Mercurial > repos > recetox > matchms_split

annotate matchms_split.py @ 2:5d9d107485ec draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 701733d99742a8e567ed6db7384be66c5ecb4a58
author recetox
date Thu, 18 May 2023 13:23:04 +0000
parents 0b2ea1dc4c8c
children 49f9aa5cfa21
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0b2ea1dc4c8c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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1 import argparse
0b2ea1dc4c8c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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2 import itertools
0b2ea1dc4c8c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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3 import os
0b2ea1dc4c8c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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4 from typing import List
0b2ea1dc4c8c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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0b2ea1dc4c8c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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6 from matchms import Spectrum
0b2ea1dc4c8c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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7 from matchms.exporting import save_as_msp
0b2ea1dc4c8c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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8 from matchms.importing import load_from_msp
0b2ea1dc4c8c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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0b2ea1dc4c8c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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0b2ea1dc4c8c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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11 def read_spectra(filename: str) -> List[Spectrum]:
0b2ea1dc4c8c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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12 """Read spectra from file.
0b2ea1dc4c8c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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0b2ea1dc4c8c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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14 Args:
0b2ea1dc4c8c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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15 filename (str): Path to .msp file from which to load the spectra.
0b2ea1dc4c8c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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0b2ea1dc4c8c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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17 Returns:
0b2ea1dc4c8c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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18 List[Spectrum]: Spectra contained in the file.
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19 """
0b2ea1dc4c8c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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20 return list(load_from_msp(filename, True))
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0b2ea1dc4c8c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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0b2ea1dc4c8c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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23 def get_spectra_names(spectra: list) -> List[str]:
0b2ea1dc4c8c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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24 """Read the keyword 'compound_name' from a spectra.
0b2ea1dc4c8c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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0b2ea1dc4c8c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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26 Args:
0b2ea1dc4c8c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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27 spectra (list): List of individual spectra.
0b2ea1dc4c8c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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0b2ea1dc4c8c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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29 Returns:
0b2ea1dc4c8c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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30 List[str]: List with 'compoud_name' of individual spectra.
0b2ea1dc4c8c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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31 """
0b2ea1dc4c8c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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32 return [x.get("compound_name") for x in spectra]
0b2ea1dc4c8c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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0b2ea1dc4c8c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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0b2ea1dc4c8c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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35 def make_outdir(outdir: str):
0b2ea1dc4c8c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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36 """Create destination directory.
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0b2ea1dc4c8c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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38 Args:
0b2ea1dc4c8c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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39 outdir (str): Path to destination directory where split spectra files are generated.
0b2ea1dc4c8c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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40 """
0b2ea1dc4c8c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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41 return os.mkdir(outdir)
0b2ea1dc4c8c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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0b2ea1dc4c8c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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0b2ea1dc4c8c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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44 def write_spectra(spectra, outdir):
0b2ea1dc4c8c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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45 """Generates MSP files of individual spectra.
0b2ea1dc4c8c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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0b2ea1dc4c8c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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47 Args:
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48 spectra (List[Spectrum]): Spectra to write to file
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49 outdir (str): Path to destination directory.
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50 """
0b2ea1dc4c8c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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51 names = get_spectra_names(spectra)
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52 for i in range(len(spectra)):
0b2ea1dc4c8c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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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 """
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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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70 def split_spectra(filename, outdir):
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71 """Save individual MSP spectra files in the destination directory.
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73 Args:
0b2ea1dc4c8c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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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 """
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77 make_outdir(outdir)
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78 return write_spectra(filename, outdir)
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81 def split_round_robin(iterable, num_chunks):
0b2ea1dc4c8c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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82 chunks = [list() for _ in range(num_chunks)]
0b2ea1dc4c8c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 5888b20035c9c782b7c94495b0760134f82f4c2e
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83 index = itertools.cycle(range(num_chunks))
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84 for value in iterable:
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85 chunks[next(index)].append(value)
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86 chunks = filter(lambda x: len(x) > 0, chunks)
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87 return chunks
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89
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90 listarg = argparse.ArgumentParser()
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91 listarg.add_argument('--filename', type=str)
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92 listarg.add_argument('--method', type=str)
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93 listarg.add_argument('--outdir', type=str)
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94 listarg.add_argument('--parameter', type=int)
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95 args = listarg.parse_args()
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96 outdir = args.outdir
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97 filename = args.filename
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98 method = args.method
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99 parameter = args.parameter
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100
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101
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102 if __name__ == "__main__":
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103 spectra = load_from_msp(filename)
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104 make_outdir(outdir)
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105
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106 if method == "one-per-file":
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107 write_spectra(list(spectra), outdir)
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108 else:
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109 if method == "chunk-size":
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110 chunks = iter(lambda: list(itertools.islice(spectra, parameter)), [])
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111 elif method == "num-chunks":
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112 chunks = split_round_robin(spectra, parameter)
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113 for i, x in enumerate(chunks):
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114 save_as_msp(x, os.path.join(outdir, f"chunk_{i}.msp"))