def test_gather(self):
# ensure the test will function as expected
for result in self.results:
for hsps in result.hsps:
assert hsps.query_id == self.gene_id
gathered = refinement.gather_by_query(self.results)
# make sure we only found the one we're interested
assert len(gathered) == 1
assert [self.gene_id] == list(gathered.keys())
for result in gathered[self.gene_id]:
assert isinstance(result, refinement.HMMResult)
def test_merges(self):
results = refinement.gather_by_query(self.results)[self.gene_id]
results = sorted(list(results), key=lambda result: result.query_start)
hit_ids = set(result.hit_id for result in results)
assert len(hit_ids) == 3
assert hit_ids == self.hit_ids
# 2 hits each for 1048 and 1237, for 5 hits total
assert len(results) == 5
new = refinement._merge_domain_list(results, self.hmm_lengths)
# after merging, only one hit should remain for each
assert len(new) == 3
# and the original list should be untouched
assert len(results) == 5
def test_incomplete_regulator(self):
results = refinement.gather_by_query(self.results)[self.gene_id]
results = sorted(list(results), key=lambda result: result.query_start)
assert len(results) == 5
regulator_id = "DUMMY:some_regulator_desc"
regulator_result = refinement.HMMResult(regulator_id, 1, 2, 1e-10, 1)
results.append(regulator_result)
new_lengths = dict(self.hmm_lengths)
new_lengths[regulator_id] = len(regulator_result) * 100 # always big
# set the thresholds to be unreachable
new = refinement._remove_incomplete(results,
new_lengths,
threshold=2.,
fallback=2.)
# ensure the tiny, but present, regulator is still in the list
assert len(new) == 1
assert new[0].hit_id == regulator_id
def test_incomplete_removal(self):
results = refinement.gather_by_query(self.results)[self.gene_id]
results = sorted(list(results), key=lambda result: result.query_start)
assert len(results) == 5
# ensure they're all too short to be caught
for result in results:
assert len(result) / self.hmm_lengths[result.hit_id] < 1
new = refinement._remove_incomplete(results, self.hmm_lengths)
# ensure all were removed
assert not new
# and original list untouched
assert len(results) == 5
longest = 0
for result in results:
proportional_length = len(result) / self.hmm_lengths[result.hit_id]
if proportional_length > longest:
longest = proportional_length
assert longest < 1. / 3.
# ensure the fallback works as intended
new = refinement._remove_incomplete(results, self.hmm_lengths)
# ensure all were removed
assert not new
new = refinement._remove_incomplete(results,
self.hmm_lengths,
fallback=longest - 0.01)
# ensure the longest, and longer than the fallback, remain
assert len(new) == 1
assert len(new[0]) / self.hmm_lengths[new[0].hit_id] == longest
# change the fallback to 0 and ensure only one comes back
new = refinement._remove_incomplete(results,
self.hmm_lengths,
fallback=0.)
assert len(new) == 1
assert len(new[0]) / self.hmm_lengths[new[0].hit_id] == longest
