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Fixed match metric difference between remote and local

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This commit is contained in:
Harrison Deng 2025-02-06 17:12:31 +00:00
parent a27e09da31
commit 85946eb110
4 changed files with 10 additions and 10 deletions
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4
src/autobigs/engine/analysis/aligners.py
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@ -8,7 +8,7 @@ from queue import Queue
from autobigs.engine.structures.alignment import AlignmentStats, PairwiseAlignment
class AsyncPairwiseAlignmentEngine(AbstractContextManager):
class AsyncBiopythonPairwiseAlignmentEngine(AbstractContextManager):
def __enter__(self):
self._thread_pool = ThreadPoolExecutor(self._max_threads, thread_name_prefix="async-pairwise-alignment")
return self
@ -46,7 +46,7 @@ class AsyncPairwiseAlignmentEngine(AbstractContextManager):
percent_identity=top_alignment_identities/top_alignment.length,
mismatches=top_alignment_mismatches,
gaps=top_alignment_gaps,
score=top_alignment_score
match_metric=top_alignment_score
)), associated_data
async def next_completed(self) -> Union[tuple[PairwiseAlignment, dict[str, Any]], None]:

8
src/autobigs/engine/analysis/bigsdb.py
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@ -11,7 +11,7 @@ from typing import Any, AsyncGenerator, AsyncIterable, Iterable, Mapping, Sequen
from aiohttp import ClientSession, ClientTimeout
from autobigs.engine.analysis.aligners import AsyncPairwiseAlignmentEngine
from autobigs.engine.analysis.aligners import AsyncBiopythonPairwiseAlignmentEngine
from autobigs.engine.reading import read_fasta
from autobigs.engine.structures.alignment import PairwiseAlignment
from autobigs.engine.structures.genomics import NamedString
@ -82,7 +82,7 @@ class RemoteBIGSdbMLSTProfiler(BIGSdbMLSTProfiler):
percent_identity=float(partial_match["identity"]),
mismatches=int(partial_match["mismatches"]),
gaps=int(partial_match["gaps"]),
score=int(partial_match["score"])
match_metric=int(partial_match["bitscore"])
)
yield Allele(
allele_locus=allele_loci,
@ -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, max_threads=2) as aligner_engine:
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)):
@ -235,7 +235,7 @@ class LocalBIGSdbMLSTProfiler(BIGSdbMLSTProfiler):
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.score)[0]
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):

2
src/autobigs/engine/structures/alignment.py
View File

@ -7,7 +7,7 @@ class AlignmentStats:
percent_identity: float
mismatches: int
gaps: int
score: int
match_metric: int
@dataclass(frozen=True)
class PairwiseAlignment:

6
tests/autobigs/engine/analysis/test_aligners.py
View File

@ -2,7 +2,7 @@ from Bio import SeqIO
from Bio.Align import PairwiseAligner
from pytest import mark
from pytest import fixture
from autobigs.engine.analysis.aligners import AsyncPairwiseAlignmentEngine
from autobigs.engine.analysis.aligners import AsyncBiopythonPairwiseAlignmentEngine
from autobigs.engine.structures.alignment import PairwiseAlignment
@fixture
@ -17,11 +17,11 @@ def tohamaI_bpertussis_genome():
def dummy_engine(request):
aligner = PairwiseAligner("blastn")
aligner.mode = "local"
with AsyncPairwiseAlignmentEngine(aligner, request.param) as engine:
with AsyncBiopythonPairwiseAlignmentEngine(aligner, request.param) as engine:
yield engine
class TestAsyncPairwiseAlignmentEngine:
async def test_single_alignment_no_errors(self, tohamaI_bpertussis_genome, tohamaI_bpertussis_adk: str, dummy_engine: AsyncPairwiseAlignmentEngine):
async def test_single_alignment_no_errors(self, tohamaI_bpertussis_genome, tohamaI_bpertussis_adk: str, dummy_engine: AsyncBiopythonPairwiseAlignmentEngine):
dummy_engine.align(tohamaI_bpertussis_genome, tohamaI_bpertussis_adk)
async for alignment, additional_information in dummy_engine:
assert isinstance(alignment, PairwiseAlignment)