comparison subsearch.py @ 15:c5de6c19eb06 draft default tip

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

14:b2569e22b40c

import subprocess
import sys
import tempfile

from openbabel import openbabel, pybel
openbabel.obErrorLog.StopLogging()


def parse_command_line():
    parser = argparse.ArgumentParser()
    parser.add_argument('-i', '--infile', required=True, help='Molecule file.')
    parser.add_argument('--iformat', help='Input format.')
    parser.add_argument('--fastsearch-index', dest="fastsearch_index", required=True,
                        help='Path to the openbabel fastsearch index.')
    parser.add_argument('-o', '--outfile', required=True, help='Path to the output file.')
    parser.add_argument('--oformat', default='smi', help='Output file format')
    parser.add_argument("--max-candidates", dest="max_candidates", type=int, default=4000,
                        help="The maximum number of candidates.")
    parser.add_argument('-p', '--processors', type=int,
                        default=multiprocessing.cpu_count())
    return parser.parse_args()


results = list()

    results.append(res)


def mp_helper(query, args):
    """
        Helper function for multiprocessing.
        That function is a wrapper around the following command:
        obabel file.fs -s"smarts" -Ooutfile.smi -al 999999999
    """

    if args.oformat == 'names':
        opts = '-osmi -xt'
    else:
        opts = '-o%s' % args.oformat

    tmp = tempfile.NamedTemporaryFile(delete=False)
    cmd = 'obabel -ifs %s -O %s %s -s%s -al %s' % (args.fastsearch_index, tmp.name, opts, query, args.max_candidates)

    child = subprocess.Popen(cmd.split(), stdout=subprocess.PIPE, stderr=subprocess.PIPE)

    stdout, stderr = child.communicate()
    return_code = child.returncode

    if return_code:

def get_smiles_or_smarts(args):
    """
    Wrapper to retrieve a striped SMILES or SMARTS string from different input formats.
    """
    if args.iformat in ['smi', 'text', 'tabular']:
        with open(args.infile) as text_file:
            for line in text_file:
                yield line.split('\t')[0].strip()
    else:
        # inchi or sdf files
        for mol in pybel.readfile(args.iformat, args.infile):
            yield mol.write('smiles').split('\t')[0]


def substructure_search(args):
    pool = multiprocessing.Pool(args.processors)
    for query in get_smiles_or_smarts(args):
        pool.apply_async(mp_helper, args=(query, args), callback=mp_callback)
        # mp_callback(mp_helper(query, args))
    pool.close()
    pool.join()

    if args.oformat == 'names':
        out_handle = open(args.outfile, 'w')
        for result_file, query in results:
            with open(result_file) as res_handle:
                for line in res_handle:
                    out_handle.write('%s\t%s\n' % (line.strip(), query))
            os.remove(result_file)
        out_handle.close()
    else:
        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()


def __main__():
    """
        Multiprocessing Open Babel Substructure Search.
    """
    args = parse_command_line()
    substructure_search(args)

15:c5de6c19eb06

import subprocess
import sys
import tempfile

from openbabel import openbabel, pybel

openbabel.obErrorLog.StopLogging()


def parse_command_line():
    parser = argparse.ArgumentParser()
    parser.add_argument("-i", "--infile", required=True, help="Molecule file.")
    parser.add_argument("--iformat", help="Input format.")
    parser.add_argument(
        "--fastsearch-index",
        dest="fastsearch_index",
        required=True,
        help="Path to the openbabel fastsearch index.",
    )
    parser.add_argument(
        "-o", "--outfile", required=True, help="Path to the output file."
    )
    parser.add_argument("--oformat", default="smi", help="Output file format")
    parser.add_argument(
        "--max-candidates",
        dest="max_candidates",
        type=int,
        default=4000,
        help="The maximum number of candidates.",
    )
    parser.add_argument(
        "-p", "--processors", type=int, default=multiprocessing.cpu_count()
    )
    return parser.parse_args()


results = list()

    results.append(res)


def mp_helper(query, args):
    """
    Helper function for multiprocessing.
    That function is a wrapper around the following command:
    obabel file.fs -s"smarts" -Ooutfile.smi -al 999999999
    """

    if args.oformat == "names":
        opts = "-osmi -xt"
    else:
        opts = "-o%s" % args.oformat

    tmp = tempfile.NamedTemporaryFile(delete=False)
    cmd = "obabel -ifs %s -O %s %s -s%s -al %s" % (
        args.fastsearch_index,
        tmp.name,
        opts,
        query,
        args.max_candidates,
    )

    child = subprocess.Popen(
        cmd.split(), stdout=subprocess.PIPE, stderr=subprocess.PIPE
    )

    stdout, stderr = child.communicate()
    return_code = child.returncode

    if return_code:

def get_smiles_or_smarts(args):
    """
    Wrapper to retrieve a striped SMILES or SMARTS string from different input formats.
    """
    if args.iformat in ["smi", "text", "tabular"]:
        with open(args.infile) as text_file:
            for line in text_file:
                yield line.split("\t")[0].strip()
    else:
        # inchi or sdf files
        for mol in pybel.readfile(args.iformat, args.infile):
            yield mol.write("smiles").split("\t")[0]


def substructure_search(args):
    pool = multiprocessing.Pool(args.processors)
    for query in get_smiles_or_smarts(args):
        pool.apply_async(mp_helper, args=(query, args), callback=mp_callback)
        # mp_callback(mp_helper(query, args))
    pool.close()
    pool.join()

    if args.oformat == "names":
        out_handle = open(args.outfile, "w")
        for result_file, query in results:
            with open(result_file) as res_handle:
                for line in res_handle:
                    out_handle.write("%s\t%s\n" % (line.strip(), query))
            os.remove(result_file)
        out_handle.close()
    else:
        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()


def __main__():
    """
    Multiprocessing Open Babel Substructure Search.
    """
    args = parse_command_line()
    substructure_search(args)