Mercurial > repos > recetox > matchms

annotate matchms_similarity_wrapper.py @ 4:ba5e9bd05d5b draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5661cf2406e0616d7b2f4bee1b57ec43716088de
author recetox
date Tue, 18 Oct 2022 11:00:55 +0000
parents 9f8532c99845
children
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1 import argparse
30e680e555d4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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2 import sys
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4 import numpy as np
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5 from matchms import calculate_scores
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6 from matchms.importing import load_from_mgf, load_from_msp
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f680068b7863 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit ca44513d50b29a4706e2a2db96c23ef6688b7c2d
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7 from matchms.similarity import CosineGreedy, CosineHungarian, MetadataMatch, ModifiedCosine, NeutralLossesCosine
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10 def convert_precursor_mz(spectrum):
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11 """
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12 Check the presence of precursor m/z since it is needed for ModifiedCosine similarity metric. Convert to float if
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13 needed, raise error if missing.
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14 """
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16 if "precursor_mz" in spectrum.metadata:
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17 metadata = spectrum.metadata
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18 metadata["precursor_mz"] = float(metadata["precursor_mz"])
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19 spectrum.metadata = metadata
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20 return spectrum
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21 else:
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22 raise ValueError("Precursor_mz missing. Apply 'add_precursor_mz' filter first.")
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25 def main(argv):
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26 parser = argparse.ArgumentParser(description="Compute MSP similarity scores")
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27 parser.add_argument("-r", dest="ri_tolerance", type=float, help="Use RI filtering with given tolerance.")
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28 parser.add_argument("-s", dest="symmetric", action='store_true', help="Computation is symmetric.")
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29 parser.add_argument("--ref", dest="references_filename", type=str, help="Path to reference spectra library.")
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30 parser.add_argument("--ref_format", dest="references_format", type=str, help="Reference spectra library file format.")
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31 parser.add_argument("queries_filename", type=str, help="Path to query spectra.")
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32 parser.add_argument("queries_format", type=str, help="Query spectra file format.")
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33 parser.add_argument("similarity_metric", type=str, help='Metric to use for matching.')
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34 parser.add_argument("tolerance", type=float, help="Tolerance to use for peak matching.")
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35 parser.add_argument("mz_power", type=float, help="The power to raise mz to in the cosine function.")
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36 parser.add_argument("intensity_power", type=float, help="The power to raise intensity to in the cosine function.")
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37 parser.add_argument("output_filename_scores", type=str, help="Path where to store the output .json scores.")
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38 args = parser.parse_args()
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40 if args.queries_format == 'msp':
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41 queries_spectra = list(load_from_msp(args.queries_filename))
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42 elif args.queries_format == 'mgf':
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43 queries_spectra = list(load_from_mgf(args.queries_filename))
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44 else:
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45 raise ValueError(f'File format {args.queries_format} not supported for query spectra.')
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47 if args.symmetric:
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48 reference_spectra = queries_spectra.copy()
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49 else:
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50 if args.references_format == 'msp':
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51 reference_spectra = list(load_from_msp(args.references_filename))
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52 elif args.references_format == 'mgf':
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53 reference_spectra = list(load_from_mgf(args.references_filename))
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54 else:
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55 raise ValueError(f'File format {args.references_format} not supported for reference spectra library.')
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57 if args.similarity_metric == 'CosineGreedy':
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58 similarity_metric = CosineGreedy(args.tolerance, args.mz_power, args.intensity_power)
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59 elif args.similarity_metric == 'CosineHungarian':
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60 similarity_metric = CosineHungarian(args.tolerance, args.mz_power, args.intensity_power)
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61 elif args.similarity_metric == 'ModifiedCosine':
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62 similarity_metric = ModifiedCosine(args.tolerance, args.mz_power, args.intensity_power)
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63 reference_spectra = list(map(convert_precursor_mz, reference_spectra))
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64 queries_spectra = list(map(convert_precursor_mz, queries_spectra))
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65 elif args.similarity_metric == 'NeutralLossesCosine':
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66 similarity_metric = NeutralLossesCosine(args.tolerance, args.mz_power, args.intensity_power)
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67 reference_spectra = list(map(convert_precursor_mz, reference_spectra))
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68 queries_spectra = list(map(convert_precursor_mz, queries_spectra))
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69 else:
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70 return -1
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72 print("Calculating scores...")
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73 scores = calculate_scores(
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74 references=reference_spectra,
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75 queries=queries_spectra,
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76 similarity_function=similarity_metric,
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77 is_symmetric=args.symmetric
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78 )
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80 if args.ri_tolerance is not None:
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81 print("RI filtering with tolerance ", args.ri_tolerance)
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82 ri_matches = calculate_scores(reference_spectra, queries_spectra, MetadataMatch("retention_index", "difference", args.ri_tolerance)).scores
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83 scores._scores["score"] = np.where(ri_matches, scores.scores["score"], 0.0)
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84
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85 write_outputs(args, scores)
30e680e555d4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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86 return 0
30e680e555d4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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87
30e680e555d4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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88
30e680e555d4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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89 def write_outputs(args, scores):
4
ba5e9bd05d5b planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5661cf2406e0616d7b2f4bee1b57ec43716088de
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90 """Write Scores to json file."""
0
30e680e555d4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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91 print("Storing outputs...")
4
ba5e9bd05d5b planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5661cf2406e0616d7b2f4bee1b57ec43716088de
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92 scores.to_json(args.output_filename_scores)
0
30e680e555d4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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93
30e680e555d4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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94
30e680e555d4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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95 if __name__ == "__main__":
30e680e555d4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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96 main(argv=sys.argv[1:])
30e680e555d4 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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97 pass