Mercurial > repos > recetox > matchms_convert
view formatter.py @ 14:72759b974615 draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 2a2f69962f84b4ff91c9739bdf7749c5097a33ed
author | recetox |
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date | Thu, 22 Feb 2024 12:31:28 +0000 |
parents | d4609fbf8ca3 |
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import click from matchms.importing import scores_from_json from pandas import DataFrame def scores_to_dataframe(scores): """Unpack scores from matchms.scores into two dataframes of scores and matches. Args: scores (matchms.scores): matchms.scores object. Returns: DataFrame: Scores DataFrame: Matches """ data = [] for i, (row, col) in enumerate(zip(scores.scores.row, scores.scores.col)): data.append([scores.queries[col].metadata['compound_name'], scores.references[row].metadata['compound_name'], *scores.scores.data[i]]) dataframe = DataFrame(data, columns=['query', 'reference', *scores.scores.score_names]) return dataframe def load_data(scores_filename: str) -> DataFrame: """Load data from filenames and join on compound id. Args: scores_filename (str): Path to json file with serialized scores. Returns: DataFrame: Joined dataframe on compounds containing scores and matches in long format. """ scores = scores_from_json(scores_filename) scores = scores_to_dataframe(scores) return scores @click.group(invoke_without_command=True) @click.option('--sf', 'scores_filename', type=click.Path(exists=True), required=True) @click.option('--o', 'output_filename', type=click.Path(writable=True), required=True) def cli(scores_filename, output_filename): result = load_data(scores_filename) result.to_csv(output_filename, sep="\t", index=False) pass if __name__ == '__main__': cli()