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Added predetermined headers feature
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Harrison Deng
2025-03-14 14:26:43 +00:00
parent 34bf02c75a
commit f8d92a4aad
5 changed files with 27 additions and 7 deletions
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9
tests/autobigs/engine/analysis/test_bigsdb.py
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@@ -222,3 +222,12 @@ class TestBIGSdbIndex:
assert isinstance(profile, MLSTProfile)
assert profile.clonal_complex == "ST-2 complex"
assert profile.sequence_type == "1"
@pytest.mark.parametrize(["bigsdb_name", "scheme_id", "expected"], [
("pubmlst_bordetella_seqdef", 3, ["adk", "fumC", "glyA", "tyrB", "icd", "pepA", "pgm"])
])
async def test_bigsdb_index_fetches_loci_names(self, bigsdb_name, scheme_id, expected):
async with BIGSdbIndex() as bigsdb_index:
loci = await bigsdb_index.get_scheme_loci(bigsdb_name, scheme_id)
assert set(loci) == set(expected)

6
tests/autobigs/engine/test_writing.py
View File

@@ -27,7 +27,7 @@ async def test_column_order_is_same_as_expected_file(dummy_alphabet_mlst_profile
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)
await write_mlst_profiles_as_csv(iterable_to_asynciterable(dummy_profiles), output_path, ["A", "D", "B", "C"])
with open(output_path) as csv_handle:
csv_reader = reader(csv_handle)
lines = list(csv_reader)
@@ -38,7 +38,7 @@ async def test_csv_writing_sample_name_not_repeated_when_single_sequence(dummy_a
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)
await write_mlst_profiles_as_csv(iterable_to_asynciterable(dummy_profiles), output_path, ["A", "D", "B", "C"])
with open(output_path) as csv_handle:
csv_reader = reader(csv_handle)
lines = list(csv_reader)
@@ -63,7 +63,7 @@ async def test_csv_writing_includes_asterisk_for_non_exact(dummy_alphabet_mlst_p
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)
await write_mlst_profiles_as_csv(iterable_to_asynciterable(dummy_profiles), output_path, ["A", "D", "B", "C"])
with open(output_path) as csv_handle:
csv_reader = reader(csv_handle)
lines = list(csv_reader)