Mercurial > repos > recetox > biotransformer

annotate wrapper_biotransformer.py @ 3:6080aee7c4f6 draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 5cdd2628a1a509b3e0ccc599eaab63d664bf031a"
author recetox
date Wed, 13 Jan 2021 11:17:53 +0000
parents 362a66a3889c
children 77f693bb14ac
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362a66a3889c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 833817386e90cca9ac4737e6857fcaf672f2a011"
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1 import subprocess
362a66a3889c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 833817386e90cca9ac4737e6857fcaf672f2a011"
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2 import sys
362a66a3889c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 833817386e90cca9ac4737e6857fcaf672f2a011"
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3 import tempfile
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6080aee7c4f6 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 5cdd2628a1a509b3e0ccc599eaab63d664bf031a"
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4 import re
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362a66a3889c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 833817386e90cca9ac4737e6857fcaf672f2a011"
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5 import pandas
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6080aee7c4f6 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 5cdd2628a1a509b3e0ccc599eaab63d664bf031a"
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6
6080aee7c4f6 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 5cdd2628a1a509b3e0ccc599eaab63d664bf031a"
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7 from openbabel import openbabel, pybel
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8 openbabel.obErrorLog.StopLogging()
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11 # function for translating inchi to smiles
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12 def InchiToSmiles(df):
362a66a3889c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 833817386e90cca9ac4737e6857fcaf672f2a011"
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13 sm = []
362a66a3889c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 833817386e90cca9ac4737e6857fcaf672f2a011"
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14 for item in df['InChI']:
362a66a3889c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 833817386e90cca9ac4737e6857fcaf672f2a011"
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15 tmp = pybel.readstring("inchi", item)
362a66a3889c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 833817386e90cca9ac4737e6857fcaf672f2a011"
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16 sm.append(tmp.write("smi"))
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17 return(sm)
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20 executable = ["biotransformer"]
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21 # executable_r = ["Rscript", "inchi_to_smiles.r"]
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23 argv = sys.argv[1:]
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24 if "-icsv" in argv:
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25 icsv = argv.pop(argv.index("-icsv") + 1)
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26 argv.remove("-icsv")
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28 if "-ocsv" not in argv:
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29 sys.stderr.write("excpected -ocsv parameter\n")
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30 sys.exit(1)
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31 ocsv = argv.pop(argv.index("-ocsv") + 1)
362a66a3889c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 833817386e90cca9ac4737e6857fcaf672f2a011"
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32 argv.remove("-ocsv")
362a66a3889c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 833817386e90cca9ac4737e6857fcaf672f2a011"
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33 ocsv_dup = argv.pop(argv.index("-ocsvDup") + 1)
362a66a3889c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 833817386e90cca9ac4737e6857fcaf672f2a011"
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34 argv.remove("-ocsvDup")
362a66a3889c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 833817386e90cca9ac4737e6857fcaf672f2a011"
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35 ocsv_dup2 = argv.pop(argv.index("-ocsvDup2") + 1)
362a66a3889c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 833817386e90cca9ac4737e6857fcaf672f2a011"
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36 argv.remove("-ocsvDup2")
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38 in_df = pandas.read_csv(icsv, header=None)
362a66a3889c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 833817386e90cca9ac4737e6857fcaf672f2a011"
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39 out_df1 = pandas.DataFrame() # all results
362a66a3889c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 833817386e90cca9ac4737e6857fcaf672f2a011"
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40 out_df2 = pandas.DataFrame() # filtered results based on 6 columns
362a66a3889c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 833817386e90cca9ac4737e6857fcaf672f2a011"
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41 out_df3 = pandas.DataFrame() # filtered results based on 3 columns
362a66a3889c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 833817386e90cca9ac4737e6857fcaf672f2a011"
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43 tmp2 = pandas.DataFrame()
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44 tmp3 = pandas.DataFrame()
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46 smList1 = [] # list with smiles string
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47 smList2 = []
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48 smList3 = []
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49 for _, (smiles,) in in_df.iterrows():
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50 with tempfile.NamedTemporaryFile() as out:
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51 print("Working on compound: " + smiles)
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52 if not re.search(r'\.', smiles):
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53 subprocess.run(executable + argv + ["-ismi", smiles] + ["-ocsv", out.name])
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54 try:
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55 tmp2 = pandas.read_csv(out.name)
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56 tmp3 = pandas.read_csv(out.name)
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57 tmp2.drop_duplicates(inplace=True, subset=["InChI", "InChIKey", "Synonyms", "Molecular formula", "Major Isotope Mass", "ALogP"])
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58 tmp3.drop_duplicates(inplace=True, subset=["Molecular formula", "Major Isotope Mass", "ALogP"])
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59 smList2.append([smiles] * tmp2.shape[0])
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60 smList3.append([smiles] * tmp3.shape[0])
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61 out_df1 = pandas.concat([out_df1, pandas.read_csv(out.name)])
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62 out_df2 = pandas.concat([out_df2, tmp2])
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63 out_df3 = pandas.concat([out_df3, tmp3])
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64 smList1.append([smiles] * pandas.read_csv(out.name).shape[0])
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65 except pandas.errors.EmptyDataError:
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66 continue
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67 else:
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68 print("ERROR: Input compound cannot be a mixture.")
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69 smList1 = sum(smList1, []) # merge sublists into one list
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70 smList2 = sum(smList2, [])
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71 smList3 = sum(smList3, [])
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73 out_df1.insert(0, "SMILES query", smList1)
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74 out_df1.drop_duplicates(inplace=True)
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75 out_df1.insert(1, "SMILES target", InchiToSmiles(out_df1))
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76 out_df1.to_csv(ocsv)
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78 out_df2.insert(0, "SMILES query", smList2)
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79 out_df3.insert(0, "SMILES query", smList3)
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80 out_df2.drop_duplicates(inplace=True)
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81 out_df3.drop_duplicates(inplace=True)
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82 out_df2.insert(1, "SMILES target", InchiToSmiles(out_df2))
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83 out_df3.insert(1, "SMILES target", InchiToSmiles(out_df3))
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84 # out_df.drop_duplicates(inplace=True, subset=["InChI", "InChIKey", "Synonyms", "Molecular formula", "Major Isotope Mass", "ALogP"])
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85 out_df2.to_csv(ocsv_dup)
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86 out_df3.to_csv(ocsv_dup2)
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87 else:
362a66a3889c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 833817386e90cca9ac4737e6857fcaf672f2a011"
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88 # code = subprocess.run(executable + argv).returncode
362a66a3889c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 833817386e90cca9ac4737e6857fcaf672f2a011"
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89 # sys.exit(code)
362a66a3889c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 833817386e90cca9ac4737e6857fcaf672f2a011"
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90 subprocess.run(executable + argv)
362a66a3889c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 833817386e90cca9ac4737e6857fcaf672f2a011"
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91 smile = argv.pop(argv.index("-ismi") + 1)
362a66a3889c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 833817386e90cca9ac4737e6857fcaf672f2a011"
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92 tmp = pandas.DataFrame()
362a66a3889c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 833817386e90cca9ac4737e6857fcaf672f2a011"
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93 out = argv.pop(argv.index("-ocsv") + 1)
362a66a3889c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 833817386e90cca9ac4737e6857fcaf672f2a011"
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94 tmp = pandas.read_csv(out) # reads created output file
362a66a3889c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 833817386e90cca9ac4737e6857fcaf672f2a011"
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95 tmp.insert(0, "SMILES query", smile) # add SMILES string for query
362a66a3889c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 833817386e90cca9ac4737e6857fcaf672f2a011"
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96 tmp.insert(1, "SMILES target", InchiToSmiles(tmp)) # add SMILES string for target
362a66a3889c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 833817386e90cca9ac4737e6857fcaf672f2a011"
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97 tmp.to_csv(out)