def check_results_relaxed_blastx(
results, correct, formatter, delta=0.01, reformatCorrect=False, allowedLengthDiff=0, identityMin=0.6
):
results = reformat_results(results, formatter)
if reformatCorrect: # reformat these data too
correct = reformat_results(correct, formatter)
else:
correct.sort()
# Length of output
assert abs(len(results) - len(correct)) <= allowedLengthDiff
# Format check
for result in results:
assert 3 * result[0] == result[2]
assert 0.0 < result[3] and result[3] <= 1.0
# High-identity comparison
results_high = []
correct_high = []
for result in results:
if result[3] > identityMin:
results_high.append(result)
for result in correct:
if result[3] > identityMin:
correct_high.append(result)
assert testutil.approximate_cmp(correct_high, results_high, delta) == 0
def check_results(results, correct, formatter, delta=0.01, reformatCorrect=False, reformatResults=True):
if reformatResults:
results = reformat_results(results, formatter)
if reformatCorrect: # reformat these data too
correct = reformat_results(correct, formatter)
else:
correct.sort()
# this is to help troubleshooting the mismatches if there are any
mismatch = [(a, b) for a, b in zip(correct, results) if testutil.approximate_cmp([a], [b], delta)]
if mismatch:
logger.warn("blast mismatches found")
for m in mismatch:
logger.warn("%s != %s" % m)
# this is the actual test
assert testutil.approximate_cmp(correct, results, delta) == 0
def check_results(results, correct, formatter, delta=0.01):
found = []
for result in results:
for t in result.edges():
found.append(formatter(t))
# order it identically
correct.sort()
found.sort()
# this is to help troubleshooting the mismatches if there are any
mismatch = [ (a, b) for a, b in zip(correct, found) if
testutil.approximate_cmp([a], [b], delta)]
if mismatch:
logger.warn('blast mismatches found')
for m in mismatch:
logger.warn('%s != %s' % m)
# this is the actual test
assert testutil.approximate_cmp(correct, found, delta) == 0
def check_results_relaxed_blastp(
results,
correct,
formatter,
delta=0.01,
reformatCorrect=False,
allowedLengthDiff=0,
identityMin=0.6,
reformatResults=True,
):
if reformatResults:
results = reformat_results(results, formatter)
if reformatCorrect: # reformat these data too
correct = reformat_results(correct, formatter)
else:
correct.sort()
# Length of output
assert abs(len(results) - len(correct)) <= allowedLengthDiff
# Format check
key_re = re.compile("^[A-Z]{3}[A-Z0-9]?_[A-Z]{2,5}$")
for result in results:
assert key_re.search(result[0])
assert key_re.search(result[1])
assert 0.0 < result[2] and result[2] <= 1.0
# High-identity comparison
results_high = []
correct_high = []
for result in results:
if result[2] > identityMin:
results_high.append(result)
for result in correct:
if result[2] > identityMin:
correct_high.append(result)
assert testutil.approximate_cmp(correct_high, results_high, delta) == 0
