Mercurial > repos > recetox > matchms_formatter

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