diff multi_obgrep.py @ 15:2956017a9244 draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf

--- a/multi_obgrep.py	Tue Nov 10 20:21:59 2020 +0000
+++ b/multi_obgrep.py	Thu Aug 15 10:53:50 2024 +0000
@@ -15,21 +15,55 @@
 
 def parse_command_line():
     parser = argparse.ArgumentParser()
-    parser.add_argument('-i', '--infile', required=True, help='Molecule file.')
-    parser.add_argument('-q', '--query', required=True, help='Query file, containing different SMARTS in each line.')
-    parser.add_argument('-o', '--outfile', required=True, help='Path to the output file.')
+    parser.add_argument("-i", "--infile", required=True, help="Molecule file.")
+    parser.add_argument(
+        "-q",
+        "--query",
+        required=True,
+        help="Query file, containing different SMARTS in each line.",
+    )
+    parser.add_argument(
+        "-o", "--outfile", required=True, help="Path to the output file."
+    )
     parser.add_argument("--iformat", help="Input format, like smi, sdf, inchi")
-    parser.add_argument("--n-times", dest="n_times", type=int,
-                        default=0, help="Print a molecule only if the pattern occurs # times inside the molecule.")
-    parser.add_argument('-p', '--processors', type=int, default=multiprocessing.cpu_count())
-    parser.add_argument("--invert-matches", dest="invert_matches", action="store_true",
-                        default=False, help="Invert the matching, print non-matching molecules.")
-    parser.add_argument("--only-name", dest="only_name", action="store_true",
-                        default=False, help="Only print the name of the molecules.")
-    parser.add_argument("--full-match", dest="full_match", action="store_true",
-                        default=False, help="Full match, print matching-molecules only when the number of heavy atoms is also equal to the number of atoms in the SMARTS pattern.")
-    parser.add_argument("--number-of-matches", dest="number_of_matches", action="store_true",
-                        default=False, help="Print the number of matches.")
+    parser.add_argument(
+        "--n-times",
+        dest="n_times",
+        type=int,
+        default=0,
+        help="Print a molecule only if the pattern occurs # times inside the molecule.",
+    )
+    parser.add_argument(
+        "-p", "--processors", type=int, default=multiprocessing.cpu_count()
+    )
+    parser.add_argument(
+        "--invert-matches",
+        dest="invert_matches",
+        action="store_true",
+        default=False,
+        help="Invert the matching, print non-matching molecules.",
+    )
+    parser.add_argument(
+        "--only-name",
+        dest="only_name",
+        action="store_true",
+        default=False,
+        help="Only print the name of the molecules.",
+    )
+    parser.add_argument(
+        "--full-match",
+        dest="full_match",
+        action="store_true",
+        default=False,
+        help="Full match, print matching-molecules only when the number of heavy atoms is also equal to the number of atoms in the SMARTS pattern.",
+    )
+    parser.add_argument(
+        "--number-of-matches",
+        dest="number_of_matches",
+        action="store_true",
+        default=False,
+        help="Print the number of matches.",
+    )
     return parser.parse_args()
 
 
@@ -42,25 +76,27 @@
 
 def mp_helper(query, args):
     """
-        Helper function for multiprocessing.
-        That function is a wrapper around obgrep.
+    Helper function for multiprocessing.
+    That function is a wrapper around obgrep.
     """
 
     cmd_list = []
     if args.invert_matches:
-        cmd_list.append('-v')
+        cmd_list.append("-v")
     if args.only_name:
-        cmd_list.append('-n')
+        cmd_list.append("-n")
     if args.full_match:
-        cmd_list.append('-f')
+        cmd_list.append("-f")
     if args.number_of_matches:
-        cmd_list.append('-c')
+        cmd_list.append("-c")
     if args.n_times:
-        cmd_list.append('-t %s' % str(args.n_times))
+        cmd_list.append("-t %s" % str(args.n_times))
 
     tmp = tempfile.NamedTemporaryFile(delete=False)
-    cmd = 'obgrep %s "%s" %s' % (' '.join(cmd_list), query, args.infile)
-    child = subprocess.Popen(shlex.split(cmd), stdout=open(tmp.name, 'w+'), stderr=subprocess.PIPE)
+    cmd = 'obgrep %s "%s" %s' % (" ".join(cmd_list), query, args.infile)
+    child = subprocess.Popen(
+        shlex.split(cmd), stdout=open(tmp.name, "w+"), stderr=subprocess.PIPE
+    )
 
     stdout, stderr = child.communicate()
     return (tmp.name, query)
@@ -80,9 +116,9 @@
     pool.close()
     pool.join()
 
-    out_handle = open(args.outfile, 'wb')
+    out_handle = open(args.outfile, "wb")
     for result_file, query in results:
-        res_handle = open(result_file, 'rb')
+        res_handle = open(result_file, "rb")
         shutil.copyfileobj(res_handle, out_handle)
         res_handle.close()
         os.remove(result_file)
@@ -93,7 +129,7 @@
 
 def __main__():
     """
-        Multiprocessing obgrep search.
+    Multiprocessing obgrep search.
     """
     args = parse_command_line()
     obgrep(args)