def test_filter(self):
# fake HSPs all in one CDS with overlap > 20 and query_ids from the same equivalence group
# not overlapping by > 20
first = FakeHSPHit("AMP-binding", "A", 50, 90, 0.1, None)
second = FakeHSPHit("A-OX", "A", 70, 100, 0.5, None)
new, by_id = hmm_detection.filter_results([first, second], {"A": [first, second]},
self.filter_file, self.signature_names)
assert new == [first, second]
assert by_id == {"A": [first, second]}
# overlapping, in same group
first.hit_end = 91
assert hmm_detection.hsp_overlap_size(first, second) == 21
new, by_id = hmm_detection.filter_results([first, second], {"A": [first, second]},
self.filter_file, self.signature_names)
assert new == [second]
assert by_id == {"A": [second]}
# overlapping, not in same group
second.query_id = "none"
new, by_id = hmm_detection.filter_results([first, second], {"A": [first, second]},
self.filter_file, self.signature_names)
assert new == [first, second]
assert by_id == {"A": [first, second]}
# not in the same CDS, but int he same group
second.hit_id = "B"
second.query_id = "A-OX"
new, by_id = hmm_detection.filter_results([first, second], {"A": [first], "B": [second]},
self.filter_file, self.signature_names)
assert new == [first, second]
assert by_id == {"A": [first], "B": [second]}
def test_filter_multiple(self):
# all in one CDS no overlap and the same query_ids -> cull all but the best score
# not overlapping, not same query_id
first = FakeHSPHit("AMP-binding", "A", 50, 60, 0.1, None)
second = FakeHSPHit("A-OX", "A", 70, 100, 0.5, None)
both = [first, second]
by_id = {"A": [first, second]}
new, by_id = hmm_detection.filter_result_multiple(
list(both), dict(by_id))
assert new == [first, second]
assert by_id == {"A": [first, second]}
# not overlapping, same query_id
first.query_id = "A-OX"
new, by_id = hmm_detection.filter_result_multiple(
list(both), dict(by_id))
assert new == [second]
assert by_id == {"A": [second]}
# not in same CDS, same query_id
second.hit_id = "B"
by_id = {"A": [first], "B": [second]}
new, by_id = hmm_detection.filter_result_multiple(
list(both), dict(by_id))
assert new == [first, second]
assert by_id == {"A": [first], "B": [second]}