diff wrapper_biotransformer.py @ 0:0b86600b715e draft

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/biotransformer commit 9b8e9941cdf0689518021bc0aa4b7196b28d25d7

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/wrapper_biotransformer.py	Tue Jun 06 11:23:51 2023 +0000
@@ -0,0 +1,75 @@
+import re
+import subprocess
+import sys
+import tempfile
+
+import pandas
+from openbabel import openbabel, pybel
+openbabel.obErrorLog.StopLogging()
+
+
+def InchiToSmiles(df):
+    '''Translate inchi to smiles'''
+    sm = []
+    for item in df['InChI']:
+        tmp = pybel.readstring("inchi", item)
+        sm.append(tmp.write("smi"))
+    return sm
+
+
+executable = ["biotransformer"]
+
+argv = sys.argv[1:]
+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")
+
+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
+
+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.append([smiles] * bio_out.shape[0])
+                smList2.append([smiles] * tmp2.shape[0])
+                smList3.append([smiles] * tmp3.shape[0])
+
+                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_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')