Exemple #1
0
def join(*args):
    flags.assert_flag('sabmark-dir')
    flags.assert_flag('sabmark-set')
    if flags.config.sabmark_set == 'twilight':
        return os.path.join(flags.config.sabmark_dir, __TWILIGHT, *args)
    else:
        return os.path.join(flags.config.sabmark_dir, __SUPERFAMILY, *args)
Exemple #2
0
def search_bowdb_pdb(prot_files, bow_db=None, chain='',
                     limit=100, min=0.0, max=1.0):
    flags.assert_flag('bow-db')

    if bow_db is None:
        bow_db = flags.config.bow_db
    else:
        bow_db = ejoin(bow_db)
    if isinstance(prot_files, basestring):
        prot_files = [prot_files]

    file_hash = hashlib.md5(''.join(prot_files)).hexdigest()
    outname = 'bowsearch_limit-%d_min-%f_max-%f_chain-%s_%s' \
        % (limit, min, max, chain, file_hash)
    outname = ejoin(outname)

    def runsearch():
        print >> open(outname, 'w+'), \
            cmd('bowsearch', '-output', 'csv',
                '-limit', '%d' % limit,
                '-min', '%f' % min,
                '-max', '%f' % max,
                '--chain', chain,
                bow_db, *prot_files)
    cached([outname], runsearch)

    print outname

    rows = []
    for row in csv.DictReader(open(outname), delimiter='\t'):
        row['Cosine'] = float(row['Cosine'])
        row['Euclid'] = float(row['Euclid'])
        rows.append(row)
    return rows