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Added a unit test for multithreaded alignments

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This commit is contained in:
Harrison Deng 2025-02-06 18:01:50 +00:00
parent 85946eb110
commit fe999f1cab
3 changed files with 29 additions and 4 deletions
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5
src/autobigs/engine/analysis/aligners.py
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@ -7,7 +7,6 @@ from queue import Queue
from autobigs.engine.structures.alignment import AlignmentStats, PairwiseAlignment from autobigs.engine.structures.alignment import AlignmentStats, PairwiseAlignment
class AsyncBiopythonPairwiseAlignmentEngine(AbstractContextManager): class AsyncBiopythonPairwiseAlignmentEngine(AbstractContextManager):
def __enter__(self): def __enter__(self):
self._thread_pool = ThreadPoolExecutor(self._max_threads, thread_name_prefix="async-pairwise-alignment") self._thread_pool = ThreadPoolExecutor(self._max_threads, thread_name_prefix="async-pairwise-alignment")
@ -52,8 +51,8 @@ class AsyncBiopythonPairwiseAlignmentEngine(AbstractContextManager):
async def next_completed(self) -> Union[tuple[PairwiseAlignment, dict[str, Any]], None]: async def next_completed(self) -> Union[tuple[PairwiseAlignment, dict[str, Any]], None]:
if self._work_complete.empty() and len(self._work_left): if self._work_complete.empty() and len(self._work_left):
return None return None
future_now = await asyncio.wrap_future(self._work_complete.get()) completed_alignment = await asyncio.wrap_future(self._work_complete.get())
return future_now return completed_alignment
def __exit__(self, exc_type, exc_value, traceback): def __exit__(self, exc_type, exc_value, traceback):
self.shutdown() self.shutdown()

17
tests/autobigs/engine/analysis/test_aligners.py
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@ -13,6 +13,15 @@ def tohamaI_bpertussis_adk():
def tohamaI_bpertussis_genome(): def tohamaI_bpertussis_genome():
return str(SeqIO.read("tests/resources/tohama_I_bpertussis.fasta", format="fasta").seq) return str(SeqIO.read("tests/resources/tohama_I_bpertussis.fasta", format="fasta").seq)
@fixture
def fdaargos_1560_hinfluenza_adk():
return str(SeqIO.read("tests/resources/fdaargos_1560_hinfluenza_adk.fasta", format="fasta").seq)
@fixture
def fdaargos_1560_hinfluenza_genome():
return str(SeqIO.read("tests/resources/fdaargos_1560_hinfluenza.fasta", format="fasta").seq)
@fixture(params=[1, 2]) @fixture(params=[1, 2])
def dummy_engine(request): def dummy_engine(request):
aligner = PairwiseAligner("blastn") aligner = PairwiseAligner("blastn")
@ -21,7 +30,13 @@ def dummy_engine(request):
yield engine yield engine
class TestAsyncPairwiseAlignmentEngine: class TestAsyncPairwiseAlignmentEngine:
async def test_single_alignment_no_errors(self, tohamaI_bpertussis_genome, tohamaI_bpertussis_adk: str, dummy_engine: AsyncBiopythonPairwiseAlignmentEngine): async def test_single_alignment_no_errors_single_alignment(self, tohamaI_bpertussis_genome, tohamaI_bpertussis_adk: str, dummy_engine: AsyncBiopythonPairwiseAlignmentEngine):
dummy_engine.align(tohamaI_bpertussis_genome, tohamaI_bpertussis_adk) dummy_engine.align(tohamaI_bpertussis_genome, tohamaI_bpertussis_adk)
async for alignment, additional_information in dummy_engine:
assert isinstance(alignment, PairwiseAlignment)
async def test_single_alignment_no_errors_multiple(self, tohamaI_bpertussis_genome, tohamaI_bpertussis_adk, fdaargos_1560_hinfluenza_genome, fdaargos_1560_hinfluenza_adk, dummy_engine: AsyncBiopythonPairwiseAlignmentEngine):
dummy_engine.align(tohamaI_bpertussis_genome, tohamaI_bpertussis_adk)
dummy_engine.align(fdaargos_1560_hinfluenza_genome, fdaargos_1560_hinfluenza_adk)
async for alignment, additional_information in dummy_engine: async for alignment, additional_information in dummy_engine:
assert isinstance(alignment, PairwiseAlignment) assert isinstance(alignment, PairwiseAlignment)

11
tests/resources/fdaargos_1560_hinfluenza_adk.fasta Normal file
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@ -0,0 +1,11 @@
>lcl|CP085952.1_gene_371 [gene=adk] [locus_tag=LK401_01855] [location=complement(365128..365772)] [gbkey=Gene]
ATGAAAATTATTCTTTTAGGTGCACCGGGTGCAGGTAAAGGCACTCAAGCACAATTTATTATGAACAAAT
TTGGTATCCCGCAAATTTCAACTGGTGATATGTTCCGTGCTGCAATCAAAGCGGGGACTGAACTTGGCAA
ACAAGCTAAAGCATTAATGGATGAAGGTAAATTAGTGCCAGATGAATTAACCGTTGCCCTTGTAAAAGAT
CGTATTGCTCAAGCTGACTGCACAAATGGTTTCTTGTTAGATGGTTTCCCTCGTACTATTCCACAAGCGG
ATGCACTGAAAGATTCAGGTGTTAAAATTGACTTTGTTTTAGAATTTGATGTGCCAGACGAAGTGATTGT
TGAACGTATGAGTGGCCGTCGCGTACACCAAGCGTCTGGCCGTTCTTACCACATCGTTTATAATCCACCA
AAAGTGGAAGGTAAAGATGATGTAACAGGCGAAGATTTAATTATTCGTGCAGACGATAAACCAGAAACTG
TATTAGATCGTTTAGCCGTATATCATAAACAAACTAGCCCATTAATTGATTATTACCAAGCAGAAGCGAA
AGCGGGGAATACTCAATATTTCCGTTTAGACGGTACACAAAAAGTAGAAGAAGTTAGCCAAGAGTTAGAT
AAAATCTTAGGCTAA