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Finished adding partial allele matching

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Harrison Deng
2025-01-10 15:25:31 +00:00
parent 03fbbe542e
commit 0c0a2c9d4c
2 changed files with 30 additions and 14 deletions
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21
src/automlst/engine/remote/databases/bigsdb.py
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@@ -59,28 +59,29 @@ class BIGSdbMLSTProfiler(AbstractAsyncContextManager):
async def fetch_mlst_st(self, alleles: AsyncIterable[Allele]) -> MLSTProfile:
async def fetch_mlst_st(self, alleles: Union[AsyncIterable[Allele], Iterable[Allele]]) -> MLSTProfile:
uri_path = "designations"
allele_request_dict: dict[str, list[dict[str, str]]] = defaultdict(list)
async for allele in alleles:
allele_request_dict[allele.allele_loci].append({"allele": str(allele.allele_variant)})
if isinstance(alleles, AsyncIterable):
async for allele in alleles:
allele_request_dict[allele.allele_loci].append({"allele": str(allele.allele_variant)})
else:
for allele in alleles:
allele_request_dict[allele.allele_loci].append({"allele": str(allele.allele_variant)})
request_json = {
"designations": allele_request_dict
}
async with self._http_client.post(uri_path, json=request_json) as response:
response_json: dict = await response.json()
if "exact_matches" not in response_json:
raise NoBIGSdbExactMatchesException(self._database_name, self._schema_id)
schema_exact_matches: dict = response_json["exact_matches"]
response_json.setdefault("fields", dict)
allele_map: dict[str, list[Allele]] = defaultdict(list)
response_json.setdefault("fields", dict())
schema_fields_returned: dict[str, str] = response_json["fields"]
schema_fields_returned.setdefault("ST", "unknown")
schema_fields_returned.setdefault("clonal_complex", "unknown")
allele_map: dict[str, list[Allele]] = defaultdict(list)
schema_exact_matches: dict = response_json["exact_matches"]
for exact_match_loci, exact_match_alleles in schema_exact_matches.items():
for exact_match_allele in exact_match_alleles:
allele_map[exact_match_loci].append(Allele(exact_match_loci, exact_match_allele["allele_id"]))
allele_map[exact_match_loci].append(Allele(exact_match_loci, exact_match_allele["allele_id"], None))
return MLSTProfile(allele_map, schema_fields_returned["ST"], schema_fields_returned["clonal_complex"])
async def profile_string(self, string: str, exact: bool = False) -> MLSTProfile: