Mercurial > repos > recetox > msp_split

annotate splitMSP.py @ 0:e7825eae651e draft default tip

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msp_split commit 0d9dfeae375a6761b52be79111e228d950e2902e"
author recetox
date Fri, 25 Mar 2022 15:37:27 +0000
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e7825eae651e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msp_split commit 0d9dfeae375a6761b52be79111e228d950e2902e"
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1 import argparse
e7825eae651e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msp_split commit 0d9dfeae375a6761b52be79111e228d950e2902e"
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2 import os
e7825eae651e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msp_split commit 0d9dfeae375a6761b52be79111e228d950e2902e"
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3 from typing import List
e7825eae651e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msp_split commit 0d9dfeae375a6761b52be79111e228d950e2902e"
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e7825eae651e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msp_split commit 0d9dfeae375a6761b52be79111e228d950e2902e"
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5 from matchms import Spectrum
e7825eae651e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msp_split commit 0d9dfeae375a6761b52be79111e228d950e2902e"
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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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e7825eae651e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msp_split commit 0d9dfeae375a6761b52be79111e228d950e2902e"
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e7825eae651e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msp_split commit 0d9dfeae375a6761b52be79111e228d950e2902e"
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10 def read_spectra(filename: str) -> List[Spectrum]:
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11 """Read spectra from file.
e7825eae651e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msp_split commit 0d9dfeae375a6761b52be79111e228d950e2902e"
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e7825eae651e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msp_split commit 0d9dfeae375a6761b52be79111e228d950e2902e"
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13 Args:
e7825eae651e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msp_split commit 0d9dfeae375a6761b52be79111e228d950e2902e"
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14 filename (str): Path to .msp file from which to load the spectra.
e7825eae651e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msp_split commit 0d9dfeae375a6761b52be79111e228d950e2902e"
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e7825eae651e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msp_split commit 0d9dfeae375a6761b52be79111e228d950e2902e"
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16 Returns:
e7825eae651e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msp_split commit 0d9dfeae375a6761b52be79111e228d950e2902e"
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17 List[Spectrum]: Spectra contained in the file.
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18 """
e7825eae651e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msp_split commit 0d9dfeae375a6761b52be79111e228d950e2902e"
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19 return list(load_from_msp(filename, True))
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e7825eae651e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msp_split commit 0d9dfeae375a6761b52be79111e228d950e2902e"
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e7825eae651e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msp_split commit 0d9dfeae375a6761b52be79111e228d950e2902e"
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22 def get_spectra_names(spectra: list) -> List[str]:
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23 """Read the keyword 'compound_name' from a spectra.
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e7825eae651e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msp_split commit 0d9dfeae375a6761b52be79111e228d950e2902e"
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25 Args:
e7825eae651e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msp_split commit 0d9dfeae375a6761b52be79111e228d950e2902e"
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26 spectra (list): List of individual spectra.
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e7825eae651e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msp_split commit 0d9dfeae375a6761b52be79111e228d950e2902e"
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28 Returns:
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29 List[str]: List with 'compoud_name' of individual spectra.
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30 """
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31 return [x.get("compound_name") for x in spectra]
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e7825eae651e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msp_split commit 0d9dfeae375a6761b52be79111e228d950e2902e"
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34 def make_outdir(outdir: str):
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35 """Create destination directory.
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37 Args:
e7825eae651e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msp_split commit 0d9dfeae375a6761b52be79111e228d950e2902e"
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38 outdir (str): Path to destination directory where split spectra files are generated.
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39 """
e7825eae651e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msp_split commit 0d9dfeae375a6761b52be79111e228d950e2902e"
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40 return os.mkdir(outdir)
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e7825eae651e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msp_split commit 0d9dfeae375a6761b52be79111e228d950e2902e"
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43 def write_spectra(filename, outdir):
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44 """Generates MSP files of individual spectra. Structure of filename is 'compound_name.msp'.
e7825eae651e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msp_split commit 0d9dfeae375a6761b52be79111e228d950e2902e"
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e7825eae651e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msp_split commit 0d9dfeae375a6761b52be79111e228d950e2902e"
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46 Args:
e7825eae651e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msp_split commit 0d9dfeae375a6761b52be79111e228d950e2902e"
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47 filename (str): MSP file that contains the spectra.
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48 outdir (str): Path to destination directory.
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49 """
e7825eae651e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msp_split commit 0d9dfeae375a6761b52be79111e228d950e2902e"
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50 spectra = read_spectra(filename)
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51 names = get_spectra_names(spectra)
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52 for i in range(len(spectra)):
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53 outpath = assemble_outpath(names[i], outdir)
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54 save_as_msp(spectra[i], outpath)
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57 def assemble_outpath(name, outdir):
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58 """Filter special chracteres from name.
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60 Args:
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61 name (str): Name to be filetered.
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62 outdir (str): Path to destination directory.
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63 """
e7825eae651e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msp_split commit 0d9dfeae375a6761b52be79111e228d950e2902e"
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64 filename = ''.join(filter(str.isalnum, name))
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65 outfile = str(filename) + ".msp"
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66 outpath = os.path.join(outdir, outfile)
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67 return outpath
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e7825eae651e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msp_split commit 0d9dfeae375a6761b52be79111e228d950e2902e"
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70 def split_spectra(filename, outdir):
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71 """Save individual MSP spectra files in the destination directory.
e7825eae651e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msp_split commit 0d9dfeae375a6761b52be79111e228d950e2902e"
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e7825eae651e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msp_split commit 0d9dfeae375a6761b52be79111e228d950e2902e"
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73 Args:
e7825eae651e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msp_split commit 0d9dfeae375a6761b52be79111e228d950e2902e"
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74 filename (str): MSP file that contains the spectra.
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75 outdir (str): Path to destination directory where split spectra files are saved.
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76 """
e7825eae651e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msp_split commit 0d9dfeae375a6761b52be79111e228d950e2902e"
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77 make_outdir(outdir)
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78 return write_spectra(filename, outdir)
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81 listarg = argparse.ArgumentParser()
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82 listarg.add_argument('--filename', type=str)
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83 listarg.add_argument('--outdir', type=str)
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84 args = listarg.parse_args()
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85 outdir = args.outdir
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86 filename = args.filename
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89 if __name__ == "__main__":
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90 split_spectra(filename, outdir)