Mercurial > repos > recetox > matchms

comparison matchms_wrapper.py @ 4:57959596262d draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 3c7f3cf3f925215a23b2f6665432c32b5ebdc2aa"
author recetox
date Tue, 08 Jun 2021 11:28:40 +0000
parents a7c9fc186f8c
children 672c22d7f004
comparison
equal deleted inserted replaced
3:72adeb3ca264 4:57959596262d
13 13
14 14
15 def main(argv): 15 def main(argv):
16 parser = argparse.ArgumentParser(description="Compute MSP similarity scores") 16 parser = argparse.ArgumentParser(description="Compute MSP similarity scores")
17 parser.add_argument( 17 parser.add_argument(
18 "references_filename", type=str, help="Path to reference MSP library." 18 "--ref", type=str, dest="references_filename", help="Path to reference MSP library."
19 ) 19 )
20 parser.add_argument("queries_filename", type=str, help="Path to query spectra.") 20 parser.add_argument("queries_filename", type=str, help="Path to query spectra.")
21 parser.add_argument("similarity_metric", type=str, help='Metric to use for matching.') 21 parser.add_argument("similarity_metric", type=str, help='Metric to use for matching.')
22 parser.add_argument("output_filename_scores", type=str, help="Path where to store the output .csv scores.") 22 parser.add_argument("output_filename_scores", type=str, help="Path where to store the output .csv scores.")
23 parser.add_argument("output_filename_matches", type=str, help="Path where to store the output .csv matches.") 23 parser.add_argument("output_filename_matches", type=str, help="Path where to store the output .csv matches.")
25 parser.add_argument("mz_power", type=float, help="The power to raise mz to in the cosine function.") 25 parser.add_argument("mz_power", type=float, help="The power to raise mz to in the cosine function.")
26 parser.add_argument("intensity_power", type=float, help="The power to raise intensity to in the cosine function.") 26 parser.add_argument("intensity_power", type=float, help="The power to raise intensity to in the cosine function.")
27 27
28 args = parser.parse_args() 28 args = parser.parse_args()
29 29
30 reference_spectra = load_from_msp(args.references_filename) 30 queries_spectra = list(load_from_msp(args.queries_filename))
31 queries_spectra = load_from_msp(args.queries_filename) 31 if(args.references_filename):
32 reference_spectra = list(load_from_msp(args.references_filename))
33 symmetric = False
34 else:
35 reference_spectra = queries_spectra.copy()
36 symmetric = True
32 37
33 if args.similarity_metric == 'CosineGreedy': 38 if args.similarity_metric == 'CosineGreedy':
34 similarity_metric = CosineGreedy(args.tolerance, args.mz_power, args.intensity_power) 39 similarity_metric = CosineGreedy(args.tolerance, args.mz_power, args.intensity_power)
35 elif args.similarity_metric == 'CosineHungarian': 40 elif args.similarity_metric == 'CosineHungarian':
36 similarity_metric = CosineHungarian(args.tolerance, args.mz_power, args.intensity_power) 41 similarity_metric = CosineHungarian(args.tolerance, args.mz_power, args.intensity_power)
43 48
44 scores = calculate_scores( 49 scores = calculate_scores(
45 references=list(reference_spectra), 50 references=list(reference_spectra),
46 queries=list(queries_spectra), 51 queries=list(queries_spectra),
47 similarity_function=similarity_metric, 52 similarity_function=similarity_metric,
53 is_symmetric=symmetric
48 ) 54 )
49 55
50 query_names = [spectra.metadata['name'] for spectra in scores.queries] 56 query_names = [spectra.metadata['name'] for spectra in scores.queries]
51 reference_names = [spectra.metadata['name'] for spectra in scores.references] 57 reference_names = [spectra.metadata['name'] for spectra in scores.references]
52 58