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Updated iteration on asynchronous aligner

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This commit is contained in:
Harrison Deng 2025-02-05 17:17:37 +00:00
parent ff8a1aff08
commit fb99526162
2 changed files with 13 additions and 12 deletions
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23
src/autobigs/engine/analysis/aligners.py
View File

@ -10,7 +10,7 @@ from autobigs.engine.structures.alignment import AlignmentStats, PairwiseAlignme
class AsyncPairwiseAlignmentEngine(AbstractContextManager):
def __enter__(self):
self._thread_pool = ThreadPoolExecutor(self._max_threads)
self._thread_pool = ThreadPoolExecutor(self._max_threads, thread_name_prefix="async-pairwise-alignment")
return self
def __init__(self, aligner: PairwiseAligner, max_threads: int = 4):
@ -29,19 +29,20 @@ class AsyncPairwiseAlignmentEngine(AbstractContextManager):
self._work_complete.put(future)
def work(self, reference, query, **associated_data):
alignment_results = sorted(self._aligner.align(reference, query))[0]
top_alignment_stats = alignment_results.counts()
alignments = self._aligner.align(reference, query)
top_alignment = sorted(alignments)[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
top_alignment_score = alignment_results.score # type: ignore
top_alignment_score = top_alignment.score # type: ignore
return PairwiseAlignment(
alignment_results.sequences[0],
alignment_results.sequences[1],
alignment_results.indices[0],
alignment_results.indices[1],
top_alignment.sequences[0],
top_alignment.sequences[1],
top_alignment.indices[0],
top_alignment.indices[1],
AlignmentStats(
percent_identity=top_alignment_identities/alignment_results.length,
percent_identity=top_alignment_identities/top_alignment.length,
mismatches=top_alignment_mismatches,
gaps=top_alignment_gaps,
score=top_alignment_score
@ -50,8 +51,8 @@ class AsyncPairwiseAlignmentEngine(AbstractContextManager):
async def next_completed(self) -> Union[tuple[PairwiseAlignment, dict[str, Any]], None]:
if self._work_complete.empty() and len(self._work_left):
return None
future_now: Future = await asyncio.wrap_future(self._work_complete.get())
completed: tuple[PairwiseAlignment, dict[str, Any]] = (future_now).result()
future_now = await asyncio.wrap_future(self._work_complete.get())
completed: tuple[PairwiseAlignment, dict[str, Any]] = future_now
self._work_left.remove(future_now)
return completed

2
src/autobigs/engine/analysis/bigsdb.py
View File

@ -209,7 +209,7 @@ class LocalBIGSdbMLSTProfiler(BIGSdbMLSTProfiler):
async def determine_mlst_allele_variants(self, query_sequence_strings: Iterable[str]) -> AsyncGenerator[Allele, Any]:
aligner = PairwiseAligner("blastn")
aligner.mode = "local"
with AsyncPairwiseAlignmentEngine(aligner) as aligner_engine:
with AsyncPairwiseAlignmentEngine(aligner, max_threads=2) 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)):