47 lines
1.7 KiB
Python
47 lines
1.7 KiB
Python
from typing import AsyncIterable, Iterable
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import pytest
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from autobigs.engine.structures.alignment import AlignmentStats
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from autobigs.engine.writing import alleles_to_text_map, write_mlst_profiles_as_csv
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from autobigs.engine.structures.mlst import Allele, MLSTProfile
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import tempfile
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from csv import reader
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from os import path
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@pytest.fixture
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def dummy_alphabet_mlst_profile():
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return MLSTProfile((
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Allele("A", "1", None),
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Allele("D", "1", None),
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Allele("B", "1", None),
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Allele("C", "1", None),
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Allele("C", "2", AlignmentStats(90, 10, 0, 90))
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), "mysterious", "very mysterious")
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async def iterable_to_asynciterable(iterable: Iterable):
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for iterated in iterable:
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yield iterated
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async def test_column_order_is_same_as_expected_file(dummy_alphabet_mlst_profile: MLSTProfile):
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dummy_profiles = [("test_1", dummy_alphabet_mlst_profile)]
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with tempfile.TemporaryDirectory() as temp_dir:
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output_path = path.join(temp_dir, "out.csv")
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await write_mlst_profiles_as_csv(iterable_to_asynciterable(dummy_profiles), output_path)
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with open(output_path) as csv_handle:
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csv_reader = reader(csv_handle)
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lines = list(csv_reader)
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target_columns = lines[4:]
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assert target_columns == sorted(target_columns)
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async def test_alleles_to_text_map_mapping_is_correct(dummy_alphabet_mlst_profile: MLSTProfile):
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mapping = alleles_to_text_map(dummy_alphabet_mlst_profile.alleles)
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expected_mapping = {
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"A": "1",
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"B": "1",
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"C": ("1", "2*"),
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"D": "1"
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}
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for allele_name, allele_ids in mapping.items():
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assert allele_name in expected_mapping
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assert allele_ids == expected_mapping[allele_name] |