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Added unit tests for pubMLST MLST profiling

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This commit is contained in:
Harrison Deng
2025-01-08 17:34:30 +00:00
parent 424beeb559
commit 645357ac58
5 changed files with 110 additions and 105 deletions
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9
tests/nsbdiagnosistoolkit/engine/remote/databases/institutpasteur/test_mlst.py
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@@ -16,7 +16,8 @@ async def test_profiling_results_in_exact_matches_when_exact():
assert len(targets_left) == 0
async def test_profiling_results_in_correct_st():
dummy_alleles = [
async def dummy_allele_generator():
dummy_alleles = [
Allele("adk", "1"),
Allele("fumC", "1"),
Allele("glyA", "1"),
@@ -24,9 +25,11 @@ async def test_profiling_results_in_correct_st():
Allele("icd", "1"),
Allele("pepA", "1"),
Allele("pgm", "1"),
]
]
for dummy_allele in dummy_alleles:
yield dummy_allele
async with InstitutPasteurProfiler(database_name="pubmlst_bordetella_seqdef") as dummy_profiler:
mlst_st_data = await dummy_profiler.fetch_mlst_st(3, dummy_alleles)
mlst_st_data = await dummy_profiler.fetch_mlst_st(3, 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"

31
tests/nsbdiagnosistoolkit/engine/remote/databases/pubmlst/test_mlst.py
View File

@@ -1,6 +1,6 @@
import asyncio
from Bio import SeqIO
from automlst.engine.data.mlst import Allele, MLSTProfile
from automlst.engine.remote.databases.institutpasteur.mlst import InstitutPasteurProfiler
from automlst.engine.remote.databases.pubmlst.mlst import PubMLSTProfiler
@@ -24,25 +24,28 @@ async def test_profiling_results_in_exact_matches_when_exact():
assert len(dummy_alleles) == 0
async def test_profiling_results_in_correct_st():
dummy_alleles = [
Allele("adk", "1"),
Allele("atpG", "1"),
Allele("frdB", "1"),
Allele("fucK", "1"),
Allele("mdh", "1"),
Allele("pgi", "1"),
Allele("recA", "5"),
]
async with InstitutPasteurProfiler(database_name="pubmlst_hinfluenzae_seqdef") as dummy_profiler:
mlst_st_data = await dummy_profiler.fetch_mlst_st(1, dummy_alleles)
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 PubMLSTProfiler(database_name="pubmlst_hinfluenzae_seqdef") as dummy_profiler:
mlst_st_data = await dummy_profiler.fetch_mlst_st(1, 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_sequence_profiling_is_correct():
sequence = str(SeqIO.read("tests/resources/tohama_I_bpertussis.fasta", "fasta").seq)
async with InstitutPasteurProfiler(database_name="pubmlst_hinfluenzae_seqdef") as dummy_profiler:
sequence = str(SeqIO.read("tests/resources/FDAARGOS_1560.fasta", "fasta").seq)
async with PubMLSTProfiler(database_name="pubmlst_hinfluenzae_seqdef") as dummy_profiler:
profile = await dummy_profiler.profile_string(1, sequence)
assert profile is not None
assert isinstance(profile, MLSTProfile)