From fe999f1cabdba774c5b89a67d3c42dc1e8f4ec34 Mon Sep 17 00:00:00 2001
From: Harrison Deng <yunyangdeng@outlook.com>
Date: Thu, 6 Feb 2025 18:01:50 +0000
Subject: [PATCH] Added a unit test for multithreaded alignments

---
 src/autobigs/engine/analysis/aligners.py        |  5 ++---
 tests/autobigs/engine/analysis/test_aligners.py | 17 ++++++++++++++++-
 .../fdaargos_1560_hinfluenza_adk.fasta          | 11 +++++++++++
 3 files changed, 29 insertions(+), 4 deletions(-)
 create mode 100644 tests/resources/fdaargos_1560_hinfluenza_adk.fasta

diff --git a/src/autobigs/engine/analysis/aligners.py b/src/autobigs/engine/analysis/aligners.py
index 85b9b9f..8909902 100644
--- a/src/autobigs/engine/analysis/aligners.py
+++ b/src/autobigs/engine/analysis/aligners.py
@@ -7,7 +7,6 @@ from queue import Queue
 
 from autobigs.engine.structures.alignment import AlignmentStats, PairwiseAlignment
 
-
 class AsyncBiopythonPairwiseAlignmentEngine(AbstractContextManager):
     def __enter__(self):
         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]:
         if self._work_complete.empty() and len(self._work_left):
             return None
-        future_now = await asyncio.wrap_future(self._work_complete.get())
-        return future_now
+        completed_alignment = await asyncio.wrap_future(self._work_complete.get())
+        return completed_alignment
 
     def __exit__(self, exc_type, exc_value, traceback):
         self.shutdown()
diff --git a/tests/autobigs/engine/analysis/test_aligners.py b/tests/autobigs/engine/analysis/test_aligners.py
index 159dfa5..6285b98 100644
--- a/tests/autobigs/engine/analysis/test_aligners.py
+++ b/tests/autobigs/engine/analysis/test_aligners.py
@@ -13,6 +13,15 @@ def tohamaI_bpertussis_adk():
 def tohamaI_bpertussis_genome():
     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])
 def dummy_engine(request):
     aligner = PairwiseAligner("blastn")
@@ -21,7 +30,13 @@ def dummy_engine(request):
         yield engine
 
 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)
+        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:
             assert isinstance(alignment, PairwiseAlignment)
\ No newline at end of file
diff --git a/tests/resources/fdaargos_1560_hinfluenza_adk.fasta b/tests/resources/fdaargos_1560_hinfluenza_adk.fasta
new file mode 100644
index 0000000..49f92bc
--- /dev/null
+++ b/tests/resources/fdaargos_1560_hinfluenza_adk.fasta
@@ -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
\ No newline at end of file