Mercurial > repos > recetox > biotransformer
diff wrapper_biotransformer.py @ 3:6080aee7c4f6 draft
"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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--- a/wrapper_biotransformer.py Fri Sep 25 14:32:24 2020 +0000 +++ b/wrapper_biotransformer.py Wed Jan 13 11:17:53 2021 +0000 @@ -1,9 +1,11 @@ import subprocess import sys import tempfile - +import re import pandas -from openbabel import pybel + +from openbabel import openbabel, pybel +openbabel.obErrorLog.StopLogging() # function for translating inchi to smiles @@ -46,17 +48,24 @@ smList3 = [] for _, (smiles,) in in_df.iterrows(): with tempfile.NamedTemporaryFile() as out: - subprocess.run(executable + argv + ["-ismi", smiles] + ["-ocsv", out.name]) - tmp2 = pandas.read_csv(out.name) - tmp3 = pandas.read_csv(out.name) - tmp2.drop_duplicates(inplace=True, subset=["InChI", "InChIKey", "Synonyms", "Molecular formula", "Major Isotope Mass", "ALogP"]) - tmp3.drop_duplicates(inplace=True, subset=["Molecular formula", "Major Isotope Mass", "ALogP"]) - smList2.append([smiles] * tmp2.shape[0]) - smList3.append([smiles] * tmp3.shape[0]) - out_df1 = pandas.concat([out_df1, pandas.read_csv(out.name)]) - out_df2 = pandas.concat([out_df2, tmp2]) - out_df3 = pandas.concat([out_df3, tmp3]) - smList1.append([smiles] * pandas.read_csv(out.name).shape[0]) + print("Working on compound: " + smiles) + if not re.search(r'\.', smiles): + subprocess.run(executable + argv + ["-ismi", smiles] + ["-ocsv", out.name]) + try: + tmp2 = pandas.read_csv(out.name) + tmp3 = pandas.read_csv(out.name) + tmp2.drop_duplicates(inplace=True, subset=["InChI", "InChIKey", "Synonyms", "Molecular formula", "Major Isotope Mass", "ALogP"]) + tmp3.drop_duplicates(inplace=True, subset=["Molecular formula", "Major Isotope Mass", "ALogP"]) + smList2.append([smiles] * tmp2.shape[0]) + smList3.append([smiles] * tmp3.shape[0]) + out_df1 = pandas.concat([out_df1, pandas.read_csv(out.name)]) + out_df2 = pandas.concat([out_df2, tmp2]) + out_df3 = pandas.concat([out_df3, tmp3]) + smList1.append([smiles] * pandas.read_csv(out.name).shape[0]) + except pandas.errors.EmptyDataError: + continue + else: + print("ERROR: Input compound cannot be a mixture.") smList1 = sum(smList1, []) # merge sublists into one list smList2 = sum(smList2, []) smList3 = sum(smList3, [])