def test_run_on_record_skips_work(self):
record = create_fake_record()
record.id = "real"
results = cassis.CassisResults(record.id)
mock("cassis.detect", returns=cassis.CassisResults("fake"))
assert cassis.run_on_record(record, results, None).record_id == "real"
assert cassis.run_on_record(record, None, None).record_id == "fake"
def test_run_on_record_skips_work(self):
record = create_fake_record()
record.id = "real"
results = cassis.CassisResults(record.id)
with patch.object(cassis,
"detect",
return_value=cassis.CassisResults("fake")):
assert cassis.run_on_record(record, results,
None).record_id == "real"
assert cassis.run_on_record(record, None, None).record_id == "fake"
def test_regeneration(self):
record = create_fake_record()
results = cassis.CassisResults(record.id)
# create a prediction, since it will generate a border with many extra qualifiers
start_marker = ClusterMarker("gene1", Motif(3, 3, score=1))
start_marker.promoter = "gene1"
start_marker.abundance = 2
end_marker = ClusterMarker("gene4", Motif(3, 3, score=1))
end_marker.promoter = "gene3+gene4"
assert end_marker.abundance == 1
cluster = cassis.ClusterPrediction(start_marker, end_marker)
results.subregions = cassis.create_subregions("gene1", [cluster],
record)
assert results.subregions
results.promoters = [
Promoter("gene1", 10, 20, seq=Seq("cgtacgtacgt")),
Promoter("gene2", 30, 40, seq=Seq("cgtacgtacgt")),
CombinedPromoter("gene3", "gene4", 50, 60, seq=Seq("cgtacgtacgt"))
]
round_trip = cassis.regenerate_previous_results(
results.to_json(), record, None)
assert isinstance(round_trip, cassis.CassisResults)
assert len(results.subregions) == len(round_trip.subregions)
for old, new in zip(results.subregions, round_trip.subregions):
assert old.location == new.location
assert old.to_biopython()[0].qualifiers == new.to_biopython(
)[0].qualifiers
assert round_trip.promoters == results.promoters
def test_changed_max_gap_length(self):
record = create_fake_record()
json = cassis.CassisResults(record.id).to_json()
assert isinstance(cassis.regenerate_previous_results(json, record, None),
cassis.CassisResults)
cassis.MAX_GAP_LENGTH += 1
assert cassis.regenerate_previous_results(json, record, None) is None
def test_changed_max_percentage(self):
record = create_fake_record()
json = cassis.CassisResults(record.id).to_json()
assert isinstance(cassis.regenerate_previous_results(json, record, None),
cassis.CassisResults)
cassis.MAX_PERCENTAGE += 5
assert cassis.regenerate_previous_results(json, record, None) is None
def test_not_same_record(self):
record = create_fake_record()
record.id = "A"
other = create_fake_record()
other.id = "B"
json = cassis.CassisResults(record.id).to_json()
assert isinstance(cassis.regenerate_previous_results(json, record, None),
cassis.CassisResults)
assert cassis.regenerate_previous_results(json, other, None) is None
def test_base(self):
results = cassis.CassisResults("test")
assert results.record_id == "test"
assert results.subregions == []
assert results.promoters == []
