Added a unit test for multithreaded alignments

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)

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