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Added test for non-exact allele matches
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Harrison Deng
2025-02-28 15:05:26 +00:00
parent bbd9e67c8c
commit 3d6f36a722
4 changed files with 277 additions and 1 deletions
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tests/autobigs/engine/test_writing.py
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@@ -47,7 +47,8 @@ async def test_csv_writing_sample_name_not_repeated_when_single_sequence(dummy_a
async def test_alleles_to_text_map_mapping_is_correct(dummy_alphabet_mlst_profile: NamedMLSTProfile):
mapping = alleles_to_text_map(dummy_alphabet_mlst_profile.mlst_profile.alleles) # type: ignore
assert dummy_alphabet_mlst_profile.mlst_profile is not None
mapping = alleles_to_text_map(dummy_alphabet_mlst_profile.mlst_profile.alleles)
expected_mapping = {
"A": "1",
"B": "1",
@@ -58,3 +59,12 @@ async def test_alleles_to_text_map_mapping_is_correct(dummy_alphabet_mlst_profil
assert allele_name in expected_mapping
assert allele_ids == expected_mapping[allele_name]
async def test_csv_writing_includes_asterisk_for_non_exact(dummy_alphabet_mlst_profile: NamedMLSTProfile):
dummy_profiles = [dummy_alphabet_mlst_profile]
with tempfile.TemporaryDirectory() as temp_dir:
output_path = path.join(temp_dir, "out.csv")
await write_mlst_profiles_as_csv(iterable_to_asynciterable(dummy_profiles), output_path)
with open(output_path) as csv_handle:
csv_reader = reader(csv_handle)
lines = list(csv_reader)
assert '*' in lines[1][5]