Mercurial > repos > recetox > matchms

annotate matchms_similarity_wrapper.py @ 10:c3dd958cc4a5 draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
author recetox
date Fri, 28 Jan 2022 16:22:06 +0000
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children ba9410f612bc
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10
c3dd958cc4a5 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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1 import argparse
c3dd958cc4a5 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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2 import sys
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3
c3dd958cc4a5 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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4 from matchms import calculate_scores
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5 from matchms.importing import load_from_mgf, load_from_msp
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6 from matchms.similarity import (
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7 CosineGreedy,
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8 CosineHungarian,
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9 ModifiedCosine,
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10 )
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11 from pandas import DataFrame
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13
c3dd958cc4a5 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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14 def convert_precursor_mz(spectrum):
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15 """
c3dd958cc4a5 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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16 Check the presence of precursor m/z since it is needed for ModifiedCosine similarity metric. Convert to float if
c3dd958cc4a5 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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17 needed, raise error if missing.
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18 """
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19
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20 if "precursor_mz" in spectrum.metadata:
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21 metadata = spectrum.metadata
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22 metadata["precursor_mz"] = float(metadata["precursor_mz"])
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23 spectrum.metadata = metadata
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24 return spectrum
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25 else:
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26 raise ValueError("Precursor_mz missing. Apply 'add_precursor_mz' filter first.")
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27
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29 def main(argv):
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30 parser = argparse.ArgumentParser(description="Compute MSP similarity scores")
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31 parser.add_argument("-s", dest="symmetric", action='store_true', help="Computation is symmetric.")
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32 parser.add_argument("--ref", dest="references_filename", type=str, help="Path to reference spectra library.")
c3dd958cc4a5 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
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33 parser.add_argument("--ref_format", dest="references_format", type=str, help="Reference spectra library file format.")
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34 parser.add_argument("queries_filename", type=str, help="Path to query spectra.")
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35 parser.add_argument("queries_format", type=str, help="Query spectra file format.")
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36 parser.add_argument("similarity_metric", type=str, help='Metric to use for matching.')
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37 parser.add_argument("tolerance", type=float, help="Tolerance to use for peak matching.")
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38 parser.add_argument("mz_power", type=float, help="The power to raise mz to in the cosine function.")
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39 parser.add_argument("intensity_power", type=float, help="The power to raise intensity to in the cosine function.")
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40 parser.add_argument("output_filename_scores", type=str, help="Path where to store the output .tsv scores.")
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41 parser.add_argument("output_filename_matches", type=str, help="Path where to store the output .tsv matches.")
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42 args = parser.parse_args()
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43
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44 if args.queries_format == 'msp':
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45 queries_spectra = list(load_from_msp(args.queries_filename))
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46 elif args.queries_format == 'mgf':
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47 queries_spectra = list(load_from_mgf(args.queries_filename))
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48 else:
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49 raise ValueError(f'File format {args.queries_format} not supported for query spectra.')
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50
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51 if args.symmetric:
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52 reference_spectra = []
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53 else:
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54 if args.references_format == 'msp':
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55 reference_spectra = list(load_from_msp(args.references_filename))
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56 elif args.references_format == 'mgf':
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57 reference_spectra = list(load_from_mgf(args.references_filename))
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58 else:
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59 raise ValueError(f'File format {args.references_format} not supported for reference spectra library.')
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60
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61 if args.similarity_metric == 'CosineGreedy':
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62 similarity_metric = CosineGreedy(args.tolerance, args.mz_power, args.intensity_power)
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63 elif args.similarity_metric == 'CosineHungarian':
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64 similarity_metric = CosineHungarian(args.tolerance, args.mz_power, args.intensity_power)
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65 elif args.similarity_metric == 'ModifiedCosine':
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66 similarity_metric = ModifiedCosine(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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71
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72 print("Calculating scores...")
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73 scores = calculate_scores(
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74 references=queries_spectra if args.symmetric else 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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79
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80 write_outputs(args, scores)
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81 return 0
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82
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83
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84 def write_outputs(args, scores):
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85 print("Storing outputs...")
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86 query_names = [spectra.metadata['name'] for spectra in scores.queries]
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87 reference_names = [spectra.metadata['name'] for spectra in scores.references]
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88
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89 # Write scores to dataframe
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90 dataframe_scores = DataFrame(data=[entry["score"] for entry in scores.scores], index=reference_names, columns=query_names)
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91 dataframe_scores.to_csv(args.output_filename_scores, sep='\t')
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92
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93 # Write number of matches to dataframe
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94 dataframe_matches = DataFrame(data=[entry["matches"] for entry in scores.scores], index=reference_names, columns=query_names)
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95 dataframe_matches.to_csv(args.output_filename_matches, sep='\t')
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96
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97
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98 if __name__ == "__main__":
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99 main(argv=sys.argv[1:])
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100 pass