
with Move(td):
with TestData('rnaseP-bsu.fa', td) as transcript, \
TestData('rnaseP-eubact.c.cm', td) as cm, \
TemporaryFile(td) as out_single,\
TemporaryFile(td) as out_multi:
for n_threads in (2, 3, 4, 5):
db_task = tasks.get_cmpress_task(cm, self.cmpress_cfg)
aln_task_single = tasks.get_cmscan_task(
transcript, out_single, cm, 1.0, 1,
self.cmscan_cfg)
aln_task_multi = tasks.get_cmscan_task(
transcript, out_multi, cm, 1.0, n_threads,
self.cmscan_cfg)
run_tasks([db_task, aln_task_single], ['run'])
run_task(aln_task_multi)
alns_single = pd.concat(cmscan_to_df_iter(out_single))
alns_multi = pd.concat(cmscan_to_df_iter(out_multi))
self.assertTrue(all(alns_single['e_value'].sort_values() == \
alns_multi['e_value'].sort_values()))
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_cmscan_task_multithreaded(self):
with TemporaryDirectory() as td:
with Move(td):
with TestData('rnaseP-bsu.fa', td) as transcript, \
TestData('rnaseP-eubact.c.cm', td) as cm, \
TemporaryFile(td) as out_single,\
TemporaryFile(td) as out_multi:
for n_threads in (2,3,4,5):
db_task = tasks.get_cmpress_task(cm, self.cmpress_cfg)
aln_task_single = tasks.get_cmscan_task(transcript, out_single,
cm, 1.0, 1,
self.cmscan_cfg)
aln_task_multi = tasks.get_cmscan_task(transcript, out_multi,
cm, 1.0,
n_threads,
self.cmscan_cfg)
run_tasks([db_task, aln_task_single], ['run'])
run_task(aln_task_multi)
alns_single = pd.concat(cmscan_to_df_iter(out_single))
alns_multi = pd.concat(cmscan_to_df_iter(out_multi))
self.assertTrue(all(alns_single['e_value'].sort_values() == \
alns_multi['e_value'].sort_values()))
def test_hmmscan_task_multithreaded(self):
with TemporaryDirectory() as td:
with Move(td):
with TestData('20aa-alitest.fa', td) as prot, \
TestData('20aa.hmm', td) as hmm, \
TemporaryFile(td) as out_single,\
TemporaryFile(td) as out_multi:
for n_threads in (2, 3, 4, 5):
db_task = tasks.get_hmmpress_task(
hmm, self.hmmpress_cfg)
aln_task_single = tasks.get_hmmscan_task(
prot, out_single, hmm, 1.0, 1, self.hmmscan_cfg)
aln_task_multi = tasks.get_hmmscan_task(
prot, out_multi, hmm, 1.0, n_threads,
self.hmmscan_cfg)
run_tasks([db_task, aln_task_single], ['run'])
run_task(aln_task_multi)
print(os.listdir(td), file=sys.stderr)
print(open(out_single).read())
alns_single = pd.concat(hmmscan_to_df_iter(out_single))
alns_multi = pd.concat(hmmscan_to_df_iter(out_multi))
self.assertTrue(all(alns_single['domain_i_evalue'].sort_values() == \
alns_multi['domain_i_evalue'].sort_values()))
def test_hmmpress_task(self):
with TemporaryDirectory() as td:
with Move(td):
with TestData('test-profile.hmm', td) as tf:
task = tasks.get_hmmpress_task(tf, self.hmmpress_cfg)
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_hmmpress_task(self):
with TemporaryDirectory() as td:
with Move(td):
with TestData('test-profile.hmm', td) as tf:
task = tasks.get_hmmpress_task(tf, self.hmmpress_cfg)
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_cmpress_task_existing(self):
with TemporaryDirectory() as td:
with Move(td):
with TestData('test-covariance-model.cm', td) as tf:
for ext in self.extensions:
touch(tf + ext)
task = tasks.get_cmpress_task(tf, self.cmpress_cfg)
run_tasks([task], ['run'])
print(os.listdir(td), file=sys.stderr)
print(task, file=sys.stderr)
status = check_status(task)
self.assertEquals(status.status, 'up-to-date')
def test_cmpress_task_existing(self):
with TemporaryDirectory() as td:
with Move(td):
with TestData('test-covariance-model.cm', td) as tf:
for ext in self.extensions:
touch(tf + ext)
task = tasks.get_cmpress_task(tf, self.cmpress_cfg)
run_tasks([task], ['run'])
print(os.listdir(td), file=sys.stderr)
print(task, file=sys.stderr)
status = check_status(task)
self.assertEquals(status.status, 'up-to-date')
def test_lastdb_task_existing(self):
with TemporaryDirectory() as td:
with Move(td):
with TestData('test-protein.fa', td) as tf:
for ext in self.extensions:
touch(tf + ext)
task = tasks.get_lastdb_task(tf, tf, self.lastdb_cfg,
prot=True)
run_tasks([task], ['run'])
print(os.listdir(td), file=sys.stderr)
print(task, file=sys.stderr)
status = check_status(task)
self.assertEquals(status.status, 'up-to-date')
def test_lastdb_task_nucl(self):
with TemporaryDirectory() as td:
with Move(td):
with TestData('test-transcript.fa', td) as tf:
task = tasks.get_lastdb_task(tf, tf, self.lastdb_cfg,
prot=False)
run_tasks([task], ['run'])
status = check_status(task)
print(os.listdir(td), file=sys.stderr)
print('PATH:', os.environ['PATH'], file=sys.stderr)
for ext in self.extensions:
self.assertTrue(os.path.isfile(tf + ext))
self.assertEquals(status.status, 'up-to-date')
def test_hmmscan_task(self):
with TemporaryDirectory() as td:
with Move(td):
with TestData('test-protein.fa', td) as prot, \
TestData('test-profile.hmm', td) as hmm, \
TemporaryFile(td) as out:
db_task = tasks.get_hmmpress_task(hmm, self.hmmpress_cfg)
aln_task = tasks.get_hmmscan_task(prot, out, hmm, 1.0, 1,
self.hmmscan_cfg)
run_tasks([db_task, aln_task], ['run'])
print(os.listdir(td), file=sys.stderr)
aln = open(out).read()
print(aln)
self.assertEquals(aln.count('accession'), 2)
self.assertIn('i-Evalue', aln)
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_hmmscan_task(self):
with TemporaryDirectory() as td:
with Move(td):
with TestData('test-protein.fa', td) as prot, \
TestData('test-profile.hmm', td) as hmm, \
TemporaryFile(td) as out:
db_task = tasks.get_hmmpress_task(hmm, self.hmmpress_cfg)
aln_task = tasks.get_hmmscan_task(prot, out, hmm, 1.0, 1,
self.hmmscan_cfg)
run_tasks([db_task, aln_task], ['run'])
print(os.listdir(td), file=sys.stderr)
aln = open(out).read()
print(aln)
self.assertEquals(aln.count('accession'), 2)
self.assertIn('i-Evalue', aln)
def test_cmscan_task(self):
with TemporaryDirectory() as td:
with Move(td):
with TestData('test-transcript.fa', td) as transcript, \
TestData('test-covariance-model.cm', td) as cm, \
TemporaryFile(td) as out:
db_task = tasks.get_cmpress_task(cm, self.cmpress_cfg)
aln_task = tasks.get_cmscan_task(transcript, out, cm, 1.0, 1,
self.cmscan_cfg)
run_tasks([db_task, aln_task], ['run'])
print(os.listdir(td), file=sys.stderr)
aln = ''.join(open(out).readlines())
print(aln, file=sys.stderr)
# TODO: better correctness check
self.assertEquals(aln.count('accession'), 2)
self.assertIn('E-value', aln)
def test_output(self):
with TemporaryDirectory() as td:
with Move(td):
with TestData('test-transcript.fa', td) as transcript:
output_fn = os.path.join(td, 'test')
tsk = tasks.get_transcriptome_stats_task(
transcript, output_fn)
run_tasks([tsk], ['run'])
with open(output_fn) as fp:
results = json.load(fp)
self.assertIn('n_ambiguous', results)
self.assertEquals(results['n_ambiguous'], 0)
self.assertIn('N', results)
self.assertEquals(results['N'], 1)
def test_cmscan_task(self):
with TemporaryDirectory() as td:
with Move(td):
with TestData('test-transcript.fa', td) as transcript, \
TestData('test-covariance-model.cm', td) as cm, \
TemporaryFile(td) as out:
db_task = tasks.get_cmpress_task(cm, self.cmpress_cfg)
aln_task = tasks.get_cmscan_task(transcript, out, cm, 1.0, 1,
self.cmscan_cfg)
run_tasks([db_task, aln_task], ['run'])
print(os.listdir(td), file=sys.stderr)
aln = ''.join(open(out).readlines())
print(aln, file=sys.stderr)
# TODO: better correctness check
self.assertEquals(aln.count('accession'), 2)
self.assertIn('E-value', aln)
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_output(self):
with TemporaryDirectory() as td:
with Move(td):
with TestData('test-transcript.fa', td) as transcript:
output_fn = os.path.join(td, 'test')
tsk = tasks.get_transcriptome_stats_task(transcript,
output_fn)
run_tasks([tsk], ['run'])
with open(output_fn) as fp:
results = json.load(fp)
self.assertIn('n_ambiguous', results)
self.assertEquals(results['n_ambiguous'], 0)
self.assertIn('N', results)
self.assertEquals(results['N'], 1)
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_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_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)
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?')
def run_task(task, cmd='run', verbosity=2):
return run_tasks([task], [cmd], config={'verbosity': verbosity})
def run_task(task, cmd='run', verbosity=2):
return run_tasks([task], [cmd], config={'verbosity': verbosity})
