def clean_sequence( sequence ):
    """Given a sequence string, return a crap-free, standardized DNA version."""
    s = sequence.replace( '\r', '' ).split( '\n' )  # separate each line
    if s[0][0] == '>': s = s[ 1 :]                  # remove defline
    s = ''.join( s )                                # make one long string
    s = s.replace( ' ', '' ).replace( '\t', '' )    # remove spaces
    return s.upper().replace( 'U', 'T' )