comparison matchms_split.py @ 10:91b4b0c9a384 draft

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit da193865f41a3a840ecc4ba0afab1d358554998a

9:05a7fc94e66c

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.

    Args:
        spectra (list): List of individual spectra.

    Returns:
        List[str]: List with 'compoud_name' of individual spectra.
    """
    return [x.get("compound_name") for x in spectra]


def make_outdir(outdir: str):
    """Create destination directory.

    Args:
        spectra (List[Spectrum]): Spectra to write to file
        outdir   (str): Path to destination directory.
    """
    names = get_spectra_names(spectra)
    for i in range(len(spectra)):
        outpath = assemble_outpath(names[i], outdir)
        save_as_msp(spectra[i], outpath)


def assemble_outpath(name, outdir):
    """Filter special chracteres from name.

    Args:
        name   (str): Name to be filetered.
        outdir (str): Path to destination directory.
    """
    filename = ''.join(filter(str.isalnum, name))
    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))

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:

10:91b4b0c9a384

import argparse
import itertools
import os

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


matchms.Metadata.set_key_replacements({})


def make_outdir(outdir: str):
    """Create destination directory.

    Args:
        spectra (List[Spectrum]): Spectra to write to file
        outdir   (str): Path to destination directory.
    """
    for i in range(len(spectra)):
        save_as_msp(spectra[i], os.path.join(outdir, f"{i}.msp"))


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

method = args.method
parameter = args.parameter


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

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