comparison matchms_filtering_wrapper.py @ 20:86d265d2a334 draft

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 113433b8b9790405c2c5d054aee4a29a21b77dc7

19:c5076cc15e8c

import argparse
import sys

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.filtering.filter_utils.smile_inchi_inchikey_conversions import is_valid_inchi, is_valid_smiles
from matchms.importing import load_from_mgf, load_from_msp


def require_key(spectrum, key, function):
    value = spectrum.get(key)
    if function(value):
        return spectrum

    return None


def main(argv):
    parser = argparse.ArgumentParser(description="Compute MSP similarity scores")
    parser.add_argument("--spectra", type=str, required=True, help="Mass spectra file to be filtered.")

    parser.add_argument("--to_intensity", type=float, help="Upper bound for intensity filter")
    parser.add_argument("-mz_range", action='store_true',
                        help="Keep only peaks between set m/z range (keep if to_mz >= m/z >= from_mz).")
    parser.add_argument("--from_mz", type=float, help="Lower bound for m/z  filter")
    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.")

    if not (args.normalise_intensities
            or args.default_filters
            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':

        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", is_valid_smiles)

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

        if spectrum is not None:
            filtered_spectra.append(spectrum)

    if args.spectra_format == 'msp':
        save_as_msp(filtered_spectra, args.output)

20:86d265d2a334

import argparse
import sys

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 main(argv):
    parser = argparse.ArgumentParser(description="Compute MSP similarity scores")
    parser.add_argument("--spectra", type=str, required=True, help="Mass spectra file to be filtered.")

    parser.add_argument("--to_intensity", type=float, help="Upper bound for intensity filter")
    parser.add_argument("-mz_range", action='store_true',
                        help="Keep only peaks between set m/z range (keep if to_mz >= m/z >= from_mz).")
    parser.add_argument("--from_mz", type=float, help="Lower bound for m/z  filter")
    parser.add_argument("--to_mz", type=float, help="Upper bound for m/z  filter")
    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.")

    if not (args.normalise_intensities
            or args.default_filters
            or args.clean_metadata
            or args.relative_intensity
            or args.mz_range
            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':

        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 spectrum is not None:
            filtered_spectra.append(spectrum)

    if args.spectra_format == 'msp':
        save_as_msp(filtered_spectra, args.output)