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Replaced local profiler with a not implemented exception

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Harrison Deng 2025-02-12 15:52:48 +00:00
parent 897f7ee922
commit 175a51f968
1 changed files with 1 additions and 136 deletions
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137
src/autobigs/engine/analysis/bigsdb.py
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@ -139,141 +139,6 @@ class RemoteBIGSdbMLSTProfiler(BIGSdbMLSTProfiler):
async def __aexit__(self, exc_type, exc_value, traceback): async def __aexit__(self, exc_type, exc_value, traceback):
await self.close() await self.close()
class LocalBIGSdbMLSTProfiler(BIGSdbMLSTProfiler):
async def __aenter__(self):
if self._prepare:
await self.update_scheme_locis()
await asyncio.gather(
self.download_alleles_cache_data(),
self.download_scheme_profiles()
)
await self.load_scheme_profiles()
return self
def __init__(self, database_api: str, database_name: str, schema_id: int, cache_path: Union[str, None] = None, prepare: bool =True):
self._database_api = database_api
self._database_name = database_name
self._schema_id = schema_id
self._base_url = f"{self._database_api}/db/{self._database_name}/schemes/{self._schema_id}/"
self._http_client = ClientSession(self._base_url, timeout=ClientTimeout(60))
if cache_path is None:
self._cache_path = tempfile.mkdtemp("BIGSdb")
self._cleanup_required = True
else:
self._cache_path = cache_path
self._cleanup_required = False
self._loci: list[str] = []
self._profiles_st_map = {}
self._prepare = prepare
async def update_scheme_locis(self):
self._loci.clear()
async with self._http_client.get(f"/api/db/{self._database_name}/schemes/{self._schema_id}") as schema_response:
schema_json = await schema_response.json()
for locus in schema_json["loci"]:
locus_name = path.basename(locus)
self._loci.append(locus_name)
self._loci.sort()
async def load_scheme_profiles(self):
self._profiles_st_map.clear()
with open(self.get_scheme_profile_path()) as profile_cache_handle:
reader = csv.DictReader(profile_cache_handle, delimiter="\t")
for line in reader:
alleles = []
for locus in self._loci:
alleles.append(line[locus])
self._profiles_st_map[tuple(alleles)] = (line["ST"], line["clonal_complex"])
def get_locus_cache_path(self, locus) -> str:
return path.join(self._cache_path, locus + "." + "fasta")
def get_scheme_profile_path(self):
return path.join(self._cache_path, "profiles.csv")
async def download_alleles_cache_data(self):
for locus in self._loci:
with open(self.get_locus_cache_path(locus), "wb") as fasta_handle:
async with self._http_client.get(f"/api/db/{self._database_name}/loci/{locus}/alleles_fasta") as fasta_response:
async for chunk, eof in fasta_response.content.iter_chunks():
fasta_handle.write(chunk)
async def download_scheme_profiles(self):
with open(self.get_scheme_profile_path(), "wb") as profile_cache_handle:
async with self._http_client.get("profiles_csv") as profiles_response:
async for chunk, eof in profiles_response.content.iter_chunks():
profile_cache_handle.write(chunk)
await self.load_scheme_profiles()
async def determine_mlst_allele_variants(self, query_sequence_strings: Iterable[str]) -> AsyncGenerator[Allele, Any]:
aligner = PairwiseAligner("blastn")
aligner.mode = "local"
with AsyncBiopythonPairwiseAlignmentEngine(aligner, max_threads=4) as aligner_engine:
for query_sequence_string in query_sequence_strings:
for locus in self._loci:
async for allele_variant in read_fasta(self.get_locus_cache_path(locus)):
aligner_engine.align(allele_variant.sequence, query_sequence_string, variant_name=allele_variant.name, full=True)
break # start a bunch of full alignments for each variant to select segments
alignment_rankings: dict[str, set[tuple[PairwiseAlignment, str]]] = defaultdict(set)
async for alignment_result, additional_information in aligner_engine:
result_variant_name = additional_information["variant_name"]
result_locus, variant_id = result_variant_name.split("_")
full_alignment = additional_information["full"]
if full_alignment:
if alignment_result.alignment_stats.gaps == 0 and alignment_result.alignment_stats.mismatches == 0:
# I.e., 100% exactly the same
yield Allele(result_locus, variant_id, None)
continue
else:
alignment_rankings[result_locus].add((alignment_result, variant_id))
interest_sequence = full_alignment[alignment_result.query_indices[0]:alignment_result.query_indices[-1]]
async for allele_variant in read_fasta(self.get_locus_cache_path(result_locus)):
if result_variant_name == allele_variant.name:
continue # Skip if we just finished aligning this
aligner_engine.align(allele_variant.sequence, interest_sequence, variant_name=result_variant_name.name, full=False)
else:
alignment_rankings[result_locus].add((alignment_result, variant_id))
for final_locus, alignments in alignment_rankings.items():
closest_alignment, closest_variant_id = sorted(alignments, key=lambda index: index[0].alignment_stats.match_metric)[0]
yield Allele(final_locus, closest_variant_id, closest_alignment.alignment_stats)
async def determine_mlst_st(self, alleles):
allele_variants: dict[str, Allele] = {}
if isinstance(alleles, AsyncIterable):
async for allele in alleles:
allele_variants[allele.allele_locus] = allele
else:
for allele in alleles:
allele_variants[allele.allele_locus] = allele
ordered_profile = []
for locus in self._loci:
ordered_profile.append(allele_variants[locus].allele_variant)
st, clonal_complex = self._profiles_st_map[tuple(ordered_profile)]
return MLSTProfile(set(allele_variants.values()), st, clonal_complex)
async def profile_string(self, query_sequence_strings: Iterable[str]) -> MLSTProfile:
alleles = self.determine_mlst_allele_variants(query_sequence_strings)
return await self.determine_mlst_st(alleles)
async def profile_multiple_strings(self, query_named_string_groups: AsyncIterable[Iterable[NamedString]], stop_on_fail: bool = False) -> AsyncGenerator[NamedMLSTProfile, Any]:
async for named_strings in query_named_string_groups:
for named_string in named_strings:
try:
yield NamedMLSTProfile(named_string.name, await self.profile_string([named_string.sequence]))
except NoBIGSdbMatchesException as e:
if stop_on_fail:
raise e
yield NamedMLSTProfile(named_string.name, None)
async def close(self):
await self._http_client.close()
if self._cleanup_required:
shutil.rmtree(self._cache_path)
async def __aexit__(self, exc_type, exc_value, traceback):
await self.close()
class BIGSdbIndex(AbstractAsyncContextManager): class BIGSdbIndex(AbstractAsyncContextManager):
KNOWN_BIGSDB_APIS = { KNOWN_BIGSDB_APIS = {
"https://bigsdb.pasteur.fr/api", "https://bigsdb.pasteur.fr/api",
@ -334,5 +199,5 @@ class BIGSdbIndex(AbstractAsyncContextManager):
def get_BIGSdb_MLST_profiler(local: bool, database_api: str, database_name: str, schema_id: int): def get_BIGSdb_MLST_profiler(local: bool, database_api: str, database_name: str, schema_id: int):
if local: if local:
return LocalBIGSdbMLSTProfiler(database_api=database_api, database_name=database_name, schema_id=schema_id) raise NotImplementedError()
return RemoteBIGSdbMLSTProfiler(database_api=database_api, database_name=database_name, schema_id=schema_id) return RemoteBIGSdbMLSTProfiler(database_api=database_api, database_name=database_name, schema_id=schema_id)