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Replaced schema with scheme
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Harrison Deng
2025-02-26 04:50:54 +00:00
parent 06dbb56c28
commit 27ae89fde7
6 changed files with 51 additions and 76 deletions
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tests/autobigs/engine/analysis/test_bigsdb.py
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@@ -71,14 +71,14 @@ hinfluenzae_2014_102_bad_profile = MLSTProfile((
), "unknown", "unknown")
@pytest.mark.parametrize("local_db,database_api,database_name,schema_id,seq_path,feature_seqs_path,expected_profile,bad_profile", [
@pytest.mark.parametrize("local_db,database_api,database_name,scheme_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://rest.pubmlst.org", "pubmlst_hinfluenzae_seqdef", 1, "2014-102_hinfluenza.fasta", "2014-102_hinfluenza_features.fasta", hinfluenzae_2014_102_profile, hinfluenzae_2014_102_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):
async def test_profiling_results_in_exact_matches_when_exact(self, local_db, database_api, database_name, scheme_id, seq_path: str, feature_seqs_path: str, expected_profile: MLSTProfile, bad_profile: MLSTProfile):
sequence = get_first_sequence_from_fasta(seq_path)
async with bigsdb.get_BIGSdb_MLST_profiler(local_db, database_api, database_name, schema_id) as dummy_profiler:
async with bigsdb.get_BIGSdb_MLST_profiler(local_db, database_api, database_name, scheme_id) as dummy_profiler:
expected_alleles = mlst.alleles_to_mapping(expected_profile.alleles)
targets_left = set(mlst.alleles_to_mapping(expected_profile.alleles).keys())
async for exact_match in dummy_profiler.determine_mlst_allele_variants(query_sequence_strings=[sequence]):
@@ -89,10 +89,10 @@ class TestBIGSdbMLSTProfiler:
assert len(targets_left) == 0
async def test_sequence_profiling_non_exact_returns_non_exact(self, local_db, database_api, database_name, schema_id, seq_path: str, feature_seqs_path: str, expected_profile: MLSTProfile, bad_profile: MLSTProfile):
async def test_sequence_profiling_non_exact_returns_non_exact(self, local_db, database_api, database_name, scheme_id, seq_path: str, feature_seqs_path: str, expected_profile: MLSTProfile, bad_profile: MLSTProfile):
target_sequences = get_multiple_sequences_from_fasta(feature_seqs_path)
mlst_targets = {x.lower() for x in mlst.alleles_to_mapping(expected_profile.alleles).keys()}
async with bigsdb.get_BIGSdb_MLST_profiler(local_db, database_api, database_name, schema_id) as profiler:
async with bigsdb.get_BIGSdb_MLST_profiler(local_db, database_api, database_name, scheme_id) as profiler:
for target_sequence in target_sequences:
match = re.fullmatch(r".*\[gene=([\w\d]+)\].*", target_sequence.description)
if match is None:
@@ -107,26 +107,26 @@ class TestBIGSdbMLSTProfiler:
assert len(mlst_targets) == 0
async def test_profiling_results_in_correct_mlst_st(self, local_db, database_api, database_name, schema_id, seq_path: str, feature_seqs_path: str, expected_profile: MLSTProfile, bad_profile: MLSTProfile):
async with bigsdb.get_BIGSdb_MLST_profiler(local_db, database_api, database_name, schema_id) as dummy_profiler:
async def test_profiling_results_in_correct_mlst_st(self, local_db, database_api, database_name, scheme_id, seq_path: str, feature_seqs_path: str, expected_profile: MLSTProfile, bad_profile: MLSTProfile):
async with bigsdb.get_BIGSdb_MLST_profiler(local_db, database_api, database_name, scheme_id) as dummy_profiler:
mlst_st_data = await dummy_profiler.determine_mlst_st(expected_profile.alleles)
assert mlst_st_data is not None
assert isinstance(mlst_st_data, MLSTProfile)
assert mlst_st_data.clonal_complex == expected_profile.clonal_complex
assert mlst_st_data.sequence_type == expected_profile.sequence_type
async def test_profiling_non_exact_results_in_list_of_mlsts(self, local_db, database_api, database_name, schema_id, seq_path: str, feature_seqs_path: str, expected_profile: MLSTProfile, bad_profile: MLSTProfile):
async def test_profiling_non_exact_results_in_list_of_mlsts(self, local_db, database_api, database_name, scheme_id, seq_path: str, feature_seqs_path: str, expected_profile: MLSTProfile, bad_profile: MLSTProfile):
dummy_alleles = bad_profile.alleles
async with bigsdb.get_BIGSdb_MLST_profiler(local_db, database_api, database_name, schema_id) as dummy_profiler:
async with bigsdb.get_BIGSdb_MLST_profiler(local_db, database_api, database_name, scheme_id) as dummy_profiler:
mlst_profile = await dummy_profiler.determine_mlst_st(dummy_alleles)
assert mlst_profile.clonal_complex == "unknown"
assert mlst_profile.sequence_type == "unknown"
async def test_bigsdb_profile_multiple_strings_same_string_twice(self, local_db, database_api, database_name, schema_id, seq_path: str, feature_seqs_path: str, expected_profile: MLSTProfile, bad_profile: MLSTProfile):
async def test_bigsdb_profile_multiple_strings_same_string_twice(self, local_db, database_api, database_name, scheme_id, seq_path: str, feature_seqs_path: str, expected_profile: MLSTProfile, bad_profile: MLSTProfile):
sequence = get_first_sequence_from_fasta(seq_path)
dummy_sequences = [[NamedString("seq1", sequence)], [NamedString("seq2", sequence)]]
async with bigsdb.get_BIGSdb_MLST_profiler(local_db, database_api, database_name, schema_id) as dummy_profiler:
async with bigsdb.get_BIGSdb_MLST_profiler(local_db, database_api, database_name, scheme_id) as dummy_profiler:
async for named_profile in dummy_profiler.profile_multiple_strings(generate_async_iterable(dummy_sequences)):
name, profile = named_profile.name, named_profile.mlst_profile
assert profile is not None
@@ -134,10 +134,10 @@ class TestBIGSdbMLSTProfiler:
assert profile.clonal_complex == expected_profile.clonal_complex
assert profile.sequence_type == expected_profile.sequence_type
async def test_bigsdb_profile_multiple_strings_exactmatch_fail_second_no_stop(self, local_db, database_api, database_name, schema_id, seq_path: str, feature_seqs_path: str, expected_profile: MLSTProfile, bad_profile: MLSTProfile):
async def test_bigsdb_profile_multiple_strings_exactmatch_fail_second_no_stop(self, local_db, database_api, database_name, scheme_id, seq_path: str, feature_seqs_path: str, expected_profile: MLSTProfile, bad_profile: MLSTProfile):
valid_seq = get_first_sequence_from_fasta(seq_path)
dummy_sequences = [[NamedString("seq1", valid_seq)], [NamedString("should_fail", gene_scrambler(valid_seq, 0.3))], [NamedString("seq3", valid_seq)]]
async with bigsdb.get_BIGSdb_MLST_profiler(local_db, database_api, database_name, schema_id) as dummy_profiler:
async with bigsdb.get_BIGSdb_MLST_profiler(local_db, database_api, database_name, scheme_id) as dummy_profiler:
async for name_profile in dummy_profiler.profile_multiple_strings(generate_async_iterable(dummy_sequences), True):
name, profile = name_profile.name, name_profile.mlst_profile
@@ -151,11 +151,11 @@ class TestBIGSdbMLSTProfiler:
assert profile.clonal_complex == expected_profile.clonal_complex
assert profile.sequence_type == expected_profile.sequence_type
async def test_bigsdb_profile_multiple_strings_nonexact_second_no_stop(self, local_db, database_api, database_name, schema_id, seq_path: str, feature_seqs_path: str, expected_profile: MLSTProfile, bad_profile: MLSTProfile):
async def test_bigsdb_profile_multiple_strings_nonexact_second_no_stop(self, local_db, database_api, database_name, scheme_id, seq_path: str, feature_seqs_path: str, expected_profile: MLSTProfile, bad_profile: MLSTProfile):
valid_seq = get_first_sequence_from_fasta(seq_path)
dummy_sequences = [[NamedString("seq1", valid_seq)], [NamedString("should_fail", gene_scrambler(valid_seq, 0.3))], [NamedString("seq3", valid_seq)]]
async with bigsdb.get_BIGSdb_MLST_profiler(local_db, database_api, database_name, schema_id) as dummy_profiler:
async with bigsdb.get_BIGSdb_MLST_profiler(local_db, database_api, database_name, scheme_id) as dummy_profiler:
async for named_profile in dummy_profiler.profile_multiple_strings(generate_async_iterable(dummy_sequences), False):
name, profile = named_profile.name, named_profile.mlst_profile
@@ -183,12 +183,12 @@ class TestBIGSdbIndex:
async with BIGSdbIndex() as bigsdb_index:
assert (await bigsdb_index.get_bigsdb_api_from_seqdefdb("pubmlst_bordetella_seqdef")) == "https://bigsdb.pasteur.fr/api"
async def test_bigsdb_index_get_schemas_for_bordetella(self):
async def test_bigsdb_index_get_schemes_for_bordetella(self):
async with BIGSdbIndex() as index:
schemas = await index.get_schemas_for_seqdefdb(seqdef_db_name="pubmlst_bordetella_seqdef")
assert len(schemas.keys()) > 0
assert "MLST" in schemas
assert isinstance(schemas["MLST"], int)
schemes = await index.get_schemes_for_seqdefdb(seqdef_db_name="pubmlst_bordetella_seqdef")
assert len(schemes.keys()) > 0
assert "MLST" in schemes
assert isinstance(schemes["MLST"], int)
async def test_bigsdb_index_get_databases_has_only_seqdef(self):
async with BIGSdbIndex() as index: