Mercurial > repos > recetox > matchms_fingerprint_similarity
view matchms_split.py @ 12:99da744050b7 draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f14275bfdc2caa760d71d307ca1803eab1adde76
author | recetox |
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date | Wed, 13 Mar 2024 10:14:23 +0000 |
parents | 5be32c7ce669 |
children |
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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"))