42 lines
2.0 KiB
Python
42 lines
2.0 KiB
Python
from Bio import SeqIO
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from Bio.Align import PairwiseAligner
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from pytest import mark
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from pytest import fixture
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from autobigs.engine.analysis.aligners import AsyncBiopythonPairwiseAlignmentEngine
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from autobigs.engine.structures.alignment import PairwiseAlignment
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@fixture
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def tohamaI_bpertussis_adk():
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return str(SeqIO.read("tests/resources/tohama_I_bpertussis_adk.fasta", format="fasta").seq)
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@fixture
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def tohamaI_bpertussis_genome():
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return str(SeqIO.read("tests/resources/tohama_I_bpertussis.fasta", format="fasta").seq)
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@fixture
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def fdaargos_1560_hinfluenza_adk():
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return str(SeqIO.read("tests/resources/fdaargos_1560_hinfluenza_adk.fasta", format="fasta").seq)
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@fixture
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def fdaargos_1560_hinfluenza_genome():
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return str(SeqIO.read("tests/resources/fdaargos_1560_hinfluenza.fasta", format="fasta").seq)
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@fixture(params=[1, 2])
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def dummy_engine(request):
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aligner = PairwiseAligner("blastn")
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aligner.mode = "local"
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with AsyncBiopythonPairwiseAlignmentEngine(aligner, request.param) as engine:
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yield engine
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class TestAsyncPairwiseAlignmentEngine:
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async def test_single_alignment_no_errors_single_alignment(self, tohamaI_bpertussis_genome, tohamaI_bpertussis_adk: str, dummy_engine: AsyncBiopythonPairwiseAlignmentEngine):
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dummy_engine.align(tohamaI_bpertussis_genome, tohamaI_bpertussis_adk)
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async for alignment, additional_information in dummy_engine:
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assert isinstance(alignment, PairwiseAlignment)
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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):
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dummy_engine.align(tohamaI_bpertussis_genome, tohamaI_bpertussis_adk)
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dummy_engine.align(fdaargos_1560_hinfluenza_genome, fdaargos_1560_hinfluenza_adk)
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async for alignment, additional_information in dummy_engine:
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assert isinstance(alignment, PairwiseAlignment) |