def from_json(json: Dict[str, Any],
record: Record) -> Optional["CassisResults"]:
# throw away the results if the conditions are different
if json["record_id"] != record.id:
logging.debug(
"Record identifiers don't match, discarding previous results")
return None
if json["max_percentage"] != MAX_PERCENTAGE:
logging.debug(
"CASSIS commonality threshold changed, discarding previous results"
)
return None
if json["max_gap_length"] != MAX_GAP_LENGTH:
logging.debug(
"CASSIS maximum island length changed, discarding previous results"
)
return None
subregions = []
promoters = [] # type: List[Promoter]
for cluster in json["subregions"]:
subregions.append(
SubRegion.from_biopython(feature_from_json(cluster)))
for promoter in json["promoters"]:
if promoter["type"] == "CombinedPromoter":
promoters.append(CombinedPromoter.from_json(promoter))
else:
promoters.append(Promoter.from_json(promoter))
results = CassisResults(record.id)
results.subregions = subregions
results.promoters = promoters
return results
def from_json(json: Dict[str, Any], record: Record) -> "RuleDetectionResults":
""" Constructs a RuleDetectionResults instance from a JSON representation """
cds_by_cluster = {}
for json_cluster, json_cds_results in json["cds_by_cluster"]:
cluster = Cluster.from_biopython(serialiser.feature_from_json(json_cluster))
cds_results = [CDSResults.from_json(result_json, record) for result_json in json_cds_results]
cds_by_cluster[cluster] = cds_results
return RuleDetectionResults(cds_by_cluster, json["tool"])
def from_json(json: Dict[str, Any], record: Record) -> Optional["RuleDetectionResults"]:
""" Constructs a RuleDetectionResults instance from a JSON representation """
if RuleDetectionResults.schema_version != json.get("schema_version", 1):
return None
cds_by_cluster = {}
for json_cluster, json_cds_results in json["cds_by_protocluster"]:
cluster = Protocluster.from_biopython(serialiser.feature_from_json(json_cluster))
cds_results = [CDSResults.from_json(result_json, record) for result_json in json_cds_results]
cds_by_cluster[cluster] = cds_results
cdses_outside = [CDSResults.from_json(chunk, record) for chunk in json["outside_protoclusters"]]
return RuleDetectionResults(cds_by_cluster, json["tool"], cdses_outside)
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)