Mercurial > repos > recetox > matchms_filtering
comparison matchms_filtering_wrapper.py @ 0:3d275fbdf741 draft
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
author | recetox |
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date | Tue, 22 Mar 2022 16:08:03 +0000 |
parents | |
children | 13de8005adba |
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-1:000000000000 | 0:3d275fbdf741 |
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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:]) |