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Finished adding partial allele matching

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This commit is contained in:
Harrison Deng
2025-01-10 15:25:31 +00:00
parent 03fbbe542e
commit 0c0a2c9d4c
2 changed files with 30 additions and 14 deletions
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23
tests/automlst/engine/remote/databases/test_bigsdb.py
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@@ -30,7 +30,7 @@ async def test_institutpasteur_profiling_results_in_exact_matches_when_exact():
assert len(targets_left) == 0
async def test_institutpasteur_sequence_profiling_non_exact_returns_non_exact():
sequences = SeqIO.parse("tests/resources/tohama_I_bpertussis_coding.fasta", "fasta")
sequences = list(SeqIO.parse("tests/resources/tohama_I_bpertussis_coding.fasta", "fasta"))
mlst_targets = {"adk", "fumc", "glya", "tyrb", "icd", "pepa", "pgm"}
async with BIGSdbMLSTProfiler(database_api="https://bigsdb.pasteur.fr/api", database_name="pubmlst_bordetella_seqdef", schema_id=3) as profiler:
for sequence in sequences:
@@ -40,13 +40,12 @@ async def test_institutpasteur_sequence_profiling_non_exact_returns_non_exact():
gene = match.group(1)
if gene.lower() not in mlst_targets:
continue
scrambled = gene_scrambler(str(sequence.seq), 0.2)
scrambled = gene_scrambler(str(sequence.seq), 0.125)
async for partial_match in profiler.fetch_mlst_allele_variants(scrambled, False):
assert partial_match.partial_match_profile is not None
assert partial_match.allele_variant == '1'
mlst_targets.remove(gene.lower())
assert len(mlst_targets) == 0
assert len(mlst_targets) == 0
async def test_institutpasteur_profiling_results_in_correct_mlst_st():
async def dummy_allele_generator():
@@ -68,6 +67,22 @@ async def test_institutpasteur_profiling_results_in_correct_mlst_st():
assert mlst_st_data.clonal_complex == "ST-2 complex"
assert mlst_st_data.sequence_type == "1"
async def test_institutpasteur_profiling_non_exact_results_in_list_of_mlsts():
dummy_alleles = [
Allele("adk", "1", None),
Allele("fumC", "2", None),
Allele("glyA", "36", None),
Allele("tyrB", "4", None),
Allele("icd", "4", None),
Allele("pepA", "1", None),
Allele("pgm", "5", None),
]
async with BIGSdbMLSTProfiler(database_api="https://bigsdb.pasteur.fr/api", database_name="pubmlst_bordetella_seqdef", schema_id=3) as dummy_profiler:
mlst_profile = await dummy_profiler.fetch_mlst_st(dummy_alleles)
assert mlst_profile.clonal_complex == "unknown"
assert mlst_profile.sequence_type == "unknown"
async def test_institutpasteur_sequence_profiling_is_correct():
sequence = str(SeqIO.read("tests/resources/tohama_I_bpertussis.fasta", "fasta").seq)
async with BIGSdbMLSTProfiler(database_api="https://bigsdb.pasteur.fr/api", database_name="pubmlst_bordetella_seqdef", schema_id=3) as dummy_profiler: