Mercurial > repos > recetox > biotransformer

diff 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
line wrap: on
line diff
--- a/wrapper_biotransformer.py	Mon Apr 11 10:09:39 2022 +0000
+++ b/wrapper_biotransformer.py	Tue Jun 06 11:23:37 2023 +0000
@@ -1,9 +1,9 @@
+import re
 import subprocess
 import sys
 import tempfile
-import re
+
 import pandas
-
 from openbabel import openbabel, pybel
 openbabel.obErrorLog.StopLogging()
 
@@ -14,7 +14,7 @@
     for item in df['InChI']:
         tmp = pybel.readstring("inchi", item)
         sm.append(tmp.write("smi"))
-    return(sm)
+    return sm
 
 
 executable = ["biotransformer"]
@@ -64,12 +64,12 @@
 
 out_df1.insert(0, "SMILES query", smList1)
 out_df1.insert(1, "SMILES target", InchiToSmiles(out_df1))
-out_df1.to_csv(ocsv, sep ='\t')
+out_df1.to_csv(ocsv, sep='\t')
 
 out_df2.insert(0, "SMILES query", smList2)
 out_df2.insert(1, "SMILES target", InchiToSmiles(out_df2))
-out_df2.to_csv(ocsv_dup, sep ='\t')
+out_df2.to_csv(ocsv_dup, sep='\t')
 
 out_df3.insert(0, "SMILES query", smList3)
 out_df3.insert(1, "SMILES target", InchiToSmiles(out_df3))
-out_df3.to_csv(ocsv_dup2, sep ='\t')
+out_df3.to_csv(ocsv_dup2, sep='\t')