def setUp(self):
self.config = get_simple_options(None, [])
self.config.genefinding_gff3 = path.get_full_path(__file__, "data", "test_gff.gff")
self.single_entry = False
contig1 = DummyRecord(seq="A"*2000)
contig1.id = "CONTIG_1"
contig2 = DummyRecord(seq="A"*2000)
contig2.id = "CONTIG_2"
self.sequences = [contig1, contig2]
def test_results_reconstruction(self):
def check_results(results):
assert results.record_id == "rec_id"
assert results.tool == "toolname"
assert isinstance(results.best_hits["cds1"], HMMResult)
assert results.best_hits["cds1"].hit_id == 'desc1'
assert results.best_hits["cds2"].bitscore == 20
assert results.function_mapping["cds2"] == GeneFunction.REGULATORY
hits = {
"cds1": HMMResult("desc1", 0, 100, 2.3e-126, 416),
"cds2": HMMResult("desc2", 5, 60, 3e-16, 20),
}
mapping = {
"cds1": GeneFunction.TRANSPORT,
"cds2": GeneFunction.REGULATORY,
}
results = self.res_class("rec_id",
"toolname",
best_hits=hits,
function_mapping=mapping)
check_results(results)
json = results.to_json()
assert json["best_hits"]["cds1"][0] == hits["cds1"].hit_id
record = DummyRecord()
record.id = "rec_id"
reconstructed = self.res_class.from_json(json, record)
check_results(reconstructed)
def test_add_to_incorrect_record(self):
results = self.create_results(record_id=self.record.id)
with self.assertRaisesRegex(
ValueError,
"Record to store in and record analysed don't match"):
other = DummyRecord()
other.id = self.record.id * 2
results.add_to_record(other)
def test_regeneration(self):
record = DummyRecord()
record.id = "rec_name"
as_json = json.loads(json.dumps(self.results.to_json()))
regenerated = structures.SideloadedResults.from_json(as_json, record)
assert regenerated.protoclusters == self.results.protoclusters
assert regenerated.subregions == self.results.subregions
assert regenerated.record_id == self.results.record_id
as_json["schema_version"] = -1
with self.assertRaisesRegex(ValueError,
"Detection results have changed"):
structures.SideloadedResults.from_json(as_json, record)
