115 lines
5.6 KiB
Python
115 lines
5.6 KiB
Python
from Bio import SeqIO
|
|
from automlst.engine.data.mlst import Allele, MLSTProfile
|
|
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:
|
|
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:
|
|
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)
|
|
|
|
assert len(targets_left) == 0
|
|
|
|
async def test_institutpasteur_profiling_results_in_correct_mlst_st():
|
|
async def dummy_allele_generator():
|
|
dummy_alleles = [
|
|
Allele("adk", "1"),
|
|
Allele("fumC", "1"),
|
|
Allele("glyA", "1"),
|
|
Allele("tyrB", "1"),
|
|
Allele("icd", "1"),
|
|
Allele("pepA", "1"),
|
|
Allele("pgm", "1"),
|
|
]
|
|
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:
|
|
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)
|
|
assert mlst_st_data.clonal_complex == "ST-2 complex"
|
|
assert mlst_st_data.sequence_type == "1"
|
|
|
|
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:
|
|
profile = await dummy_profiler.profile_string(sequence)
|
|
assert profile is not None
|
|
assert isinstance(profile, MLSTProfile)
|
|
assert profile.clonal_complex == "ST-2 complex"
|
|
assert profile.sequence_type == "1"
|
|
|
|
|
|
async def test_pubmlst_profiling_results_in_exact_matches_when_exact():
|
|
dummy_alleles = {
|
|
Allele("adk", "1"),
|
|
Allele("atpG", "1"),
|
|
Allele("frdB", "1"),
|
|
Allele("fucK", "1"),
|
|
Allele("mdh", "1"),
|
|
Allele("pgi", "1"),
|
|
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:
|
|
exact_matches = dummy_profiler.fetch_mlst_allele_variants(sequence_string=sequence)
|
|
async for exact_match in exact_matches:
|
|
assert isinstance(exact_match, Allele)
|
|
dummy_alleles.remove(exact_match)
|
|
|
|
assert len(dummy_alleles) == 0
|
|
|
|
async def test_pubmlst_profiling_results_in_correct_st():
|
|
async def generate_dummy_targets():
|
|
dummy_alleles = [
|
|
Allele("adk", "1"),
|
|
Allele("atpG", "1"),
|
|
Allele("frdB", "1"),
|
|
Allele("fucK", "1"),
|
|
Allele("mdh", "1"),
|
|
Allele("pgi", "1"),
|
|
Allele("recA", "5"),
|
|
]
|
|
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:
|
|
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)
|
|
assert mlst_st_data.clonal_complex == "ST-3 complex"
|
|
assert mlst_st_data.sequence_type == "3"
|
|
|
|
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:
|
|
profile = await dummy_profiler.profile_string(sequence)
|
|
assert profile is not None
|
|
assert isinstance(profile, MLSTProfile)
|
|
assert profile.clonal_complex == "ST-3 complex"
|
|
assert profile.sequence_type == "3"
|
|
|
|
async def test_bigsdb_index_all_databases_is_not_empty():
|
|
async with BIGSdbIndex() as bigsdb_index:
|
|
assert len(await bigsdb_index.get_known_seqdef_dbs()) > 0
|
|
|
|
async def test_bigsdb_index_references_pubmlst_correctly():
|
|
async with BIGSdbIndex() as bigsdb_index:
|
|
assert (await bigsdb_index.get_bigsdb_api_from_seqdefdb("pubmlst_hinfluenzae_seqdef")) == "https://rest.pubmlst.org"
|
|
|
|
async def test_bigsdb_index_references_institutpasteur_correctly():
|
|
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_instantiates_correct_profiler():
|
|
sequence = str(SeqIO.read("tests/resources/tohama_I_bpertussis.fasta", "fasta").seq)
|
|
async with BIGSdbIndex() as bigsdb_index:
|
|
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" |