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annotate matchms_split.py @ 21:500f473df7e4 draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 8db07edd3b0d2ff778036dec410027ad58365488
author recetox
date Mon, 15 Jul 2024 07:59:51 +0000
parents 114617e6ad33
children 7676700d7c4f
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169c72b2ce79 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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1 import argparse
169c72b2ce79 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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2 import itertools
169c72b2ce79 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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3 import os
169c72b2ce79 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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5 import matchms
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169c72b2ce79 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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6 from matchms.exporting import save_as_msp
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7 from matchms.importing import load_from_msp
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10 matchms.Metadata.set_key_replacements({})
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169c72b2ce79 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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13 def make_outdir(outdir: str):
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14 """Create destination directory.
169c72b2ce79 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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169c72b2ce79 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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16 Args:
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17 outdir (str): Path to destination directory where split spectra files are generated.
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18 """
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19 return os.mkdir(outdir)
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22 def write_spectra(spectra, outdir):
169c72b2ce79 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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23 """Generates MSP files of individual spectra.
169c72b2ce79 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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25 Args:
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26 spectra (List[Spectrum]): Spectra to write to file
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27 outdir (str): Path to destination directory.
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28 """
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29 for i in range(len(spectra)):
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30 save_as_msp(spectra[i], os.path.join(outdir, f"{i}.msp"))
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33 def split_round_robin(iterable, num_chunks):
169c72b2ce79 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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34 chunks = [list() for _ in range(num_chunks)]
169c72b2ce79 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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35 index = itertools.cycle(range(num_chunks))
169c72b2ce79 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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36 for value in iterable:
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37 chunks[next(index)].append(value)
169c72b2ce79 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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38 chunks = filter(lambda x: len(x) > 0, chunks)
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39 return chunks
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42 listarg = argparse.ArgumentParser()
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43 listarg.add_argument('--filename', type=str)
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44 listarg.add_argument('--method', type=str)
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45 listarg.add_argument('--outdir', type=str)
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46 listarg.add_argument('--parameter', type=int)
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47 args = listarg.parse_args()
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48 outdir = args.outdir
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49 filename = args.filename
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50 method = args.method
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51 parameter = args.parameter
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54 if __name__ == "__main__":
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55 spectra = load_from_msp(filename, metadata_harmonization=False)
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56 make_outdir(outdir)
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58 if method == "one-per-file":
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59 write_spectra(list(spectra), outdir)
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60 else:
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61 if method == "chunk-size":
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62 chunks = iter(lambda: list(itertools.islice(spectra, parameter)), [])
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63 elif method == "num-chunks":
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64 chunks = split_round_robin(spectra, parameter)
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65 for i, x in enumerate(chunks):
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66 save_as_msp(x, os.path.join(outdir, f"chunk_{i}.msp"))