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annotate msp_merge.py @ 0:c2862090e321 draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge commit 51ff658aecc8738ef57af512229cd155763082d1
author recetox
date Thu, 19 May 2022 12:04:25 +0000
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c2862090e321 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge commit 51ff658aecc8738ef57af512229cd155763082d1
recetox
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1 import argparse
c2862090e321 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge commit 51ff658aecc8738ef57af512229cd155763082d1
recetox
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2 from itertools import chain
c2862090e321 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge commit 51ff658aecc8738ef57af512229cd155763082d1
recetox
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3 from typing import List
c2862090e321 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge commit 51ff658aecc8738ef57af512229cd155763082d1
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c2862090e321 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge commit 51ff658aecc8738ef57af512229cd155763082d1
recetox
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5 from matchms import Spectrum
c2862090e321 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge commit 51ff658aecc8738ef57af512229cd155763082d1
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6 from matchms.exporting import save_as_msp
c2862090e321 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge commit 51ff658aecc8738ef57af512229cd155763082d1
recetox
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7 from matchms.importing import load_from_msp
c2862090e321 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge commit 51ff658aecc8738ef57af512229cd155763082d1
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c2862090e321 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge commit 51ff658aecc8738ef57af512229cd155763082d1
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c2862090e321 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge commit 51ff658aecc8738ef57af512229cd155763082d1
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10 def read_spectra(filenames: str) -> List[Spectrum]:
c2862090e321 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge commit 51ff658aecc8738ef57af512229cd155763082d1
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11 """Read spectra from files.
c2862090e321 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge commit 51ff658aecc8738ef57af512229cd155763082d1
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c2862090e321 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge commit 51ff658aecc8738ef57af512229cd155763082d1
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13 Args:
c2862090e321 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge commit 51ff658aecc8738ef57af512229cd155763082d1
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14 filenames (str): Paths to MSP files from which to load each spectrum.
c2862090e321 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge commit 51ff658aecc8738ef57af512229cd155763082d1
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c2862090e321 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge commit 51ff658aecc8738ef57af512229cd155763082d1
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16 Returns:
c2862090e321 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge commit 51ff658aecc8738ef57af512229cd155763082d1
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17 List[Spectrum]: Spectra stored in the file.
c2862090e321 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge commit 51ff658aecc8738ef57af512229cd155763082d1
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18 """
c2862090e321 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge commit 51ff658aecc8738ef57af512229cd155763082d1
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19 spectra = list(chain(*[load_from_msp(file) for file in filenames]))
c2862090e321 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge commit 51ff658aecc8738ef57af512229cd155763082d1
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20 return spectra
c2862090e321 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge commit 51ff658aecc8738ef57af512229cd155763082d1
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c2862090e321 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge commit 51ff658aecc8738ef57af512229cd155763082d1
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c2862090e321 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge commit 51ff658aecc8738ef57af512229cd155763082d1
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23 listarg = argparse.ArgumentParser()
c2862090e321 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge commit 51ff658aecc8738ef57af512229cd155763082d1
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24 listarg.add_argument('--filenames', nargs='+', type=str)
c2862090e321 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge commit 51ff658aecc8738ef57af512229cd155763082d1
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25 listarg.add_argument('--outfilename', type=str)
c2862090e321 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge commit 51ff658aecc8738ef57af512229cd155763082d1
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26 args = listarg.parse_args()
c2862090e321 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge commit 51ff658aecc8738ef57af512229cd155763082d1
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c2862090e321 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge commit 51ff658aecc8738ef57af512229cd155763082d1
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28 if __name__ == "__main__":
c2862090e321 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge commit 51ff658aecc8738ef57af512229cd155763082d1
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29 spectra = read_spectra(args.filenames)
c2862090e321 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msp_merge commit 51ff658aecc8738ef57af512229cd155763082d1
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30 save_as_msp(spectra, args.outfilename)