comparison matchms_split.py @ 4:0cf68b536cd1 draft

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e

3:9dfcee100f48

import argparse
import itertools
import os
from typing import List

from matchms import Spectrum
from matchms.exporting import save_as_msp
from matchms.importing import load_from_msp


def read_spectra(filename: str) -> List[Spectrum]:
    """Read spectra from file.

    Args:
        filename (str): Path to .msp file from which to load the spectra.

    Returns:
        List[Spectrum]: Spectra contained in the file.
    """
    return list(load_from_msp(filename, True))


def get_spectra_names(spectra: list) -> List[str]:
    """Read the keyword 'compound_name' from a spectra.

    outfile = str(filename) + ".msp"
    outpath = os.path.join(outdir, outfile)
    return outpath


def split_spectra(filename, outdir):
    """Save individual MSP spectra files in the destination directory.

    Args:
        filename (str): MSP file that contains the spectra.
        outdir   (str): Path to destination directory where split spectra files are saved.
    """
    make_outdir(outdir)
    return write_spectra(filename, outdir)


def split_round_robin(iterable, num_chunks):
    chunks = [list() for _ in range(num_chunks)]
    index = itertools.cycle(range(num_chunks))
    for value in iterable:
        chunks[next(index)].append(value)

method = args.method
parameter = args.parameter


if __name__ == "__main__":
    spectra = load_from_msp(filename)
    make_outdir(outdir)

    if method == "one-per-file":
        write_spectra(list(spectra), outdir)
    else:

4:0cf68b536cd1

import argparse
import itertools
import os
from typing import List

from matchms.exporting import save_as_msp
from matchms.importing import load_from_msp


def get_spectra_names(spectra: list) -> List[str]:
    """Read the keyword 'compound_name' from a spectra.

    outfile = str(filename) + ".msp"
    outpath = os.path.join(outdir, outfile)
    return outpath


def split_round_robin(iterable, num_chunks):
    chunks = [list() for _ in range(num_chunks)]
    index = itertools.cycle(range(num_chunks))
    for value in iterable:
        chunks[next(index)].append(value)

method = args.method
parameter = args.parameter


if __name__ == "__main__":
    spectra = load_from_msp(filename, metadata_harmonization=True)
    make_outdir(outdir)

    if method == "one-per-file":
        write_spectra(list(spectra), outdir)
    else: