annotate matchms_networking_wrapper.py @ 3:358a151ab81e draft

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit da193865f41a3a840ecc4ba0afab1d358554998a
author recetox
date Mon, 05 Feb 2024 10:41:13 +0000
parents ea891750acfc
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
ea891750acfc planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
recetox
parents:
diff changeset
1 import argparse
ea891750acfc planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
recetox
parents:
diff changeset
2 import sys
ea891750acfc planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
recetox
parents:
diff changeset
3
ea891750acfc planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
recetox
parents:
diff changeset
4 from matchms.importing import scores_from_json
ea891750acfc planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
recetox
parents:
diff changeset
5 from matchms.networking import SimilarityNetwork
ea891750acfc planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
recetox
parents:
diff changeset
6
ea891750acfc planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
recetox
parents:
diff changeset
7
ea891750acfc planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
recetox
parents:
diff changeset
8 def main(argv):
ea891750acfc planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
recetox
parents:
diff changeset
9 parser = argparse.ArgumentParser(description="Create network-graph from similarity scores.")
ea891750acfc planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
recetox
parents:
diff changeset
10 parser.add_argument("--graph_format", type=str, help="Format of the output similarity network.")
ea891750acfc planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
recetox
parents:
diff changeset
11 parser.add_argument("--score_name", type=str, help="Name of the score layer to use for creating the network graph.")
ea891750acfc planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
recetox
parents:
diff changeset
12 parser.add_argument("--identifier", type=str, help="Unique metadata identifier of each spectrum from which scores are computed.")
ea891750acfc planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
recetox
parents:
diff changeset
13 parser.add_argument("--top_n", type=int, help="Number of highest-score edges to keep.")
ea891750acfc planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
recetox
parents:
diff changeset
14 parser.add_argument("--max_links", type=int, help="Maximum number of links to add per node.")
ea891750acfc planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
recetox
parents:
diff changeset
15 parser.add_argument("--score_cutoff", type=float, help="Minimum similarity score value to link two spectra.")
ea891750acfc planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
recetox
parents:
diff changeset
16 parser.add_argument("--link_method", type=str, help="Method for selecting top N edges for each node.")
ea891750acfc planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
recetox
parents:
diff changeset
17 parser.add_argument("--keep_unconnected_nodes", help="Keep unconnected nodes in the network.", action="store_true")
ea891750acfc planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
recetox
parents:
diff changeset
18 parser.add_argument("scores", type=str, help="Path to matchms similarity-scores .json file.")
ea891750acfc planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
recetox
parents:
diff changeset
19 parser.add_argument("output_filename", type=str, help="Path where to store the output similarity network.")
ea891750acfc planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
recetox
parents:
diff changeset
20 args = parser.parse_args()
ea891750acfc planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
recetox
parents:
diff changeset
21
ea891750acfc planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
recetox
parents:
diff changeset
22 scores = scores_from_json(args.scores)
ea891750acfc planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
recetox
parents:
diff changeset
23
ea891750acfc planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
recetox
parents:
diff changeset
24 network = SimilarityNetwork(identifier_key=args.identifier,
ea891750acfc planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
recetox
parents:
diff changeset
25 top_n=args.top_n,
ea891750acfc planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
recetox
parents:
diff changeset
26 max_links=args.max_links,
ea891750acfc planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
recetox
parents:
diff changeset
27 score_cutoff=args.score_cutoff,
ea891750acfc planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
recetox
parents:
diff changeset
28 link_method=args.link_method,
ea891750acfc planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
recetox
parents:
diff changeset
29 keep_unconnected_nodes=args.keep_unconnected_nodes)
ea891750acfc planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
recetox
parents:
diff changeset
30 score_name = next((s for s in scores.score_names if args.score_name in s and "score" in s), None)
ea891750acfc planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
recetox
parents:
diff changeset
31 if score_name is None:
ea891750acfc planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
recetox
parents:
diff changeset
32 raise ValueError(f"Could not find any score name containing '{args.score_name}'.")
ea891750acfc planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
recetox
parents:
diff changeset
33
ea891750acfc planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
recetox
parents:
diff changeset
34 network.create_network(scores, score_name)
ea891750acfc planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
recetox
parents:
diff changeset
35 network.export_to_file(filename=args.output_filename, graph_format=args.graph_format)
ea891750acfc planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
recetox
parents:
diff changeset
36
ea891750acfc planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
recetox
parents:
diff changeset
37 return 0
ea891750acfc planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
recetox
parents:
diff changeset
38
ea891750acfc planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
recetox
parents:
diff changeset
39
ea891750acfc planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
recetox
parents:
diff changeset
40 if __name__ == "__main__":
ea891750acfc planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
recetox
parents:
diff changeset
41 main(argv=sys.argv[1:])
ea891750acfc planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 970c7dc210faacd545c740ddae0e5e78c2cecce4
recetox
parents:
diff changeset
42 pass