annotate multi_obgrep.py @ 7:fac2c28b4c55 draft default tip

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

#!/usr/bin/env python
"""
    Input: Molecules in SDF, SMILES ...
    Output: Molecule file filtered with obgrep.
    Copyright 2013, Bjoern Gruening and Xavier Lucas
"""
import argparse
import multiprocessing
import os
import shlex
import shutil
import subprocess
import tempfile


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__()