Mercurial > repos > recetox > matchms_remove_key
annotate formatter.py @ 0:ea891750acfc draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
author | recetox |
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date | Mon, 04 Dec 2023 19:17:25 +0000 |
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ea891750acfc
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
recetox
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1 import click |
ea891750acfc
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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2 from matchms.importing import scores_from_json |
ea891750acfc
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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3 from pandas import DataFrame |
ea891750acfc
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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4 |
ea891750acfc
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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5 |
ea891750acfc
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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6 def scores_to_dataframe(scores): |
ea891750acfc
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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7 """Unpack scores from matchms.scores into two dataframes of scores and matches. |
ea891750acfc
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
recetox
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8 |
ea891750acfc
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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9 Args: |
ea891750acfc
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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10 scores (matchms.scores): matchms.scores object. |
ea891750acfc
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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11 |
ea891750acfc
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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12 Returns: |
ea891750acfc
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
recetox
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13 DataFrame: Scores |
ea891750acfc
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
recetox
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14 DataFrame: Matches |
ea891750acfc
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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15 """ |
ea891750acfc
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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16 data = [] |
ea891750acfc
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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17 |
ea891750acfc
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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18 for i, (row, col) in enumerate(zip(scores.scores.row, scores.scores.col)): |
ea891750acfc
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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19 data.append([scores.queries[col].metadata['compound_name'], scores.references[row].metadata['compound_name'], *scores.scores.data[i]]) |
ea891750acfc
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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20 |
ea891750acfc
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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21 dataframe = DataFrame(data, columns=['query', 'reference', *scores.scores.score_names]) |
ea891750acfc
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
recetox
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22 |
ea891750acfc
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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23 return dataframe |
ea891750acfc
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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24 |
ea891750acfc
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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25 |
ea891750acfc
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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26 def load_data(scores_filename: str) -> DataFrame: |
ea891750acfc
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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27 """Load data from filenames and join on compound id. |
ea891750acfc
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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28 |
ea891750acfc
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
recetox
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29 Args: |
ea891750acfc
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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30 scores_filename (str): Path to json file with serialized scores. |
ea891750acfc
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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31 |
ea891750acfc
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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32 Returns: |
ea891750acfc
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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33 DataFrame: Joined dataframe on compounds containing scores and matches in long format. |
ea891750acfc
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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34 """ |
ea891750acfc
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
recetox
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35 scores = scores_from_json(scores_filename) |
ea891750acfc
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
recetox
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36 scores = scores_to_dataframe(scores) |
ea891750acfc
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
recetox
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37 |
ea891750acfc
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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38 return scores |
ea891750acfc
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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39 |
ea891750acfc
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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40 |
ea891750acfc
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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41 @click.group(invoke_without_command=True) |
ea891750acfc
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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42 @click.option('--sf', 'scores_filename', type=click.Path(exists=True), required=True) |
ea891750acfc
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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43 @click.option('--o', 'output_filename', type=click.Path(writable=True), required=True) |
ea891750acfc
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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44 def cli(scores_filename, output_filename): |
ea891750acfc
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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45 result = load_data(scores_filename) |
ea891750acfc
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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46 result.to_csv(output_filename, sep="\t", index=False) |
ea891750acfc
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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47 pass |
ea891750acfc
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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48 |
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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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49 |
ea891750acfc
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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50 if __name__ == '__main__': |
ea891750acfc
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
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51 cli() |