Mercurial > repos > recetox > matchms_formatter

annotate matchms_filtering_wrapper.py @ 22:f76a397afbe1 draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b797ce0fea5cb3d9a0cf0ec31a21f9b73f112b4e
author recetox
date Mon, 15 Jan 2024 12:25:49 +0000
parents 23d4bc72c505
children 8bd942dcf1ad
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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
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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
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7 from matchms.filtering import default_filters, normalize_intensities, reduce_to_number_of_peaks, select_by_mz, \
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8 select_by_relative_intensity
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9 from matchms.filtering.filter_utils.derive_precursor_mz_and_parent_mass import derive_precursor_mz_from_parent_mass
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10 from matchms.filtering.filter_utils.smile_inchi_inchikey_conversions import is_valid_inchi, is_valid_smiles
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11 from matchms.importing import load_from_mgf, load_from_msp
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14 def require_key(spectrum, key, function):
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15 value = spectrum.get(key)
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16 if function(value):
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17 return spectrum
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19 return None
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22 def main(argv):
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23 parser = argparse.ArgumentParser(description="Compute MSP similarity scores")
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24 parser.add_argument("--spectra", type=str, required=True, help="Mass spectra file to be filtered.")
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25 parser.add_argument("--spectra_format", type=str, required=True, help="Format of spectra file.")
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26 parser.add_argument("--output", type=str, required=True, help="Filtered mass spectra file.")
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27 parser.add_argument("-normalise_intensities", action='store_true',
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28 help="Normalize intensities of peaks (and losses) to unit height.")
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29 parser.add_argument("-default_filters", action='store_true',
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30 help="Collection of filters that are considered default and that do no require any (factory) arguments.")
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31 parser.add_argument("-clean_metadata", action='store_true',
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32 help="Apply all adding and cleaning filters if possible, so that the spectra have canonical metadata.")
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33 parser.add_argument("-relative_intensity", action='store_true',
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34 help="Keep only peaks within set relative intensity range (keep if to_intensity >= intensity >= from_intensity).")
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35 parser.add_argument("--from_intensity", type=float, help="Lower bound for intensity filter")
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36 parser.add_argument("--to_intensity", type=float, help="Upper bound for intensity filter")
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37 parser.add_argument("-mz_range", action='store_true',
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38 help="Keep only peaks between set m/z range (keep if to_mz >= m/z >= from_mz).")
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39 parser.add_argument("--from_mz", type=float, help="Lower bound for m/z filter")
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40 parser.add_argument("--to_mz", type=float, help="Upper bound for m/z filter")
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41 parser.add_argument("-require_smiles", action='store_true',
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42 help="Remove spectra that does not contain SMILES.")
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43 parser.add_argument("-require_inchi", action='store_true',
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44 help="Remove spectra that does not contain INCHI.")
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45 parser.add_argument("-derive_precursor_mz_from_parent_mass", action='store_true',
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46 help="Derives the precursor_mz from the parent mass and adduct or charge.")
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47 parser.add_argument("--estimate_from_adduct", type=str, help="estimate from adduct.")
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48 parser.add_argument("-reduce_to_top_n_peaks", action='store_true',
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49 help="reduce to top n peaks filter.")
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50 parser.add_argument("--n_max", type=int, help="Maximum number of peaks. Remove peaks if more peaks are found.")
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51 args = parser.parse_args()
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52
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53 if not (args.normalise_intensities
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54 or args.default_filters
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55 or args.clean_metadata
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56 or args.relative_intensity
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57 or args.mz_range
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58 or args.require_smiles
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59 or args.require_inchi
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60 or args.derive_precursor_mz_from_parent_mass
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61 or args.reduce_to_top_n_peaks):
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62 raise ValueError('No filter selected.')
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63
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64 if args.spectra_format == 'msp':
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65 spectra = list(load_from_msp(args.spectra))
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66 elif args.queries_format == 'mgf':
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67 spectra = list(load_from_mgf(args.spectra))
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68 else:
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69 raise ValueError(f'File format {args.spectra_format} not supported for mass spectra file.')
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70
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71 filtered_spectra = []
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72 for spectrum in spectra:
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73 if args.normalise_intensities:
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74 spectrum = normalize_intensities(spectrum)
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75
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76 if args.default_filters:
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77 spectrum = default_filters(spectrum)
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78
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79 if args.clean_metadata:
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80 filters = [add_compound_name, add_precursor_mz, add_fingerprint, add_losses, add_parent_mass,
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81 add_retention_index, add_retention_time, clean_compound_name]
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82 for metadata_filter in filters:
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83 spectrum = metadata_filter(spectrum)
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84
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85 if args.relative_intensity:
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86 spectrum = select_by_relative_intensity(spectrum, args.from_intensity, args.to_intensity)
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87
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88 if args.mz_range:
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89 spectrum = select_by_mz(spectrum, args.from_mz, args.to_mz)
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90
11
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91 if args.reduce_to_top_n_peaks:
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92 spectrum = reduce_to_number_of_peaks(spectrum_in=spectrum, n_max=args.n_max)
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93
21
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94 if args.derive_precursor_mz_from_parent_mass:
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95 spectrum.set("parent_mass", float(spectrum.get('parent_mass')))
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96 precursor_mz = derive_precursor_mz_from_parent_mass(spectrum, args.estimate_from_adduct)
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97 spectrum.set("precursor_mz", precursor_mz)
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98
11
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99 if args.require_smiles and spectrum is not None:
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100 spectrum = require_key(spectrum, "smiles", is_valid_smiles)
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101
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102 if args.require_inchi and spectrum is not None:
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103 spectrum = require_key(spectrum, "inchi", is_valid_inchi)
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104
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105 if spectrum is not None:
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106 filtered_spectra.append(spectrum)
10
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107
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108 if args.spectra_format == 'msp':
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109 save_as_msp(filtered_spectra, args.output)
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110 else:
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111 save_as_mgf(filtered_spectra, args.output)
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112
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113 return 0
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114
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115
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116 if __name__ == "__main__":
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117 main(argv=sys.argv[1:])