Mercurial > repos > recetox > matchms_formatter

comparison matchms_filtering_wrapper.py @ 10:1b09315a3f87 draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
author recetox
date Tue, 27 Jun 2023 14:25:59 +0000
parents
children ae45992f969e
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9:715fe77be601 10:1b09315a3f87
1 import argparse
2 import sys
3
4 from matchms.exporting import save_as_mgf, save_as_msp
5 from matchms.filtering import add_compound_name, add_fingerprint, add_losses, add_parent_mass, add_precursor_mz,\
6 add_retention_index, add_retention_time, clean_compound_name
7 from matchms.filtering import default_filters, normalize_intensities, select_by_mz, select_by_relative_intensity
8 from matchms.importing import load_from_mgf, load_from_msp
9
10
11 def main(argv):
12 parser = argparse.ArgumentParser(description="Compute MSP similarity scores")
13 parser.add_argument("--spectra", type=str, required=True, help="Mass spectra file to be filtered.")
14 parser.add_argument("--spectra_format", type=str, required=True, help="Format of spectra file.")
15 parser.add_argument("--output", type=str, required=True, help="Filtered mass spectra file.")
16 parser.add_argument("-normalise_intensities", action='store_true',
17 help="Normalize intensities of peaks (and losses) to unit height.")
18 parser.add_argument("-default_filters", action='store_true',
19 help="Collection of filters that are considered default and that do no require any (factory) arguments.")
20 parser.add_argument("-clean_metadata", action='store_true',
21 help="Apply all adding and cleaning filters if possible, so that the spectra have canonical metadata.")
22 parser.add_argument("-relative_intensity", action='store_true',
23 help="Keep only peaks within set relative intensity range (keep if to_intensity >= intensity >= from_intensity).")
24 parser.add_argument("--from_intensity", type=float, help="Lower bound for intensity filter")
25 parser.add_argument("--to_intensity", type=float, help="Upper bound for intensity filter")
26 parser.add_argument("-mz_range", action='store_true',
27 help="Keep only peaks between set m/z range (keep if to_mz >= m/z >= from_mz).")
28 parser.add_argument("--from_mz", type=float, help="Lower bound for m/z filter")
29 parser.add_argument("--to_mz", type=float, help="Upper bound for m/z filter")
30 args = parser.parse_args()
31
32 if not (args.normalise_intensities
33 or args.default_filters
34 or args.clean_metadata
35 or args.relative_intensity
36 or args.mz_range):
37 raise ValueError('No filter selected.')
38
39 if args.spectra_format == 'msp':
40 spectra = list(load_from_msp(args.spectra))
41 elif args.queries_format == 'mgf':
42 spectra = list(load_from_mgf(args.spectra))
43 else:
44 raise ValueError(f'File format {args.spectra_format} not supported for mass spectra file.')
45
46 filtered_spectra = []
47 for spectrum in spectra:
48 if args.normalise_intensities:
49 spectrum = normalize_intensities(spectrum)
50
51 if args.default_filters:
52 spectrum = default_filters(spectrum)
53
54 if args.clean_metadata:
55 filters = [add_compound_name, add_precursor_mz, add_fingerprint, add_losses, add_parent_mass,
56 add_retention_index, add_retention_time, clean_compound_name]
57 for metadata_filter in filters:
58 spectrum = metadata_filter(spectrum)
59
60 if args.relative_intensity:
61 spectrum = select_by_relative_intensity(spectrum, args.from_intensity, args.to_intensity)
62
63 if args.mz_range:
64 spectrum = select_by_mz(spectrum, args.from_mz, args.to_mz)
65
66 filtered_spectra.append(spectrum)
67
68 if args.spectra_format == 'msp':
69 save_as_msp(filtered_spectra, args.output)
70 else:
71 save_as_mgf(filtered_spectra, args.output)
72
73 return 0
74
75
76 if __name__ == "__main__":
77 main(argv=sys.argv[1:])