def test_from_json(self):
res_object = RREFinderResults.from_json(self.json_dict, self.record,
self.min_length,
self.bitscore_cutoff)
assert res_object
assert res_object.hits_per_protocluster == self.hits_per_protocluster
assert res_object.hit_info == self.hit_info
assert res_object.bitscore_cutoff == self.bitscore_cutoff
assert res_object.min_length == self.min_length
assert res_object.record_id == self.record_id
json_dict2 = dict(self.json_dict)
json_dict2['record_id'] = 'another_record'
assert not RREFinderResults.from_json(
json_dict2, self.record, self.min_length, self.bitscore_cutoff)
json_dict3 = dict(self.json_dict)
json_dict3['schema_version'] = 'not_a_valid_schema'
assert not RREFinderResults.from_json(
json_dict3, self.record, self.min_length, self.bitscore_cutoff)
# Invalid arguments should return None
json_dict4 = dict(self.json_dict)
_ = json_dict4.pop('bitscore_cutoff')
with self.assertRaises(ValueError):
_ = RREFinderResults.from_json(json_dict4, self.record,
self.min_length,
self.bitscore_cutoff)
json_dict5 = dict(self.json_dict)
_ = json_dict5.pop('min_length')
with self.assertRaises(ValueError):
_ = RREFinderResults.from_json(json_dict5, self.record,
self.min_length,
self.bitscore_cutoff)
# More lenient settings shouldn't return results
assert not RREFinderResults.from_json(self.json_dict, self.record, 25,
self.bitscore_cutoff)
assert not RREFinderResults.from_json(self.json_dict, self.record,
self.min_length, 15.0)
# Stricter settings should filter
res_object2 = RREFinderResults.from_json(self.json_dict, self.record,
self.min_length, 35.0)
assert res_object2.hit_info['locus_tag_a'] == [self.hit_a1]
assert len(res_object2.hit_info) == 1
assert res_object2.hits_per_protocluster[1] == ['locus_tag_a']
assert len(res_object2.hits_per_protocluster) == 1
res_object3 = RREFinderResults.from_json(self.json_dict, self.record,
80, self.bitscore_cutoff)
assert res_object3.hits_per_protocluster[2] == ['locus_tag_b']
assert len(res_object3.hits_per_protocluster) == 1
assert res_object3.hit_info['locus_tag_b'] == [self.hit_b1]
assert len(res_object3.hit_info) == 1
def test_json_conversion(self):
results = self.create_results()
json = jsonlib.loads(jsonlib.dumps(results.to_json()))
regenerated = RREFinderResults.from_json(json, self.record)
assert regenerated.hits_by_protocluster == results.hits_by_protocluster
assert regenerated.hits_by_cds == results.hits_by_cds
assert regenerated.bitscore_cutoff == results.bitscore_cutoff
assert regenerated.min_length == results.min_length
assert regenerated.record_id == results.record_id
def test_from_json_higher_bitscore(self):
json = self.create_results().to_json()
assert get_config().rre_cutoff == 25.
new = 35.
assert self.hits[0].score > new
assert self.hits[1].score < new
update_config({"rre_cutoff": new})
result = RREFinderResults.from_json(json, self.record)
assert len(result.hits_by_cds) == 1
assert result.hits_by_cds[self.hits[0].locus_tag] == [self.hits[0]]
assert len(result.hits_by_protocluster) == 1
assert result.hits_by_protocluster[1] == [self.hits[0].locus_tag]
def test_from_json_higher_min_length(self):
json = self.create_results().to_json()
assert get_config().rre_min_length == 50
new = 80
assert len(self.hits[0]) < new
assert len(self.hits[1]) > new
update_config({"rre_min_length": new})
results = RREFinderResults.from_json(json, self.record)
assert len(results.hits_by_cds) == 1
assert results.hits_by_cds[self.hits[1].locus_tag] == [self.hits[1]]
assert len(results.hits_by_protocluster) == 1
assert results.hits_by_protocluster[2] == [self.hits[1].locus_tag]
def test_from_json_lower_bitscore(self):
json = self.create_results().to_json()
assert get_config().rre_cutoff == 25.
update_config({"rre_cutoff": 15.})
assert not RREFinderResults.from_json(json, self.record)
def test_from_json_lower_min_length(self):
json = self.create_results().to_json()
assert get_config().rre_min_length == 50
update_config({"rre_min_length": 25})
assert not RREFinderResults.from_json(json, self.record)
def test_from_json_wrong_schema_version(self):
json = self.create_results().to_json()
json['schema_version'] = 'not_a_valid_schema'
assert not RREFinderResults.from_json(json, self.record)
def test_from_json_wrong_record(self):
json = self.create_results().to_json()
json['record_id'] = 'another_record'
assert not RREFinderResults.from_json(json, self.record)