comparison subsearch/subsearch.py @ 7:12822efbd4a4

Uploaded

6:9d1f982555ba

import shutil

def parse_command_line():
    parser = argparse.ArgumentParser()
    parser.add_argument('-i', '--infile', required=True, help='Molecule file.')
    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')

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

    tmp = tempfile.NamedTemporaryFile(delete=False)
    cmd = 'obabel %s -O %s %s -ifs -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()

        sys.stdout.write(stdout)
        sys.stdout.write(stderr)
    return (tmp.name, query)


def substructure_search( args ):

    pool = multiprocessing.Pool( args.processors )
    for query in open( args.infile ):
        pool.apply_async(mp_helper, args=(query.strip(), args), callback=mp_callback)
        #mp_callback( mp_helper(query.strip(), args) )
    pool.close()
    pool.join()

    if args.oformat == 'names':
        out_handle = open( args.outfile, 'w' )

7:12822efbd4a4

import shutil

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')

        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()

        sys.stdout.write(stdout)
        sys.stdout.write(stderr)
    return (tmp.name, query)


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.wrtie('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' )