Mercurial > repos > recetox > matchms_filtering

comparison matchms_filtering_wrapper.py @ 14:da15e8ea3b28 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 12:29:06 +0000
parents ca5a8db023e1
children 86d265d2a334
comparison
equal deleted inserted replaced
13:ca5a8db023e1 14:da15e8ea3b28
5 from matchms.filtering import add_compound_name, add_fingerprint, add_losses, add_parent_mass, add_precursor_mz,\ 5 from matchms.filtering import add_compound_name, add_fingerprint, add_losses, add_parent_mass, add_precursor_mz,\
6 add_retention_index, add_retention_time, clean_compound_name 6 add_retention_index, add_retention_time, clean_compound_name
7 from matchms.filtering import default_filters, normalize_intensities, reduce_to_number_of_peaks, select_by_mz, \ 7 from matchms.filtering import default_filters, normalize_intensities, reduce_to_number_of_peaks, select_by_mz, \
8 select_by_relative_intensity 8 select_by_relative_intensity
9 from matchms.filtering.filter_utils.derive_precursor_mz_and_parent_mass import derive_precursor_mz_from_parent_mass 9 from matchms.filtering.filter_utils.derive_precursor_mz_and_parent_mass import derive_precursor_mz_from_parent_mass
10 from matchms.filtering.filter_utils.smile_inchi_inchikey_conversions import is_valid_inchi, is_valid_smiles
10 from matchms.importing import load_from_mgf, load_from_msp 11 from matchms.importing import load_from_mgf, load_from_msp
11 12
12 13
13 def require_key(spectrum, key): 14 def require_key(spectrum, key, function):
14 if spectrum.get(key): 15 value = spectrum.get(key)
16 if function(value):
15 return spectrum 17 return spectrum
16 18
17 return None 19 return None
18 20
19 21
93 spectrum.set("parent_mass", float(spectrum.get('parent_mass'))) 95 spectrum.set("parent_mass", float(spectrum.get('parent_mass')))
94 precursor_mz = derive_precursor_mz_from_parent_mass(spectrum, args.estimate_from_adduct) 96 precursor_mz = derive_precursor_mz_from_parent_mass(spectrum, args.estimate_from_adduct)
95 spectrum.set("precursor_mz", precursor_mz) 97 spectrum.set("precursor_mz", precursor_mz)
96 98
97 if args.require_smiles and spectrum is not None: 99 if args.require_smiles and spectrum is not None:
98 spectrum = require_key(spectrum, "smiles") 100 spectrum = require_key(spectrum, "smiles", is_valid_smiles)
99 101
100 if args.require_inchi and spectrum is not None: 102 if args.require_inchi and spectrum is not None:
101 spectrum = require_key(spectrum, "inchi") 103 spectrum = require_key(spectrum, "inchi", is_valid_inchi)
102 104
103 if spectrum is not None: 105 if spectrum is not None:
104 filtered_spectra.append(spectrum) 106 filtered_spectra.append(spectrum)
105 107
106 if args.spectra_format == 'msp': 108 if args.spectra_format == 'msp':