Mercurial > repos > recetox > matchms

comparison matchms_similarity_wrapper.py @ 1:f680068b7863 draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit ca44513d50b29a4706e2a2db96c23ef6688b7c2d
author recetox
date Fri, 22 Jul 2022 16:48:21 +0000
parents 30e680e555d4
children 67ed0d4f3724
comparison
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0:30e680e555d4 1:f680068b7863
2 import sys 2 import sys
3 3
4 import numpy as np 4 import numpy as np
5 from matchms import calculate_scores 5 from matchms import calculate_scores
6 from matchms.importing import load_from_mgf, load_from_msp 6 from matchms.importing import load_from_mgf, load_from_msp
7 from matchms.similarity import CosineGreedy, CosineHungarian, MetadataMatch, ModifiedCosine 7 from matchms.similarity import CosineGreedy, CosineHungarian, MetadataMatch, ModifiedCosine, NeutralLossesCosine
8 from pandas import DataFrame 8 from pandas import DataFrame
9 9
10 10
11 def convert_precursor_mz(spectrum): 11 def convert_precursor_mz(spectrum):
12 """ 12 """
62 similarity_metric = CosineHungarian(args.tolerance, args.mz_power, args.intensity_power) 62 similarity_metric = CosineHungarian(args.tolerance, args.mz_power, args.intensity_power)
63 elif args.similarity_metric == 'ModifiedCosine': 63 elif args.similarity_metric == 'ModifiedCosine':
64 similarity_metric = ModifiedCosine(args.tolerance, args.mz_power, args.intensity_power) 64 similarity_metric = ModifiedCosine(args.tolerance, args.mz_power, args.intensity_power)
65 reference_spectra = list(map(convert_precursor_mz, reference_spectra)) 65 reference_spectra = list(map(convert_precursor_mz, reference_spectra))
66 queries_spectra = list(map(convert_precursor_mz, queries_spectra)) 66 queries_spectra = list(map(convert_precursor_mz, queries_spectra))
67 elif args.similarity_metric == 'NeutralLossesCosine':
68 similarity_metric = NeutralLossesCosine(args.tolerance, args.mz_power, args.intensity_power)
69 reference_spectra = list(map(convert_precursor_mz, reference_spectra))
70 queries_spectra = list(map(convert_precursor_mz, queries_spectra))
67 else: 71 else:
68 return -1 72 return -1
69 73
70 print("Calculating scores...") 74 print("Calculating scores...")
71 scores = calculate_scores( 75 scores = calculate_scores(