Source code for twobitreader.download

"""
downloads a .2bit genome from UCSC
.. note:: please comply with the restrictions of use at
http://hgdownload.cse.ucsc.edu/downloads.html

and do not over-use this module

By default, genomes are saved to the current directory
"""
from urllib2 import urlopen, URLError
from shutil import copyfileobj
from os.path import exists, join
from os import getcwd

def save_genome(name, destdir=None, mode='ftp'):
    """
    tries to download a genome from UCSC by name
    
    for example, 'hg19' is at
    ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/hg19.2bit
    """
    urlpath = "%s://hgdownload.cse.ucsc.edu/goldenPath/%s/bigZips/%s.2bit" % \
              (mode, name, name)
    if destdir is None: destdir = getcwd()
    remotefile = urlopen(urlpath)
    assert exists(destdir), 'Desination directory %s does not exist' % destdir
    with open(join(destdir,"%s.2bit" % name), 'wb') as destfile:
        copyfileobj(remotefile, destfile)
    return

def main():
    import sys
    if len(sys.argv)!=2:
        sys.exit('Example: python -m twobitreader.download hg19')
    else:
        save_genome(sys.argv[1])

if __name__ == '__main__': main()