diff --git a/src/autobigs/engine/data/remote/databases/bigsdb.py b/src/autobigs/engine/data/remote/databases/bigsdb.py index f7ba79a..206a9f1 100644 --- a/src/autobigs/engine/data/remote/databases/bigsdb.py +++ b/src/autobigs/engine/data/remote/databases/bigsdb.py @@ -131,116 +131,6 @@ class OnlineBIGSdbMLSTProfiler(BIGSdbMLSTProfiler): async def __aexit__(self, exc_type, exc_value, traceback): await self.close() -class LazyPersistentCachedBIGSdbMLSTProfiler(BIGSdbMLSTProfiler): - def __init__(self, database_api: str, database_name: str, schema_id: int, cache_path: str): - self._database_api = database_api - self._database_name = database_name - self._schema_id = schema_id - self._base_url = f"{database_api}/db/{self._database_name}/schemes/{self._schema_id}/" - self._http_client = ClientSession(self._base_url, timeout=ClientTimeout(10000)) - self._cache_path = cache_path - self._loci: list[str] = [] - self._profiles = {} - - async def load_scheme_locis(self): - self._loci.clear() - async with self._http_client.get("") 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.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[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"/db/{self._database_name}/loci/{locus}/alleles_fasta") as fasta_response: - async for chunk, eof in fasta_response.content.iter_chunks(): # TODO maybe allow chunking to be configurable - 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) - - async def fetch_mlst_allele_variants(self, sequence_strings: Iterable[str]) -> AsyncGenerator[Allele, Any]: - aligner = PairwiseAligner("blastn") - aligner.mode = "local" - for sequence_string in sequence_strings: - for locus in self._loci: - async for fasta_seq in read_fasta(self.get_locus_cache_path(locus)): - allele_variant = fasta_seq.name - alignment_results = aligner.align(sequence_string, fasta_seq.sequence) - top_alignment = sorted(alignment_results)[0] - top_alignment_stats = top_alignment.counts() - top_alignment_gaps = top_alignment_stats.gaps - top_alignment_identities = top_alignment_stats.identities - top_alignment_mismatches = top_alignment_stats.mismatches - if top_alignment_gaps == 0 and top_alignment_mismatches == 0: - yield Allele(locus, allele_variant, None) - else: - yield Allele( - locus, - allele_variant, - PartialAllelicMatchProfile( - percent_identity=top_alignment_identities/top_alignment.length, - mismatches=top_alignment_mismatches, - gaps=top_alignment_gaps - ) - ) - - async def fetch_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[tuple(ordered_profile)] - return MLSTProfile(allele_variants, st, clonal_complex) - - async def profile_string(self, sequence_strings: Iterable[str]) -> MLSTProfile: - alleles = self.fetch_mlst_allele_variants(sequence_strings) - return await self.fetch_mlst_st(alleles) - - async def profile_multiple_strings(self, named_string_groups: AsyncIterable[Iterable[NamedString]], stop_on_fail: bool = False) -> AsyncGenerator[NamedMLSTProfile, Any]: - async for named_strings in 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() - - async def __aexit__(self, exc_type, exc_value, traceback): - await self.close() - class BIGSdbIndex(AbstractAsyncContextManager): KNOWN_BIGSDB_APIS = { "https://bigsdb.pasteur.fr/api",