Mercurial > repos > recetox > matchms_spectral_similarity
annotate matchms_networking_wrapper.py @ 4:d6176cfda8e8 draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 0f836e483fe3727580d6d1239135203b20812504
author | recetox |
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date | Wed, 22 Nov 2023 14:21:55 +0000 |
parents | 32a8826ed367 |
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9ff95a1a2705
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
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1 import argparse |
9ff95a1a2705
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
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2 import sys |
9ff95a1a2705
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
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3 |
9ff95a1a2705
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
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4 from matchms.importing import scores_from_json |
9ff95a1a2705
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
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5 from matchms.networking import SimilarityNetwork |
9ff95a1a2705
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
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6 |
9ff95a1a2705
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
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7 |
9ff95a1a2705
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
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8 def main(argv): |
9ff95a1a2705
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
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9 parser = argparse.ArgumentParser(description="Create network-graph from similarity scores.") |
9ff95a1a2705
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
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10 parser.add_argument("--graph_format", type=str, help="Format of the output similarity network.") |
9ff95a1a2705
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
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11 parser.add_argument("--score_name", type=str, help="Name of the score layer to use for creating the network graph.") |
9ff95a1a2705
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
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12 parser.add_argument("--identifier", type=str, help="Unique metadata identifier of each spectrum from which scores are computed.") |
9ff95a1a2705
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
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13 parser.add_argument("--top_n", type=int, help="Number of highest-score edges to keep.") |
9ff95a1a2705
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
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14 parser.add_argument("--max_links", type=int, help="Maximum number of links to add per node.") |
9ff95a1a2705
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
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15 parser.add_argument("--score_cutoff", type=float, help="Minimum similarity score value to link two spectra.") |
9ff95a1a2705
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
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16 parser.add_argument("--link_method", type=str, help="Method for selecting top N edges for each node.") |
9ff95a1a2705
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
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17 parser.add_argument("--keep_unconnected_nodes", help="Keep unconnected nodes in the network.", action="store_true") |
9ff95a1a2705
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
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diff
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18 parser.add_argument("scores", type=str, help="Path to matchms similarity-scores .json file.") |
9ff95a1a2705
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
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19 parser.add_argument("output_filename", type=str, help="Path where to store the output similarity network.") |
9ff95a1a2705
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
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20 args = parser.parse_args() |
9ff95a1a2705
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
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21 |
9ff95a1a2705
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
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22 scores = scores_from_json(args.scores) |
9ff95a1a2705
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
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23 |
9ff95a1a2705
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
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24 network = SimilarityNetwork(identifier_key=args.identifier, |
9ff95a1a2705
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
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changeset
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25 top_n=args.top_n, |
9ff95a1a2705
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
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26 max_links=args.max_links, |
9ff95a1a2705
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents:
diff
changeset
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27 score_cutoff=args.score_cutoff, |
9ff95a1a2705
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
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diff
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28 link_method=args.link_method, |
9ff95a1a2705
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents:
diff
changeset
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29 keep_unconnected_nodes=args.keep_unconnected_nodes) |
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32a8826ed367
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 13f4f7af12ec694a5f4ab7b3e52f46a4f67a245e
recetox
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30 score_name = next((s for s in scores.score_names if args.score_name in s and "score" in s), None) |
32a8826ed367
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 13f4f7af12ec694a5f4ab7b3e52f46a4f67a245e
recetox
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31 if score_name is None: |
32a8826ed367
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 13f4f7af12ec694a5f4ab7b3e52f46a4f67a245e
recetox
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32 raise ValueError(f"Could not find any score name containing '{args.score_name}'.") |
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9ff95a1a2705
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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33 |
3
32a8826ed367
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 13f4f7af12ec694a5f4ab7b3e52f46a4f67a245e
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34 network.create_network(scores, score_name) |
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9ff95a1a2705
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
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35 network.export_to_file(filename=args.output_filename, graph_format=args.graph_format) |
9ff95a1a2705
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
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36 |
9ff95a1a2705
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
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37 return 0 |
9ff95a1a2705
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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38 |
9ff95a1a2705
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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39 |
9ff95a1a2705
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
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40 if __name__ == "__main__": |
9ff95a1a2705
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
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41 main(argv=sys.argv[1:]) |
9ff95a1a2705
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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42 pass |