Mercurial > repos > recetox > matchms_networking

annotate formatter.py @ 9:bd6a398a05e9 draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 0f836e483fe3727580d6d1239135203b20812504
author recetox
date Wed, 22 Nov 2023 14:24:37 +0000
parents 9982b85ff4e7
children
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8147d93d372d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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1 import click
8147d93d372d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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2 from matchms.importing import scores_from_json
8147d93d372d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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3 from pandas import DataFrame
8147d93d372d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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8147d93d372d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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8147d93d372d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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6 def scores_to_dataframe(scores):
8147d93d372d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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7 """Unpack scores from matchms.scores into two dataframes of scores and matches.
8147d93d372d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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8147d93d372d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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9 Args:
8147d93d372d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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10 scores (matchms.scores): matchms.scores object.
8147d93d372d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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12 Returns:
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13 DataFrame: Scores
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14 DataFrame: Matches
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15 """
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16 data = []
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8147d93d372d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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8147d93d372d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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18 for i, (row, col) in enumerate(zip(scores.scores.row, scores.scores.col)):
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19 data.append([scores.queries[col].metadata['compound_name'], scores.references[row].metadata['compound_name'], *scores.scores.data[i]])
9982b85ff4e7 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
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21 dataframe = DataFrame(data, columns=['query', 'reference', *scores.scores.score_names])
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8147d93d372d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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8147d93d372d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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23 return dataframe
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8147d93d372d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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8147d93d372d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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26 def load_data(scores_filename: str) -> DataFrame:
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27 """Load data from filenames and join on compound id.
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8147d93d372d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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29 Args:
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30 scores_filename (str): Path to json file with serialized scores.
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32 Returns:
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33 DataFrame: Joined dataframe on compounds containing scores and matches in long format.
8147d93d372d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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34 """
8147d93d372d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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35 scores = scores_from_json(scores_filename)
8147d93d372d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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36 scores = scores_to_dataframe(scores)
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8147d93d372d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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38 return scores
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41 @click.group(invoke_without_command=True)
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42 @click.option('--sf', 'scores_filename', type=click.Path(exists=True), required=True)
8147d93d372d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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43 @click.option('--o', 'output_filename', type=click.Path(writable=True), required=True)
8147d93d372d planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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44 def cli(scores_filename, output_filename):
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45 result = load_data(scores_filename)
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46 result.to_csv(output_filename, sep="\t", index=False)
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47 pass
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50 if __name__ == '__main__':
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51 cli()