def test_antismash_comment(self):
rec = DummyRecord()
options = Namespace()
options.start = -1
options.end = -1
options.version = "5.dummy"
bio = rec.to_biopython()
main.add_antismash_comments([(rec, bio)], options)
assert "##antiSMASH-Data-START##" in bio.annotations["comment"]
assert "##antiSMASH-Data-END##" in bio.annotations["comment"]
assert "Version" in bio.annotations["comment"] and options.version in bio.annotations["comment"]
assert "Original ID" not in bio.annotations["comment"]
assert "Starting at" not in bio.annotations["comment"]
assert "Ending at" not in bio.annotations["comment"]
bio.annotations["comment"] = ""
options.start = 7
main.add_antismash_comments([(rec, bio)], options)
assert "Original ID" not in bio.annotations["comment"]
assert "Starting at :: 7\n" in bio.annotations["comment"]
bio.annotations["comment"] = ""
options.start = -1
options.end = 1000
main.add_antismash_comments([(rec, bio)], options)
assert "Original ID" not in bio.annotations["comment"]
assert "Ending at :: 1000\n" in bio.annotations["comment"]
bio.annotations["comment"] = ""
options.end = -1
rec.original_id = "something else"
main.add_antismash_comments([(rec, bio)], options)
assert "Original ID" in bio.annotations["comment"] and "something else" in bio.annotations["comment"]
def test_complex(self):
protos = [
helpers.DummyProtocluster(core_start=3,
core_end=22,
neighbourhood_range=1,
product='a'),
helpers.DummyProtocluster(core_start=33,
core_end=48,
neighbourhood_range=2,
product='b'),
]
candidates = [
helpers.DummyCandidateCluster(clusters=protos[:1]),
helpers.DummyCandidateCluster(
clusters=protos,
kind=helpers.DummyCandidateCluster.kinds.INTERLEAVED)
]
subregion = helpers.DummySubRegion(start=55, end=90)
regions = [
helpers.DummyRegion(candidate_clusters=candidates, subregions=[]),
helpers.DummyRegion(candidate_clusters=[], subregions=[subregion]),
]
record = DummyRecord(record_id="test",
seq="A" * 90,
features=regions + [subregion] + candidates +
protos)
results = serialiser.gather_record_areas(record)
assert results
assert len(results) == 2
res = results[0]
assert res["end"] == protos[1].location.end
assert res["products"] == [p.product for p in protos]
assert res["subregions"] == []
assert len(res["protoclusters"]) == 2
assert list(res["protoclusters"]) == [0, 1]
assert res["protoclusters"][1]["product"] == protos[1].product
assert len(res["candidates"]) == 2
assert res["candidates"][0]["protoclusters"] == [0]
assert res["candidates"][1]["protoclusters"] == [0, 1]
res = results[1]
assert res["start"] == subregion.location.start
assert res["subregions"]
assert res["subregions"][0]["start"] == subregion.location.start
assert res["subregions"][0]["tool"] == subregion.tool
assert res["subregions"][0]["label"] == subregion.label
assert not res["protoclusters"]
# lastly, check all this is properly embedded in the final JSON
bio = record.to_biopython()
full = serialiser.dump_records([bio], [{}], [record])
assert full[0]["areas"] == results
