diff multi_obgrep.py @ 0:98e12cc1f3a8 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/multi_obgrep.py	Sat May 20 08:40:52 2017 -0400
@@ -0,0 +1,101 @@
+#!/usr/bin/env python
+"""
+    Input: Molecules in SDF, SMILES ...
+    Output: Molecule file filtered with obgrep.
+    Copyright 2013, Bjoern Gruening and Xavier Lucas
+"""
+import sys, os
+import argparse
+import openbabel
+openbabel.obErrorLog.StopLogging()
+import pybel
+import multiprocessing
+import tempfile
+import subprocess
+import shutil
+import shlex
+
+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("--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.")
+    return parser.parse_args()
+
+results = list()
+def mp_callback(res):
+    results.append(res)
+
+def mp_helper( query, args ):
+    """
+        Helper function for multiprocessing.
+        That function is a wrapper around obgrep.
+    """
+
+    cmd_list = []
+    if args.invert_matches:
+        cmd_list.append('-v')
+    if args.only_name:
+        cmd_list.append('-n')
+    if args.full_match:
+        cmd_list.append('-f')
+    if args.number_of_matches:
+        cmd_list.append('-c')
+    if 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)
+
+    stdout, stderr = child.communicate()
+    return (tmp.name, query)
+
+
+def obgrep( args ):
+
+    temp_file = tempfile.NamedTemporaryFile()
+    temp_link = "%s.%s" % (temp_file.name, args.iformat)
+    temp_file.close()
+    os.symlink(args.infile, temp_link)
+    args.infile = temp_link
+
+    pool = multiprocessing.Pool( args.processors )
+    for query in open( args.query ):
+        pool.apply_async(mp_helper, args=(query.strip(), args), callback=mp_callback)
+        #mp_callback( mp_helper(query.strip(), args) )
+    pool.close()
+    pool.join()
+
+    out_handle = open( args.outfile, 'wb' )
+    for result_file, query in results:
+        res_handle = open(result_file,'rb')
+        shutil.copyfileobj( res_handle, out_handle )
+        res_handle.close()
+        os.remove( result_file )
+    out_handle.close()
+
+    os.remove( temp_link )
+
+def __main__():
+    """
+        Multiprocessing obgrep search.
+    """
+    args = parse_command_line()
+    obgrep( args )
+
+if __name__ == "__main__" :
+    __main__()