annotate matchms_split.py @ 17:3370f5b08d19 draft

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f14275bfdc2caa760d71d307ca1803eab1adde76

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:
        outdir (str): Path to destination directory where split spectra files are generated.
    """
    return os.mkdir(outdir)


def write_spectra(spectra, outdir):
    """Generates MSP files of individual spectra.

    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))
    for value in iterable:
        chunks[next(index)].append(value)
    chunks = filter(lambda x: len(x) > 0, chunks)
    return chunks


listarg = argparse.ArgumentParser()
listarg.add_argument('--filename', type=str)
listarg.add_argument('--method', type=str)
listarg.add_argument('--outdir', type=str)
listarg.add_argument('--parameter', type=int)
args = listarg.parse_args()
outdir = args.outdir
filename = args.filename
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:
        if method == "chunk-size":
            chunks = iter(lambda: list(itertools.islice(spectra, parameter)), [])
        elif method == "num-chunks":
            chunks = split_round_robin(spectra, parameter)
        for i, x in enumerate(chunks):
            save_as_msp(x, os.path.join(outdir, f"chunk_{i}.msp"))