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Merge branch 'features/improved-oop-architecture' into features/non-exact-notation

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Harrison Deng
2025-02-12 17:02:22 +00:00
parent fbfd993269 09a693b696
commit 36bca1b70d
4 changed files with 7 additions and 145 deletions
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42
tests/autobigs/engine/analysis/test_aligners.py
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@@ -1,42 +0,0 @@
from Bio import SeqIO
from Bio.Align import PairwiseAligner
from pytest import mark
from pytest import fixture
from autobigs.engine.analysis.aligners import AsyncBiopythonPairwiseAlignmentEngine
from autobigs.engine.structures.alignment import PairwiseAlignment
@fixture
def tohamaI_bpertussis_adk():
return str(SeqIO.read("tests/resources/tohama_I_bpertussis_adk.fasta", format="fasta").seq)
@fixture
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")
aligner.mode = "local"
with AsyncBiopythonPairwiseAlignmentEngine(aligner, request.param) as engine:
yield engine
class TestAsyncPairwiseAlignmentEngine:
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)

14
tests/autobigs/engine/analysis/test_bigsdb.py
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@@ -61,12 +61,12 @@ hinfluenzae_fdaargos_profile = MLSTProfile((
), "3", "ST-3 complex")
hinfluenzae_fdaargos_bad_profile = MLSTProfile((
Allele("adk", "1", None),
Allele("atpG", "1", None),
Allele("frdB", "1", None),
Allele("fucK", "1", None),
Allele("mdh", "1", None),
Allele("pgi", "1", None),
Allele("adk", "3", None),
Allele("atpG", "121", None),
Allele("frdB", "6", None),
Allele("fucK", "5", None),
Allele("mdh", "12", None),
Allele("pgi", "4", None),
Allele("recA", "5", None)
), "3", "ST-3 complex")
@@ -76,7 +76,7 @@ hinfluenzae_fdaargos_fragmented_sequence = tuple(SeqIO.parse("tests/resources/to
@pytest.mark.parametrize("local_db,database_api,database_name,schema_id,seq_path,feature_seqs_path,expected_profile,bad_profile", [
(False, "https://bigsdb.pasteur.fr/api", "pubmlst_bordetella_seqdef", 3, "tohama_I_bpertussis.fasta", "tohama_I_bpertussis_features.fasta", bpertussis_tohamaI_profile, bpertussis_tohamaI_bad_profile),
(False, "https://bigsdb.pasteur.fr/api", "pubmlst_hinfluenzae_seqdef", 1, "fdaargos_1560_hinfluenza.fasta", "fdaargos_1560_hinfluenza_features.fasta", hinfluenzae_fdaargos_profile, hinfluenzae_fdaargos_bad_profile),
(False, "https://rest.pubmlst.org", "pubmlst_hinfluenzae_seqdef", 1, "fdaargos_1560_hinfluenza.fasta", "fdaargos_1560_hinfluenza_features.fasta", hinfluenzae_fdaargos_profile, hinfluenzae_fdaargos_bad_profile),
])
class TestBIGSdbMLSTProfiler:
async def test_profiling_results_in_exact_matches_when_exact(self, local_db, database_api, database_name, schema_id, seq_path: str, feature_seqs_path: str, expected_profile: MLSTProfile, bad_profile: MLSTProfile):