Mercurial > repos > recetox > matchms

comparison matchms_wrapper.py @ 9:f06923bdd2f2 draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5bd7d3aa1063b0a5a90577dd6c79504fdd93f73c"
author recetox
date Mon, 10 Jan 2022 12:21:43 +0000
parents 4571641de47a
children
comparison
equal deleted inserted replaced
8:8b1e1b2edecc 9:f06923bdd2f2
1 import argparse 1 import argparse
2 import sys 2 import sys
3 3
4 from matchms import calculate_scores 4 from matchms import calculate_scores
5 from matchms.filtering import add_precursor_mz, default_filters, normalize_intensities 5 from matchms.filtering import add_precursor_mz, default_filters, normalize_intensities
6 from matchms.importing import load_from_msp 6 from matchms.importing import load_from_mgf, load_from_msp
7 from matchms.similarity import ( 7 from matchms.similarity import (
8 CosineGreedy, 8 CosineGreedy,
9 CosineHungarian, 9 CosineHungarian,
10 ModifiedCosine, 10 ModifiedCosine,
11 ) 11 )
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("-f", dest="default_filters", action='store_true', help="Apply default filters") 17 parser.add_argument("-f", dest="default_filters", action='store_true', help="Apply default filters")
18 parser.add_argument("-n", dest="normalize_intensities", action='store_true', help="Normalize intensities.") 18 parser.add_argument("-n", dest="normalize_intensities", action='store_true', help="Normalize intensities.")
19 parser.add_argument("-s", dest="symmetric", action='store_true', help="Computation is symmetric.") 19 parser.add_argument("-s", dest="symmetric", action='store_true', help="Computation is symmetric.")
20 parser.add_argument("--ref", dest="references_filename", type=str, help="Path to reference MSP library.") 20 parser.add_argument("--ref", dest="references_filename", type=str, help="Path to reference spectra library.")
21 parser.add_argument("--ref_format", dest="references_format", type=str, help="Reference spectra library file format.")
21 parser.add_argument("queries_filename", type=str, help="Path to query spectra.") 22 parser.add_argument("queries_filename", type=str, help="Path to query spectra.")
23 parser.add_argument("queries_format", type=str, help="Query spectra file format.")
22 parser.add_argument("similarity_metric", type=str, help='Metric to use for matching.') 24 parser.add_argument("similarity_metric", type=str, help='Metric to use for matching.')
23 parser.add_argument("tolerance", type=float, help="Tolerance to use for peak matching.") 25 parser.add_argument("tolerance", type=float, help="Tolerance to use for peak matching.")
24 parser.add_argument("mz_power", type=float, help="The power to raise mz to in the cosine function.") 26 parser.add_argument("mz_power", type=float, help="The power to raise mz to in the cosine function.")
25 parser.add_argument("intensity_power", type=float, help="The power to raise intensity to in the cosine function.") 27 parser.add_argument("intensity_power", type=float, help="The power to raise intensity to in the cosine function.")
26 parser.add_argument("output_filename_scores", type=str, help="Path where to store the output .csv scores.") 28 parser.add_argument("output_filename_scores", type=str, help="Path where to store the output .tsv scores.")
27 parser.add_argument("output_filename_matches", type=str, help="Path where to store the output .csv matches.") 29 parser.add_argument("output_filename_matches", type=str, help="Path where to store the output .tsv matches.")
28 args = parser.parse_args() 30 args = parser.parse_args()
29 31
30 queries_spectra = list(load_from_msp(args.queries_filename)) 32 if args.queries_format == 'msp':
33 queries_spectra = list(load_from_msp(args.queries_filename))
34 elif args.queries_format == 'mgf':
35 queries_spectra = list(load_from_mgf(args.queries_filename))
36 else:
37 raise ValueError(f'File format {args.queries_format} not supported for query spectra.')
38
31 if args.symmetric: 39 if args.symmetric:
32 reference_spectra = [] 40 reference_spectra = []
33 else: 41 else:
34 reference_spectra = list(load_from_msp(args.references_filename)) 42 if args.references_format == 'msp':
43 reference_spectra = list(load_from_msp(args.references_filename))
44 elif args.references_format == 'mgf':
45 reference_spectra = list(load_from_mgf(args.references_filename))
46 else:
47 raise ValueError(f'File format {args.references_format} not supported for reference spectra library.')
35 48
36 if args.default_filters is True: 49 if args.default_filters is True:
37 print("Applying default filters...") 50 print("Applying default filters...")
38 queries_spectra = list(map(default_filters, queries_spectra)) 51 queries_spectra = list(map(default_filters, queries_spectra))
39 reference_spectra = list(map(default_filters, reference_spectra)) 52 reference_spectra = list(map(default_filters, reference_spectra))