33 lines
763 B
Python
33 lines
763 B
Python
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from glob import glob
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from typing import List
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from pandas import DataFrame, read_html
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def find_html_files(path) -> List:
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file_list = glob(path + "/*fastqc.html")
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return file_list
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def extract_adapters(files) -> DataFrame:
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all_adapters = DataFrame()
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for entry in files:
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tables = read_html(entry)
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adapter_sequences = tables[1].Sequence
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all_adapters = all_adapters.append(adapter_sequences)
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return all_adapters.dropna()
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def save_to_file(filename, adapters) -> None:
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adapters.to_csv(filename, index=False, header=False, sep="\n")
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def main():
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file_list = find_html_files("data")
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adapters = extract_adapters(file_list)
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save_to_file("placeholder.txt", adapters)
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if __name__ == "__main__":
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main()
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