Mercurial > repos > recetox > matchms_formatter
diff matchms_split.py @ 23:34439ffa6a60 draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit da193865f41a3a840ecc4ba0afab1d358554998a
author | recetox |
---|---|
date | Mon, 05 Feb 2024 10:39:25 +0000 |
parents | 1b09315a3f87 |
children |
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--- a/matchms_split.py Mon Jan 15 12:25:49 2024 +0000 +++ b/matchms_split.py Mon Feb 05 10:39:25 2024 +0000 @@ -1,22 +1,13 @@ import argparse import itertools import os -from typing import List +import matchms 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] +matchms.Metadata.set_key_replacements({}) def make_outdir(outdir: str): @@ -35,23 +26,8 @@ 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 + save_as_msp(spectra[i], os.path.join(outdir, f"{i}.msp")) def split_round_robin(iterable, num_chunks): @@ -76,7 +52,7 @@ if __name__ == "__main__": - spectra = load_from_msp(filename, metadata_harmonization=True) + spectra = load_from_msp(filename, metadata_harmonization=False) make_outdir(outdir) if method == "one-per-file":