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Began implementing LazyPersistentCachedBIGSdbMLSTProfiler

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Harrison Deng
2025-01-27 22:03:49 +00:00
parent ba1f0aa318
commit 3e3898334f
5 changed files with 230 additions and 86 deletions
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55
tests/autobigs/engine/data/remote/databases/test_bigsdb.py
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@@ -6,7 +6,7 @@ import pytest
from autobigs.engine.data.structures.genomics import NamedString
from autobigs.engine.data.structures.mlst import Allele, MLSTProfile
from autobigs.engine.exceptions.database import NoBIGSdbExactMatchesException, NoBIGSdbMatchesException
from autobigs.engine.data.remote.databases.bigsdb import BIGSdbIndex, BIGSdbMLSTProfiler
from autobigs.engine.data.remote.databases.bigsdb import BIGSdbIndex, OnlineBIGSdbMLSTProfiler
def gene_scrambler(gene: str, mutation_site_count: Union[int, float], alphabet: Sequence[str] = ["A", "T", "C", "G"]):
rand = random.Random(gene)
@@ -20,19 +20,19 @@ def gene_scrambler(gene: str, mutation_site_count: Union[int, float], alphabet:
async def test_institutpasteur_profiling_results_in_exact_matches_when_exact():
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:
async with OnlineBIGSdbMLSTProfiler(database_api="https://bigsdb.pasteur.fr/api", database_name="pubmlst_bordetella_seqdef", schema_id=3) as dummy_profiler:
targets_left = {"adk", "fumC", "glyA", "tyrB", "icd", "pepA", "pgm"}
async for exact_match in dummy_profiler.fetch_mlst_allele_variants(sequence_string=sequence, exact=True):
async for exact_match in dummy_profiler.fetch_mlst_allele_variants(sequence_strings=[sequence]):
assert isinstance(exact_match, Allele)
assert exact_match.allele_variant == '1' # All of Tohama I has allele id I
targets_left.remove(exact_match.allele_loci)
targets_left.remove(exact_match.allele_locus)
assert len(targets_left) == 0
async def test_institutpasteur_sequence_profiling_non_exact_returns_non_exact():
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:
async with OnlineBIGSdbMLSTProfiler(database_api="https://bigsdb.pasteur.fr/api", database_name="pubmlst_bordetella_seqdef", schema_id=3) as profiler:
for sequence in sequences:
match = re.fullmatch(r".*\[gene=([\w\d]+)\].*", sequence.description)
if match is None:
@@ -41,7 +41,7 @@ async def test_institutpasteur_sequence_profiling_non_exact_returns_non_exact():
if gene.lower() not in mlst_targets:
continue
scrambled = gene_scrambler(str(sequence.seq), 0.125)
async for partial_match in profiler.fetch_mlst_allele_variants(scrambled, False):
async for partial_match in profiler.fetch_mlst_allele_variants(scrambled):
assert partial_match.partial_match_profile is not None
mlst_targets.remove(gene.lower())
@@ -60,7 +60,7 @@ async def test_institutpasteur_profiling_results_in_correct_mlst_st():
]
for dummy_allele in dummy_alleles:
yield dummy_allele
async with BIGSdbMLSTProfiler(database_api="https://bigsdb.pasteur.fr/api", database_name="pubmlst_bordetella_seqdef", schema_id=3) as dummy_profiler:
async with OnlineBIGSdbMLSTProfiler(database_api="https://bigsdb.pasteur.fr/api", database_name="pubmlst_bordetella_seqdef", schema_id=3) as dummy_profiler:
mlst_st_data = await dummy_profiler.fetch_mlst_st(dummy_allele_generator())
assert mlst_st_data is not None
assert isinstance(mlst_st_data, MLSTProfile)
@@ -77,7 +77,7 @@ async def test_institutpasteur_profiling_non_exact_results_in_list_of_mlsts():
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:
async with OnlineBIGSdbMLSTProfiler(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"
@@ -85,7 +85,7 @@ async def test_institutpasteur_profiling_non_exact_results_in_list_of_mlsts():
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:
async with OnlineBIGSdbMLSTProfiler(database_api="https://bigsdb.pasteur.fr/api", database_name="pubmlst_bordetella_seqdef", schema_id=3) as dummy_profiler:
profile = await dummy_profiler.profile_string(sequence)
assert profile is not None
assert isinstance(profile, MLSTProfile)
@@ -104,8 +104,8 @@ async def test_pubmlst_profiling_results_in_exact_matches_when_exact():
Allele("recA", "5", None),
}
sequence = str(SeqIO.read("tests/resources/FDAARGOS_1560.fasta", "fasta").seq)
async with BIGSdbMLSTProfiler(database_api="https://rest.pubmlst.org/", database_name="pubmlst_hinfluenzae_seqdef", schema_id=1) as dummy_profiler:
exact_matches = dummy_profiler.fetch_mlst_allele_variants(sequence_string=sequence, exact=True)
async with OnlineBIGSdbMLSTProfiler(database_api="https://rest.pubmlst.org/", database_name="pubmlst_hinfluenzae_seqdef", schema_id=1) as dummy_profiler:
exact_matches = dummy_profiler.fetch_mlst_allele_variants(sequence_strings=sequence)
async for exact_match in exact_matches:
assert isinstance(exact_match, Allele)
dummy_alleles.remove(exact_match)
@@ -125,7 +125,7 @@ async def test_pubmlst_profiling_results_in_correct_st():
]
for dummy_allele in dummy_alleles:
yield dummy_allele
async with BIGSdbMLSTProfiler(database_api="https://rest.pubmlst.org/", database_name="pubmlst_hinfluenzae_seqdef", schema_id=1) as dummy_profiler:
async with OnlineBIGSdbMLSTProfiler(database_api="https://rest.pubmlst.org/", database_name="pubmlst_hinfluenzae_seqdef", schema_id=1) as dummy_profiler:
mlst_st_data = await dummy_profiler.fetch_mlst_st(generate_dummy_targets())
assert mlst_st_data is not None
assert isinstance(mlst_st_data, MLSTProfile)
@@ -134,7 +134,7 @@ async def test_pubmlst_profiling_results_in_correct_st():
async def test_pubmlst_sequence_profiling_is_correct():
sequence = str(SeqIO.read("tests/resources/FDAARGOS_1560.fasta", "fasta").seq)
async with BIGSdbMLSTProfiler(database_api="https://rest.pubmlst.org/", database_name="pubmlst_hinfluenzae_seqdef", schema_id=1) as dummy_profiler:
async with OnlineBIGSdbMLSTProfiler(database_api="https://rest.pubmlst.org/", database_name="pubmlst_hinfluenzae_seqdef", schema_id=1) as dummy_profiler:
profile = await dummy_profiler.profile_string(sequence)
assert profile is not None
assert isinstance(profile, MLSTProfile)
@@ -167,9 +167,10 @@ async def test_bigsdb_profile_multiple_strings_same_string_twice():
dummy_sequences = [NamedString("seq1", sequence), NamedString("seq2", sequence)]
async def generate_async_iterable_sequences():
for dummy_sequence in dummy_sequences:
yield dummy_sequence
async with BIGSdbMLSTProfiler(database_api="https://bigsdb.pasteur.fr/api", database_name="pubmlst_bordetella_seqdef", schema_id=3) as dummy_profiler:
async for name, profile in dummy_profiler.profile_multiple_strings(generate_async_iterable_sequences()):
yield [dummy_sequence]
async with OnlineBIGSdbMLSTProfiler(database_api="https://bigsdb.pasteur.fr/api", database_name="pubmlst_bordetella_seqdef", schema_id=3) as dummy_profiler:
async for named_profile in dummy_profiler.profile_multiple_strings(generate_async_iterable_sequences()):
name, profile = named_profile.name, named_profile.mlst_profile
assert profile is not None
assert isinstance(profile, MLSTProfile)
assert profile.clonal_complex == "ST-2 complex"
@@ -180,9 +181,11 @@ async def test_bigsdb_profile_multiple_strings_exactmatch_fail_second_no_stop():
dummy_sequences = [NamedString("seq1", valid_seq), NamedString("should_fail", gene_scrambler(valid_seq, 0.3)), NamedString("seq3", valid_seq)]
async def generate_async_iterable_sequences():
for dummy_sequence in dummy_sequences:
yield dummy_sequence
async with BIGSdbMLSTProfiler(database_api="https://bigsdb.pasteur.fr/api", database_name="pubmlst_bordetella_seqdef", schema_id=3) as dummy_profiler:
async for name, profile in dummy_profiler.profile_multiple_strings(generate_async_iterable_sequences(), True):
yield [dummy_sequence]
async with OnlineBIGSdbMLSTProfiler(database_api="https://bigsdb.pasteur.fr/api", database_name="pubmlst_bordetella_seqdef", schema_id=3) as dummy_profiler:
async for name_profile in dummy_profiler.profile_multiple_strings(generate_async_iterable_sequences(), True):
name, profile = name_profile.name, name_profile.mlst_profile
if name == "should_fail":
assert profile is None
else:
@@ -196,9 +199,10 @@ async def test_bigsdb_profile_multiple_strings_nonexact_second_no_stop():
dummy_sequences = [NamedString("seq1", valid_seq), NamedString("should_fail", gene_scrambler(valid_seq, 0.3)), NamedString("seq3", valid_seq)]
async def generate_async_iterable_sequences():
for dummy_sequence in dummy_sequences:
yield dummy_sequence
async with BIGSdbMLSTProfiler(database_api="https://bigsdb.pasteur.fr/api", database_name="pubmlst_bordetella_seqdef", schema_id=3) as dummy_profiler:
async for name, profile in dummy_profiler.profile_multiple_strings(generate_async_iterable_sequences(), False):
yield [dummy_sequence]
async with OnlineBIGSdbMLSTProfiler(database_api="https://bigsdb.pasteur.fr/api", database_name="pubmlst_bordetella_seqdef", schema_id=3) as dummy_profiler:
async for named_profile in dummy_profiler.profile_multiple_strings(generate_async_iterable_sequences(), False):
name, profile = named_profile.name, named_profile.mlst_profile
if name == "should_fail":
assert profile is not None
assert profile.clonal_complex == "unknown"
@@ -216,10 +220,11 @@ async def test_bigsdb_profile_multiple_strings_fail_second_stop():
dummy_sequences = [NamedString("seq1", valid_seq), NamedString("should_fail", invalid_seq), NamedString("seq3", valid_seq)]
async def generate_async_iterable_sequences():
for dummy_sequence in dummy_sequences:
yield dummy_sequence
async with BIGSdbMLSTProfiler(database_api="https://bigsdb.pasteur.fr/api", database_name="pubmlst_bordetella_seqdef", schema_id=3) as dummy_profiler:
yield [dummy_sequence]
async with OnlineBIGSdbMLSTProfiler(database_api="https://bigsdb.pasteur.fr/api", database_name="pubmlst_bordetella_seqdef", schema_id=3) as dummy_profiler:
with pytest.raises(NoBIGSdbMatchesException):
async for name, profile in dummy_profiler.profile_multiple_strings(generate_async_iterable_sequences(), exact=True, stop_on_fail=True):
async for named_profile in dummy_profiler.profile_multiple_strings(generate_async_iterable_sequences(), stop_on_fail=True):
name, profile = named_profile.name, named_profile.mlst_profile
if name == "should_fail":
pytest.fail("Exception should have been thrown, no exception was thrown.")
else: