BioCompass.py 文件源码

def download_mibig(outputdir, version='1.3'):
    """ Download and extract MIBiG files into outputdir
    """
    assert version in ['1.0', '1.1', '1.2', '1.3'], \
            "Invalid version of MIBiG"

    server = 'http://mibig.secondarymetabolites.org'
    filename = "mibig_gbk_%s.tar.gz" % version
    url = urlparse.urljoin(server, filename)

    with tempfile.NamedTemporaryFile(delete=True) as f:
        u = urllib2.urlopen(url)
        f.write(u.read())
        f.file.flush()
        tar = tarfile.open(f.name)
        tar.extractall(path=outputdir)
        tar.close()

    # MIBiG was packed with strange files ._*gbk. Let's remove it
    for f in [f for f in os.listdir(outputdir) if f[:2] == '._']:
        os.remove(os.path.join(outputdir, f))

#def gbk2tablegen(gb_file, strain_id=None):
#def cds_from_gbk(gb_file, strain_id=None):