24 lines
713 B
Python
24 lines
713 B
Python
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from fuzzysearch import find_near_matches_customized_levenshtein, find_near_matches_with_ngrams
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def custom_search(subsequence, sequence, max_l_dist):
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return list(find_near_matches_customized_levenshtein(subsequence, sequence, max_l_dist))
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search_functions = {
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'custom': custom_search,
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'ngrams': find_near_matches_with_ngrams,
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}
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benchmarks = {
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'dna_no_match': lambda: dict(
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subsequence = 'GCTAGCTAGCTA',
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sequence = '"ATCG" * (10**3)',
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max_l_dist = 1,
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),
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}
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def run_benchmark(search_func_name, benchmark_name, **params):
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search_func = search_functions[search_func_name]
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search_args = benchmarks[benchmark_name](**params)
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return search_func(**search_args)
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