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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit b757d35278216a1f43bd53ea687a951b005e47df
author recetox
date Wed, 20 Mar 2024 12:20:17 +0000
parents 72b687d21f65
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
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1 import argparse
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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2 import re
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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4 from openbabel import openbabel, pybel
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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5 openbabel.obErrorLog.StopLogging()
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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8 def parse_command_line():
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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9 parser = argparse.ArgumentParser()
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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10 parser.add_argument('-i', '--input', required=True, help='Input file name')
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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11 parser.add_argument('-o', '--output', required=True, help='Output file name')
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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12 parser.add_argument('-m', '--met', required=False, action='store_true', help='Remove organometallic compounds')
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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13 parser.add_argument('-a', '--anorg', required=False, action='store_true', help='Remove anorganic compounds')
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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14 return parser.parse_args()
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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17 def filter_compounds(args, pattern):
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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18 print(pattern)
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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19 with open(args.input, "r") as infile, open(args.output, "w") as outfile:
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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20 for line in infile:
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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21 values = line.split('\t', 1)
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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23 # check if input is list of SMILES or indexed table of SMILES
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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24 if values[0].isnumeric():
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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25 mol = pybel.readstring('smi', values[1]).write('inchi').split('/')[1] if values[1].strip() else ''
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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27 # check if both organometallic and anorganic filtering passes
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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28 # write original line if compound is organic without metals
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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29 if False not in ([bool(re.search(rf'{x}', mol)) for x in pattern]):
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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30 outfile.write(line)
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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31 else:
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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32 outfile.write(f'{values[0]}\t{""}\n')
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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33 else:
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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34 mol = pybel.readstring('smi', values[0]).write('inchi').split('/')[1]
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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35 if False not in ([bool(re.search(rf'{x}', mol)) for x in pattern]):
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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36 outfile.write(line)
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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39 def __main__():
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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40 """
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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41 Filter organometallics and/or anorganic compounds.
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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42 """
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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43 args = parse_command_line()
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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45 # check if user selected something to filter out, if not output file == input file
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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46 sel_pattern = []
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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47 if args.met is False and args.anorg is False:
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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48 print("No filtering selected - user did not specify what to filter out.")
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49 sel_pattern = r'^[a-zA-Z]+$'
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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50 # select patterns for filtering
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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51 if args.met:
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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52 sel_pattern.append(r'^(?:C|N|O|P|F|S|I|B|Si|Se|Cl|Br|Li|Na|H|K|[0-9]|\.)+$')
72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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53 if args.anorg:
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54 sel_pattern.append(r'[C][^abd-z]')
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72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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56 filter_compounds(args, sel_pattern)
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72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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72b687d21f65 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/filter_compounds commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
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59 if __name__ == "__main__":
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60 __main__()