def to_json(self) -> Dict[str, Any]:
""" Constructs a JSON representation from the RuleDetectionResults instance """
cds_results_json = [
] # type: List[Tuple[Dict[str, Any], List[Dict[str, Any]]]]
json = {"tool": self.tool, "cds_by_cluster": cds_results_json}
for border, cds_results in self.cds_by_cluster.items():
json_border = serialiser.feature_to_json(border.to_biopython()[0])
json_cds_results = [result.to_json() for result in cds_results]
cds_results_json.append((json_border, json_cds_results))
return json
def to_json(self) -> Dict[str, Any]:
""" Constructs a JSON representation from the RuleDetectionResults instance """
cds_results_json: List[Tuple[Dict[str, Any], List[Dict[str, Any]]]] = []
json = {
"schema_version": self.schema_version,
"tool": self.tool,
"cds_by_protocluster": cds_results_json,
"outside_protoclusters": [result.to_json() for result in self.cdses_outside_clusters],
}
for cluster, cds_results in self.cds_by_cluster.items():
json_cluster = serialiser.feature_to_json(cluster.to_biopython()[0])
json_cds_results = [result.to_json() for result in cds_results]
cds_results_json.append((json_cluster, json_cds_results))
return json
def to_json(self) -> Dict[str, Any]:
subregions = []
promoters = []
for cluster in self.subregions:
subregions.append(feature_to_json(cluster.to_biopython()[0]))
for promoter in self.promoters:
promoters.append(promoter.to_json())
return {
"record_id": self.record_id,
"subregions": subregions,
"promoters": promoters,
"max_percentage": MAX_PERCENTAGE,
"max_gap_length": MAX_GAP_LENGTH
}
def test_simple_feature(self):
location = FeatureLocation(1, 6, strand=1)
f_type = "test type"
qualifiers = {"a": ["1", "2"], "b": ["3", "4"]}
f_id = "dummy id"
# skipping biopython deprecated members: ref, ref_db, strand, location_operator
feature = SeqFeature(location=location,
type=f_type,
qualifiers=qualifiers,
id=f_id)
print(str(feature))
json = serialiser.feature_to_json(feature)
print(json) # for debugging failures
new_feature = serialiser.feature_from_json(json)
print(str(new_feature))
assert new_feature.qualifiers == feature.qualifiers
assert new_feature.id == feature.id
assert new_feature.type == feature.type
assert str(new_feature.location) == str(new_feature.location)
