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Added automatic handling of strings instead of arrays of sequences to typing

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This commit is contained in:
Harrison Deng
2025-02-06 21:15:50 +00:00
parent fe999f1cab
commit b4845fab34
2 changed files with 14 additions and 10 deletions
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9
tests/autobigs/engine/analysis/test_bigsdb.py
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@@ -201,10 +201,15 @@ class TestBIGSdbIndex:
assert database_name.endswith("seqdef")
assert databases["pubmlst_bordetella_seqdef"] == "https://bigsdb.pasteur.fr/api"
async def test_bigsdb_index_instantiates_correct_profiler(self):
@pytest.mark.parametrize("local", [
(True),
(False)
])
async def test_bigsdb_index_instantiates_correct_profiler(self, local):
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:
async with await bigsdb_index.build_profiler_from_seqdefdb(local, "pubmlst_bordetella_seqdef", 3) as profiler:
assert isinstance(profiler, BIGSdbMLSTProfiler)
profile = await profiler.profile_string(sequence)
assert profile.clonal_complex == "ST-2 complex"
assert profile.sequence_type == "1"