def test_anim_delta():
"""Test parsing of NUCmer delta file.
"""
aln, sim = anim.parse_delta(
os.path.join('test_ani_data', 'NC_002696_vs_NC_011916.delta'))
assert_equal(aln, 4073917)
assert_equal(sim, 2191)
print("Alignment length: {0}\nSimilarity Errors: {1}".format(aln, sim))
def test_anim_delta():
"""Test parsing of NUCmer delta file.
"""
aln, sim = anim.parse_delta(os.path.join('test_ani_data',
'NC_002696_vs_NC_011916.delta'))
assert_equal(aln, 4073917)
assert_equal(sim, 2191)
print("Alignment length: {0}\nSimilarity Errors: {1}".format(aln, sim))
def update_comparison_results(
joblist: List[ComparisonJob],
run,
session,
nucmer_version: str,
args: Namespace,
) -> None:
"""Update the Comparison table with the completed result set.
:param joblist: list of ComparisonJob namedtuples
:param run: Run ORM object for the current ANIm run
:param session: active pyanidb session via ORM
:param nucmer_version: version of nucmer used for the comparison
:param args: command-line arguments for this run
The Comparison table stores individual comparison results, one per row.
"""
logger = logging.getLogger(__name__)
# Add individual results to Comparison table
for job in tqdm(joblist, disable=args.disable_tqdm):
logger.debug("\t%s vs %s", job.query.description,
job.subject.description)
aln_length, sim_errs = anim.parse_delta(job.outfile)
qcov = aln_length / job.query.length
scov = aln_length / job.subject.length
try:
pid = 1 - sim_errs / aln_length
except ZeroDivisionError: # aln_length was zero (no alignment)
pid = 0
run.comparisons.append(
Comparison(
query=job.query,
subject=job.subject,
aln_length=aln_length,
sim_errs=sim_errs,
identity=pid,
cov_query=qcov,
cov_subject=scov,
program="nucmer",
version=nucmer_version,
fragsize=None,
maxmatch=args.maxmatch,
))
# Populate db
logger.debug("Committing results to database")
session.commit()
def test_anim_delta():
"""Test parsing of NUCmer delta file."""
aln, sim = anim.parse_delta(DELTAFILE)
assert_equal(aln, 4073917)
assert_equal(sim, 2191)
print("Alignment length: {0}\nSimilarity Errors: {1}".format(aln, sim))
def test_deltafile_import(self):
"""parses NUCmer .delta/.filter file."""
result = anim.parse_delta(self.deltafile)
assert_equal(result, (4073917, 2191))
def test_deltafile_import(self):
"""Parse test NUCmer .delta/.filter file."""
result = anim.parse_delta(self.deltafile)
self.assertEqual(result, (4074001, 2191))
def test_deltafile_parsing(deltafile_parsed):
"""Check parsing of test NUCmer .delta/.filter file."""
result = anim.parse_delta(deltafile_parsed.filename)
assert result == deltafile_parsed.data
def test_deltafile_import(self):
"""parses NUCmer .delta/.filter file."""
result = anim.parse_delta(self.deltafile)
assert_equal(result, (4073917, 2191))
def test_anim_delta(dir_anim_in):
"""Test parsing of NUCmer delta file."""
aln, sim = parse_delta(dir_anim_in / "NC_002696_vs_NC_011916.delta")
assert (aln, sim) == (4074148, 2191)
def test_anim_delta():
"""Test parsing of NUCmer delta file."""
aln, sim = anim.parse_delta(DELTAFILE)
assert_equal(aln, 4073917)
assert_equal(sim, 2191)
print("Alignment length: {0}\nSimilarity Errors: {1}".format(aln, sim))