ydeng/autoBIGS.engine
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Added specific tests for BIGSdbIndex

Browse Source
This commit is contained in:
Harrison Deng 2025-01-09 16:23:42 +00:00
parent 022200f197
commit d4f890a150
1 changed files with 37 additions and 8 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

45
tests/automlst/engine/remote/databases/test_bigsdb.py
View File

@ -1,11 +1,12 @@
from Bio import SeqIO
from automlst.engine.data.genomics import NamedString
from automlst.engine.data.mlst import Allele, MLSTProfile
from automlst.engine.remote.databases.bigsdb import BIGSdbIndex, BigSDBMLSTProfiler
from automlst.engine.remote.databases.bigsdb import BIGSdbIndex, BIGSdbMLSTProfiler
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 BIGSdbMLSTProfiler(database_api="https://bigsdb.pasteur.fr/api", database_name="pubmlst_bordetella_seqdef", schema_id=3) as dummy_profiler:
exact_matches = dummy_profiler.fetch_mlst_allele_variants(sequence_string=sequence)
targets_left = {"adk", "fumC", "glyA", "tyrB", "icd", "pepA", "pgm"}
async for exact_match in exact_matches:
@ -28,7 +29,7 @@ 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 BIGSdbMLSTProfiler(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)
@ -37,7 +38,7 @@ async def test_institutpasteur_profiling_results_in_correct_mlst_st():
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 BIGSdbMLSTProfiler(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)
@ -56,7 +57,7 @@ async def test_pubmlst_profiling_results_in_exact_matches_when_exact():
Allele("recA", "5"),
}
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 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)
async for exact_match in exact_matches:
assert isinstance(exact_match, Allele)
@ -77,7 +78,7 @@ 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 BIGSdbMLSTProfiler(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)
@ -86,7 +87,7 @@ 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 BIGSdbMLSTProfiler(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)
@ -112,4 +113,32 @@ async def test_bigsdb_index_instantiates_correct_profiler():
async with await bigsdb_index.build_profiler_from_seqdefdb("pubmlst_bordetella_seqdef", 3) as profiler:
profile = await profiler.profile_string(sequence)
assert profile.clonal_complex == "ST-2 complex"
assert profile.sequence_type == "1"
assert profile.sequence_type == "1"
async def test_bigsdb_profile_multiple_strings_same_string_twice():
sequence = str(SeqIO.read("tests/resources/tohama_I_bpertussis.fasta", "fasta").seq)
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()):
assert profile is not None
assert isinstance(profile, MLSTProfile)
assert profile.clonal_complex == "ST-2 complex"
assert profile.sequence_type == "1"
async def test_bigsdb_index_get_schemas_for_bordetella():
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)
async def test_bigsdb_index_get_databases_has_only_seqdef():
async with BIGSdbIndex() as index:
databases = await index.get_known_seqdef_dbs()
assert len(databases.keys()) > 0
for database_name in databases.keys():
assert database_name.endswith("seqdef")
assert databases["pubmlst_bordetella_seqdef"] == "https://bigsdb.pasteur.fr/api"