Mercurial > repos > recetox > matchms_remove_spectra

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a57d984a9850c1faa44b6948981eb1303881ba9c
author recetox
date Thu, 14 Aug 2025 12:39:28 +0000
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80df426e7e47 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 113433b8b9790405c2c5d054aee4a29a21b77dc7
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1 import argparse
80df426e7e47 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 113433b8b9790405c2c5d054aee4a29a21b77dc7
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2 import itertools
80df426e7e47 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 113433b8b9790405c2c5d054aee4a29a21b77dc7
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3 import os
80df426e7e47 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 113433b8b9790405c2c5d054aee4a29a21b77dc7
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c7be8e58a6af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a57d984a9850c1faa44b6948981eb1303881ba9c
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5 from matchms import Metadata
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80df426e7e47 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 113433b8b9790405c2c5d054aee4a29a21b77dc7
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6 from matchms.exporting import save_as_msp
80df426e7e47 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 113433b8b9790405c2c5d054aee4a29a21b77dc7
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7 from matchms.importing import load_from_msp
80df426e7e47 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 113433b8b9790405c2c5d054aee4a29a21b77dc7
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8
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c7be8e58a6af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a57d984a9850c1faa44b6948981eb1303881ba9c
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9 Metadata.set_key_replacements({})
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12 def make_outdir(outdir: str):
80df426e7e47 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 113433b8b9790405c2c5d054aee4a29a21b77dc7
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13 """Create destination directory.
80df426e7e47 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 113433b8b9790405c2c5d054aee4a29a21b77dc7
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80df426e7e47 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 113433b8b9790405c2c5d054aee4a29a21b77dc7
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15 Args:
80df426e7e47 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 113433b8b9790405c2c5d054aee4a29a21b77dc7
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16 outdir (str): Path to destination directory where split spectra files are generated.
80df426e7e47 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 113433b8b9790405c2c5d054aee4a29a21b77dc7
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17 """
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18 return os.mkdir(outdir)
80df426e7e47 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 113433b8b9790405c2c5d054aee4a29a21b77dc7
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21 def write_spectra(spectra, outdir):
80df426e7e47 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 113433b8b9790405c2c5d054aee4a29a21b77dc7
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22 """Generates MSP files of individual spectra.
80df426e7e47 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 113433b8b9790405c2c5d054aee4a29a21b77dc7
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24 Args:
80df426e7e47 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 113433b8b9790405c2c5d054aee4a29a21b77dc7
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25 spectra (List[Spectrum]): Spectra to write to file
80df426e7e47 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 113433b8b9790405c2c5d054aee4a29a21b77dc7
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26 outdir (str): Path to destination directory.
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27 """
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28 for i in range(len(spectra)):
80df426e7e47 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 113433b8b9790405c2c5d054aee4a29a21b77dc7
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29 save_as_msp(spectra[i], os.path.join(outdir, f"{i}.msp"))
80df426e7e47 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 113433b8b9790405c2c5d054aee4a29a21b77dc7
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32 def split_round_robin(iterable, num_chunks):
80df426e7e47 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 113433b8b9790405c2c5d054aee4a29a21b77dc7
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33 chunks = [list() for _ in range(num_chunks)]
80df426e7e47 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 113433b8b9790405c2c5d054aee4a29a21b77dc7
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34 index = itertools.cycle(range(num_chunks))
80df426e7e47 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 113433b8b9790405c2c5d054aee4a29a21b77dc7
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35 for value in iterable:
80df426e7e47 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 113433b8b9790405c2c5d054aee4a29a21b77dc7
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36 chunks[next(index)].append(value)
80df426e7e47 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 113433b8b9790405c2c5d054aee4a29a21b77dc7
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37 chunks = filter(lambda x: len(x) > 0, chunks)
80df426e7e47 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 113433b8b9790405c2c5d054aee4a29a21b77dc7
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38 return chunks
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41 listarg = argparse.ArgumentParser()
80df426e7e47 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 113433b8b9790405c2c5d054aee4a29a21b77dc7
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42 listarg.add_argument('--filename', type=str)
80df426e7e47 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 113433b8b9790405c2c5d054aee4a29a21b77dc7
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43 listarg.add_argument('--method', type=str)
80df426e7e47 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 113433b8b9790405c2c5d054aee4a29a21b77dc7
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44 listarg.add_argument('--outdir', type=str)
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c7be8e58a6af planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit a57d984a9850c1faa44b6948981eb1303881ba9c
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45 listarg.add_argument('--parameter', type=int, required=False)
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46 args = listarg.parse_args()
80df426e7e47 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 113433b8b9790405c2c5d054aee4a29a21b77dc7
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47 outdir = args.outdir
80df426e7e47 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 113433b8b9790405c2c5d054aee4a29a21b77dc7
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48 filename = args.filename
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49 method = args.method
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50 parameter = args.parameter
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53 if __name__ == "__main__":
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54 spectra = load_from_msp(filename, metadata_harmonization=False)
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55 make_outdir(outdir)
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57 if method == "one-per-file":
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58 write_spectra(list(spectra), outdir)
80df426e7e47 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 113433b8b9790405c2c5d054aee4a29a21b77dc7
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59 else:
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60 if method == "chunk-size":
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61 chunks = iter(lambda: list(itertools.islice(spectra, parameter)), [])
80df426e7e47 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 113433b8b9790405c2c5d054aee4a29a21b77dc7
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62 elif method == "num-chunks":
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63 chunks = split_round_robin(spectra, parameter)
80df426e7e47 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 113433b8b9790405c2c5d054aee4a29a21b77dc7
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64 for i, x in enumerate(chunks):
80df426e7e47 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 113433b8b9790405c2c5d054aee4a29a21b77dc7
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65 save_as_msp(x, os.path.join(outdir, f"chunk_{i}.msp"))