view @ 12:171c94786a56 draft

"planemo upload for repository commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
author bgruening
date Tue, 28 Jul 2020 08:32:24 -0400
parents 98e12cc1f3a8
children bd678d7db2ae
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#!/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 multiprocessing
import tempfile
import subprocess
import shutil
import shlex

from openbabel import openbabel, pybel
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):

def mp_helper( query, args ):
        Helper function for multiprocessing.
        That function is a wrapper around obgrep.

    cmd_list = []
    if args.invert_matches:
    if args.only_name:
    if args.full_match:
    if args.number_of_matches:
    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(, 'w+'), stderr=subprocess.PIPE)

    stdout, stderr = child.communicate()
    return (, query)

def obgrep( args ):

    temp_file = tempfile.NamedTemporaryFile()
    temp_link = "%s.%s" % (, args.iformat)
    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) )

    out_handle = open( args.outfile, 'wb' )
    for result_file, query in results:
        res_handle = open(result_file,'rb')
        shutil.copyfileobj( res_handle, out_handle )
        os.remove( result_file )

    os.remove( temp_link )

def __main__():
        Multiprocessing obgrep search.
    args = parse_command_line()
    obgrep( args )

if __name__ == "__main__" :