Mercurial > repos > recetox > matchms_formatter

annotate matchms_networking_wrapper.py @ 25:9287136a396a draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f14275bfdc2caa760d71d307ca1803eab1adde76
author recetox
date Wed, 13 Mar 2024 10:17:42 +0000
parents 3dad3f53402f
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1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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1 import argparse
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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2 import sys
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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4 from matchms.importing import scores_from_json
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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5 from matchms.networking import SimilarityNetwork
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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8 def main(argv):
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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9 parser = argparse.ArgumentParser(description="Create network-graph from similarity scores.")
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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10 parser.add_argument("--graph_format", type=str, help="Format of the output similarity network.")
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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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.")
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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12 parser.add_argument("--identifier", type=str, help="Unique metadata identifier of each spectrum from which scores are computed.")
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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13 parser.add_argument("--top_n", type=int, help="Number of highest-score edges to keep.")
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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14 parser.add_argument("--max_links", type=int, help="Maximum number of links to add per node.")
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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15 parser.add_argument("--score_cutoff", type=float, help="Minimum similarity score value to link two spectra.")
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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16 parser.add_argument("--link_method", type=str, help="Method for selecting top N edges for each node.")
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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17 parser.add_argument("--keep_unconnected_nodes", help="Keep unconnected nodes in the network.", action="store_true")
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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18 parser.add_argument("scores", type=str, help="Path to matchms similarity-scores .json file.")
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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19 parser.add_argument("output_filename", type=str, help="Path where to store the output similarity network.")
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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20 args = parser.parse_args()
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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22 scores = scores_from_json(args.scores)
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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24 network = SimilarityNetwork(identifier_key=args.identifier,
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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25 top_n=args.top_n,
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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26 max_links=args.max_links,
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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27 score_cutoff=args.score_cutoff,
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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28 link_method=args.link_method,
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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29 keep_unconnected_nodes=args.keep_unconnected_nodes)
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3dad3f53402f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 13f4f7af12ec694a5f4ab7b3e52f46a4f67a245e
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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)
3dad3f53402f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 13f4f7af12ec694a5f4ab7b3e52f46a4f67a245e
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31 if score_name is None:
3dad3f53402f planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 13f4f7af12ec694a5f4ab7b3e52f46a4f67a245e
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32 raise ValueError(f"Could not find any score name containing '{args.score_name}'.")
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1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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3dad3f53402f 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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1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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35 network.export_to_file(filename=args.output_filename, graph_format=args.graph_format)
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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37 return 0
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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40 if __name__ == "__main__":
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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41 main(argv=sys.argv[1:])
1b09315a3f87 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
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42 pass