44 lines
1.7 KiB
Python
44 lines
1.7 KiB
Python
from typing import AsyncIterable, Iterable
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from autobigs.engine.data.local.csv import dict_loci_alleles_variants_from_loci, write_mlst_profiles_as_csv
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from autobigs.engine.data.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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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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def test_dict_loci_alleles_variants_from_loci_single_loci_not_list():
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alleles_map = {
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"adk": [Allele("adk", "1", None)]
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}
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results = dict_loci_alleles_variants_from_loci(alleles_map)
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for loci, variant in results.items():
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assert isinstance(variant, str)
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assert variant == "1"
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def test_dict_loci_alleles_variants_from_loci_multi_loci_is_list():
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alleles_map = {
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"adk": [Allele("adk", "1", None), Allele("adk", "2", None)]
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}
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results = dict_loci_alleles_variants_from_loci(alleles_map)
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for loci, variant in results.items():
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assert isinstance(variant, list)
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assert len(variant) == 2
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async def test_column_order_is_same_as_expected_file():
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dummy_profiles = [("test_1", MLSTProfile({
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"A": Allele("A", "1", None),
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"D": Allele("D", "1", None),
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"B": Allele("B", "1", None),
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"C": Allele("C", "1", None)
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}, "mysterious", "very mysterious"))]
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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) |