Moved "LazyPersistentCachedBIGSdbMLSTProfiler" to separate branch and deleted from current branch
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@ -131,116 +131,6 @@ class OnlineBIGSdbMLSTProfiler(BIGSdbMLSTProfiler):
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async def __aexit__(self, exc_type, exc_value, traceback):
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await self.close()
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class LazyPersistentCachedBIGSdbMLSTProfiler(BIGSdbMLSTProfiler):
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def __init__(self, database_api: str, database_name: str, schema_id: int, cache_path: str):
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self._database_api = database_api
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self._database_name = database_name
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self._schema_id = schema_id
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self._base_url = f"{database_api}/db/{self._database_name}/schemes/{self._schema_id}/"
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self._http_client = ClientSession(self._base_url, timeout=ClientTimeout(10000))
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self._cache_path = cache_path
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self._loci: list[str] = []
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self._profiles = {}
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async def load_scheme_locis(self):
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self._loci.clear()
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async with self._http_client.get("") as schema_response:
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schema_json = await schema_response.json()
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for locus in schema_json["loci"]:
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locus_name = path.basename(locus)
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self._loci.append(locus_name)
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self._loci.sort()
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async def load_scheme_profiles(self):
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self._profiles.clear()
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with open(self.get_scheme_profile_path()) as profile_cache_handle:
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reader = csv.DictReader(profile_cache_handle, delimiter="\t")
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for line in reader:
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alleles = []
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for locus in self._loci:
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alleles.append(line[locus])
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self._profiles[tuple(alleles)] = (line["ST"], line["clonal_complex"])
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def get_locus_cache_path(self, locus) -> str:
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return path.join(self._cache_path, locus + "." + "fasta")
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def get_scheme_profile_path(self):
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return path.join(self._cache_path, "profiles.csv")
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async def download_alleles_cache_data(self):
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for locus in self._loci:
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with open(self.get_locus_cache_path(locus), "wb") as fasta_handle:
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async with self._http_client.get(f"/db/{self._database_name}/loci/{locus}/alleles_fasta") as fasta_response:
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async for chunk, eof in fasta_response.content.iter_chunks(): # TODO maybe allow chunking to be configurable
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fasta_handle.write(chunk)
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async def download_scheme_profiles(self):
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with open(self.get_scheme_profile_path(), "wb") as profile_cache_handle:
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async with self._http_client.get("profiles_csv") as profiles_response:
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async for chunk, eof in profiles_response.content.iter_chunks():
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profile_cache_handle.write(chunk)
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async def fetch_mlst_allele_variants(self, sequence_strings: Iterable[str]) -> AsyncGenerator[Allele, Any]:
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aligner = PairwiseAligner("blastn")
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aligner.mode = "local"
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for sequence_string in sequence_strings:
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for locus in self._loci:
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async for fasta_seq in read_fasta(self.get_locus_cache_path(locus)):
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allele_variant = fasta_seq.name
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alignment_results = aligner.align(sequence_string, fasta_seq.sequence)
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top_alignment = sorted(alignment_results)[0]
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top_alignment_stats = top_alignment.counts()
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top_alignment_gaps = top_alignment_stats.gaps
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top_alignment_identities = top_alignment_stats.identities
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top_alignment_mismatches = top_alignment_stats.mismatches
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if top_alignment_gaps == 0 and top_alignment_mismatches == 0:
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yield Allele(locus, allele_variant, None)
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else:
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yield Allele(
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locus,
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allele_variant,
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PartialAllelicMatchProfile(
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percent_identity=top_alignment_identities/top_alignment.length,
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mismatches=top_alignment_mismatches,
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gaps=top_alignment_gaps
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)
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)
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async def fetch_mlst_st(self, alleles):
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allele_variants: dict[str, Allele] = {}
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if isinstance(alleles, AsyncIterable):
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async for allele in alleles:
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allele_variants[allele.allele_locus] = allele
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else:
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for allele in alleles:
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allele_variants[allele.allele_locus] = allele
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ordered_profile = []
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for locus in self._loci:
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ordered_profile.append(allele_variants[locus].allele_variant)
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st, clonal_complex = self._profiles[tuple(ordered_profile)]
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return MLSTProfile(allele_variants, st, clonal_complex)
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async def profile_string(self, sequence_strings: Iterable[str]) -> MLSTProfile:
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alleles = self.fetch_mlst_allele_variants(sequence_strings)
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return await self.fetch_mlst_st(alleles)
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async def profile_multiple_strings(self, named_string_groups: AsyncIterable[Iterable[NamedString]], stop_on_fail: bool = False) -> AsyncGenerator[NamedMLSTProfile, Any]:
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async for named_strings in named_string_groups:
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for named_string in named_strings:
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try:
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yield NamedMLSTProfile(named_string.name, await self.profile_string([named_string.sequence]))
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except NoBIGSdbMatchesException as e:
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if stop_on_fail:
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raise e
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yield NamedMLSTProfile(named_string.name, None)
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async def close(self):
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await self._http_client.close()
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async def __aexit__(self, exc_type, exc_value, traceback):
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await self.close()
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class BIGSdbIndex(AbstractAsyncContextManager):
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KNOWN_BIGSDB_APIS = {
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"https://bigsdb.pasteur.fr/api",
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