Mercurial > repos > recetox > msmetaenhancer

annotate msmetaenhancer_wrapper.py @ 3:f387ebd6b734 draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 6858f7bc3c3cf68fd5002a2241c79923b2ca9acd"
author recetox
date Fri, 06 May 2022 12:21:30 +0000
parents 8338640d8676
children 2ada1099f42e
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ce612a11b455 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 26bede767f65ec97ac84b8cc3309db0aced22d53"
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1 import argparse
ce612a11b455 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 26bede767f65ec97ac84b8cc3309db0aced22d53"
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2 import asyncio
ce612a11b455 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 26bede767f65ec97ac84b8cc3309db0aced22d53"
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3 import sys
ce612a11b455 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 26bede767f65ec97ac84b8cc3309db0aced22d53"
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5 from matchms import set_matchms_logger_level
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ce612a11b455 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 26bede767f65ec97ac84b8cc3309db0aced22d53"
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6 from MSMetaEnhancer import Application
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9 def main(argv):
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10 parser = argparse.ArgumentParser(description="Annotate MSP file.")
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11 parser.add_argument("--input_file", type=str, help="Path to query spectra file in MSP format.")
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12 parser.add_argument("--output_file", type=str, help="Path to output spectra file.")
ce612a11b455 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 26bede767f65ec97ac84b8cc3309db0aced22d53"
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13 parser.add_argument("--jobs", type=str, help="Sequence of conversion jobs to be used.")
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14 parser.add_argument("--log_file", type=str, help="Path to log with details of the annotation process.")
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f387ebd6b734 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 6858f7bc3c3cf68fd5002a2241c79923b2ca9acd"
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15 parser.add_argument("--log_level", type=str, default='info',
f387ebd6b734 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 6858f7bc3c3cf68fd5002a2241c79923b2ca9acd"
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16 help="Severity of log messages present in the log file.")
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17 args = parser.parse_args()
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19 app = Application(log_level=args.log_level, log_file=args.log_file)
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21 # set matchms logging level to avoid extensive messages in stdout while reading file
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22 set_matchms_logger_level("ERROR")
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23 # import .msp file
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24 app.load_spectra(args.input_file, file_format='msp')
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26 # set matchms logging level back to warning
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27 set_matchms_logger_level("WARNING")
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29 # curate given metadata
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30 app.curate_spectra()
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32 # specify requested services and jobs
ce612a11b455 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 26bede767f65ec97ac84b8cc3309db0aced22d53"
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33 services = ['PubChem', 'CTS', 'CIR', 'NLM', 'RDKit', 'IDSM', 'BridgeDB']
ce612a11b455 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 26bede767f65ec97ac84b8cc3309db0aced22d53"
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35 if len(args.jobs) != 0:
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36 jobs = []
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37 for job in args.jobs.split(","):
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38 if len(job) != 0:
ce612a11b455 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 26bede767f65ec97ac84b8cc3309db0aced22d53"
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39 jobs.append(job.split())
ce612a11b455 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 26bede767f65ec97ac84b8cc3309db0aced22d53"
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40 asyncio.run(app.annotate_spectra(services, jobs))
ce612a11b455 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 26bede767f65ec97ac84b8cc3309db0aced22d53"
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41 else:
ce612a11b455 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 26bede767f65ec97ac84b8cc3309db0aced22d53"
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42 # execute without jobs parameter to run all possible jobs
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43 asyncio.run(app.annotate_spectra(services))
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45 # export .msp file
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46 app.save_spectra(args.output_file, file_format="msp")
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47 return 0
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50 if __name__ == "__main__":
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51 main(argv=sys.argv[1:])