--- a/wrapper_biotransformer.py	Wed Jan 13 11:17:53 2021 +0000
+++ b/wrapper_biotransformer.py	Mon Apr 11 10:09:39 2022 +0000
@@ -8,8 +8,8 @@
 openbabel.obErrorLog.StopLogging()
 
 
-# function for translating inchi to smiles
 def InchiToSmiles(df):
+    '''Translate inchi to smiles'''
     sm = []
     for item in df['InChI']:
         tmp = pybel.readstring("inchi", item)
@@ -18,80 +18,58 @@
 
 
 executable = ["biotransformer"]
-# executable_r = ["Rscript", "inchi_to_smiles.r"]
 
 argv = sys.argv[1:]
-if "-icsv" in argv:
-    icsv = argv.pop(argv.index("-icsv") + 1)
-    argv.remove("-icsv")
+icsv = argv.pop(argv.index("-icsv") + 1)
+argv.remove("-icsv")
+ocsv = argv.pop(argv.index("-ocsv") + 1)
+argv.remove("-ocsv")
+ocsv_dup = argv.pop(argv.index("-ocsvDup") + 1)
+argv.remove("-ocsvDup")
+ocsv_dup2 = argv.pop(argv.index("-ocsvDup2") + 1)
+argv.remove("-ocsvDup2")
 
-    if "-ocsv" not in argv:
-        sys.stderr.write("excpected -ocsv parameter\n")
-        sys.exit(1)
-    ocsv = argv.pop(argv.index("-ocsv") + 1)
-    argv.remove("-ocsv")
-    ocsv_dup = argv.pop(argv.index("-ocsvDup") + 1)
-    argv.remove("-ocsvDup")
-    ocsv_dup2 = argv.pop(argv.index("-ocsvDup2") + 1)
-    argv.remove("-ocsvDup2")
+in_df = pandas.read_csv(icsv, header=None)
+out_df1 = pandas.DataFrame()  # all results
+out_df2 = pandas.DataFrame()  # filtered results based on 6 columns
+out_df3 = pandas.DataFrame()  # filtered results based on 3 columns
 
-    in_df = pandas.read_csv(icsv, header=None)
-    out_df1 = pandas.DataFrame()  # all results
-    out_df2 = pandas.DataFrame()  # filtered results based on 6 columns
-    out_df3 = pandas.DataFrame()  # filtered results based on 3 columns
-
-    tmp2 = pandas.DataFrame()
-    tmp3 = pandas.DataFrame()
+smList1 = []  # list with smiles string
+smList2 = []
+smList3 = []
+for _, (smiles,) in in_df.iterrows():
+    with tempfile.NamedTemporaryFile() as out:
+        print("Working on compound: " + smiles)
+        if not re.search(r'\.', smiles):
+            subprocess.run(executable + argv + ["-ismi", smiles] + ["-ocsv", out.name])
+            try:
+                bio_out = pandas.read_csv(out.name)
+                tmp2 = bio_out.drop_duplicates(subset=["InChI", "InChIKey", "Synonyms", "Molecular formula", "Major Isotope Mass", "ALogP"])
+                tmp3 = bio_out.drop_duplicates(subset=["Molecular formula", "Major Isotope Mass", "ALogP"])
 
-    smList1 = []  # list with smiles string
-    smList2 = []
-    smList3 = []
-    for _, (smiles,) in in_df.iterrows():
-        with tempfile.NamedTemporaryFile() as out:
-            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, [])
+                smList1.append([smiles] * bio_out.shape[0])
+                smList2.append([smiles] * tmp2.shape[0])
+                smList3.append([smiles] * tmp3.shape[0])
 
-    out_df1.insert(0, "SMILES query", smList1)
-    out_df1.drop_duplicates(inplace=True)
-    out_df1.insert(1, "SMILES target", InchiToSmiles(out_df1))
-    out_df1.to_csv(ocsv)
+                out_df1 = pandas.concat([out_df1, bio_out])
+                out_df2 = pandas.concat([out_df2, tmp2])
+                out_df3 = pandas.concat([out_df3, tmp3])
+            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, [])
 
-    out_df2.insert(0, "SMILES query", smList2)
-    out_df3.insert(0, "SMILES query", smList3)
-    out_df2.drop_duplicates(inplace=True)
-    out_df3.drop_duplicates(inplace=True)
-    out_df2.insert(1, "SMILES target", InchiToSmiles(out_df2))
-    out_df3.insert(1, "SMILES target", InchiToSmiles(out_df3))
-    # out_df.drop_duplicates(inplace=True, subset=["InChI", "InChIKey", "Synonyms", "Molecular formula", "Major Isotope Mass", "ALogP"])
-    out_df2.to_csv(ocsv_dup)
-    out_df3.to_csv(ocsv_dup2)
-else:
-    # code = subprocess.run(executable + argv).returncode
-    # sys.exit(code)
-    subprocess.run(executable + argv)
-    smile = argv.pop(argv.index("-ismi") + 1)
-    tmp = pandas.DataFrame()
-    out = argv.pop(argv.index("-ocsv") + 1)
-    tmp = pandas.read_csv(out)   # reads created output file
-    tmp.insert(0, "SMILES query", smile)  # add SMILES string for query
-    tmp.insert(1, "SMILES target", InchiToSmiles(tmp))  # add SMILES string for target
-    tmp.to_csv(out)
+out_df1.insert(0, "SMILES query", smList1)
+out_df1.insert(1, "SMILES target", InchiToSmiles(out_df1))
+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_df3.insert(0, "SMILES query", smList3)
+out_df3.insert(1, "SMILES target", InchiToSmiles(out_df3))
+out_df3.to_csv(ocsv_dup2, sep ='\t')