Mercurial > repos > recetox > biotransformer

annotate wrapper_biotransformer.py @ 5:c0fe7ad30ade draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9b8e9941cdf0689518021bc0aa4b7196b28d25d7
author recetox
date Tue, 06 Jun 2023 11:23:37 +0000
parents 77f693bb14ac
children
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c0fe7ad30ade planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9b8e9941cdf0689518021bc0aa4b7196b28d25d7
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1 import re
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2 import subprocess
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3 import sys
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4 import tempfile
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c0fe7ad30ade planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9b8e9941cdf0689518021bc0aa4b7196b28d25d7
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5
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6 import pandas
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7 from openbabel import openbabel, pybel
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8 openbabel.obErrorLog.StopLogging()
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11 def InchiToSmiles(df):
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12 '''Translate inchi to smiles'''
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13 sm = []
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14 for item in df['InChI']:
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15 tmp = pybel.readstring("inchi", item)
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16 sm.append(tmp.write("smi"))
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c0fe7ad30ade planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9b8e9941cdf0689518021bc0aa4b7196b28d25d7
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17 return sm
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20 executable = ["biotransformer"]
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22 argv = sys.argv[1:]
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23 icsv = argv.pop(argv.index("-icsv") + 1)
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24 argv.remove("-icsv")
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25 ocsv = argv.pop(argv.index("-ocsv") + 1)
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26 argv.remove("-ocsv")
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27 ocsv_dup = argv.pop(argv.index("-ocsvDup") + 1)
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28 argv.remove("-ocsvDup")
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29 ocsv_dup2 = argv.pop(argv.index("-ocsvDup2") + 1)
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30 argv.remove("-ocsvDup2")
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32 in_df = pandas.read_csv(icsv, header=None)
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33 out_df1 = pandas.DataFrame() # all results
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34 out_df2 = pandas.DataFrame() # filtered results based on 6 columns
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35 out_df3 = pandas.DataFrame() # filtered results based on 3 columns
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37 smList1 = [] # list with smiles string
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38 smList2 = []
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39 smList3 = []
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40 for _, (smiles,) in in_df.iterrows():
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41 with tempfile.NamedTemporaryFile() as out:
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42 print("Working on compound: " + smiles)
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43 if not re.search(r'\.', smiles):
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44 subprocess.run(executable + argv + ["-ismi", smiles] + ["-ocsv", out.name])
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45 try:
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46 bio_out = pandas.read_csv(out.name)
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47 tmp2 = bio_out.drop_duplicates(subset=["InChI", "InChIKey", "Synonyms", "Molecular formula", "Major Isotope Mass", "ALogP"])
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48 tmp3 = bio_out.drop_duplicates(subset=["Molecular formula", "Major Isotope Mass", "ALogP"])
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50 smList1.append([smiles] * bio_out.shape[0])
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51 smList2.append([smiles] * tmp2.shape[0])
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52 smList3.append([smiles] * tmp3.shape[0])
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54 out_df1 = pandas.concat([out_df1, bio_out])
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55 out_df2 = pandas.concat([out_df2, tmp2])
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56 out_df3 = pandas.concat([out_df3, tmp3])
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57 except pandas.errors.EmptyDataError:
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58 continue
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59 else:
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60 print("ERROR: Input compound cannot be a mixture.")
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61 smList1 = sum(smList1, []) # merge sublists into one list
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62 smList2 = sum(smList2, [])
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63 smList3 = sum(smList3, [])
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64
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65 out_df1.insert(0, "SMILES query", smList1)
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66 out_df1.insert(1, "SMILES target", InchiToSmiles(out_df1))
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67 out_df1.to_csv(ocsv, sep='\t')
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69 out_df2.insert(0, "SMILES query", smList2)
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70 out_df2.insert(1, "SMILES target", InchiToSmiles(out_df2))
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71 out_df2.to_csv(ocsv_dup, sep='\t')
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73 out_df3.insert(0, "SMILES query", smList3)
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74 out_df3.insert(1, "SMILES target", InchiToSmiles(out_df3))
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75 out_df3.to_csv(ocsv_dup2, sep='\t')