comparison matchms_filtering_wrapper.py @ 8:f30b53a817af draft

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 98223db312c30b0e121a1422a9534a3db3fbf0c0

7:9782eb7a22b7

from matchms.exporting import save_as_mgf, save_as_msp
from matchms.filtering import add_compound_name, add_fingerprint, add_losses, add_parent_mass, add_precursor_mz,\
    add_retention_index, add_retention_time, clean_compound_name
from matchms.filtering import default_filters, normalize_intensities, reduce_to_number_of_peaks, select_by_mz, \
    select_by_relative_intensity
from matchms.importing import load_from_mgf, load_from_msp


def require_key(spectrum, key):
    if spectrum.get(key):

    parser.add_argument("--to_mz", type=float, help="Upper bound for m/z  filter")
    parser.add_argument("-require_smiles", action='store_true',
                        help="Remove spectra that does not contain SMILES.")
    parser.add_argument("-require_inchi", action='store_true',
                        help="Remove spectra that does not contain INCHI.")
    parser.add_argument("-reduce_to_top_n_peaks", action='store_true',
                        help="reduce to top n peaks filter.")
    parser.add_argument("--n_max", type=int, help="Maximum number of peaks. Remove peaks if more peaks are found.")
    args = parser.parse_args()

            or args.clean_metadata
            or args.relative_intensity
            or args.mz_range
            or args.require_smiles
            or args.require_inchi
            or args.reduce_to_top_n_peaks):
        raise ValueError('No filter selected.')

    if args.spectra_format == 'msp':
        spectra = list(load_from_msp(args.spectra))

            spectrum = select_by_mz(spectrum, args.from_mz, args.to_mz)

        if args.reduce_to_top_n_peaks:
            spectrum = reduce_to_number_of_peaks(spectrum_in=spectrum, n_max=args.n_max)

        if args.require_smiles and spectrum is not None:
            spectrum = require_key(spectrum, "smiles")

        if args.require_inchi and spectrum is not None:
            spectrum = require_key(spectrum, "inchi")

8:f30b53a817af

from matchms.exporting import save_as_mgf, save_as_msp
from matchms.filtering import add_compound_name, add_fingerprint, add_losses, add_parent_mass, add_precursor_mz,\
    add_retention_index, add_retention_time, clean_compound_name
from matchms.filtering import default_filters, normalize_intensities, reduce_to_number_of_peaks, select_by_mz, \
    select_by_relative_intensity
from matchms.filtering.filter_utils.derive_precursor_mz_and_parent_mass import derive_precursor_mz_from_parent_mass
from matchms.importing import load_from_mgf, load_from_msp


def require_key(spectrum, key):
    if spectrum.get(key):

    parser.add_argument("--to_mz", type=float, help="Upper bound for m/z  filter")
    parser.add_argument("-require_smiles", action='store_true',
                        help="Remove spectra that does not contain SMILES.")
    parser.add_argument("-require_inchi", action='store_true',
                        help="Remove spectra that does not contain INCHI.")
    parser.add_argument("-derive_precursor_mz_from_parent_mass", action='store_true',
                        help="Derives the precursor_mz from the parent mass and adduct or charge.")
    parser.add_argument("--estimate_from_adduct", type=str, help="estimate from adduct.")
    parser.add_argument("-reduce_to_top_n_peaks", action='store_true',
                        help="reduce to top n peaks filter.")
    parser.add_argument("--n_max", type=int, help="Maximum number of peaks. Remove peaks if more peaks are found.")
    args = parser.parse_args()

            or args.clean_metadata
            or args.relative_intensity
            or args.mz_range
            or args.require_smiles
            or args.require_inchi
            or args.derive_precursor_mz_from_parent_mass
            or args.reduce_to_top_n_peaks):
        raise ValueError('No filter selected.')

    if args.spectra_format == 'msp':
        spectra = list(load_from_msp(args.spectra))

            spectrum = select_by_mz(spectrum, args.from_mz, args.to_mz)

        if args.reduce_to_top_n_peaks:
            spectrum = reduce_to_number_of_peaks(spectrum_in=spectrum, n_max=args.n_max)

        if args.derive_precursor_mz_from_parent_mass:
            spectrum.set("parent_mass", float(spectrum.get('parent_mass')))
            precursor_mz = derive_precursor_mz_from_parent_mass(spectrum, args.estimate_from_adduct)
            spectrum.set("precursor_mz", precursor_mz)

        if args.require_smiles and spectrum is not None:
            spectrum = require_key(spectrum, "smiles")

        if args.require_inchi and spectrum is not None:
            spectrum = require_key(spectrum, "inchi")