def bed(args):
    """
    %prog bed bedfile bamfiles

    Convert bam files to bed.
    """
    p = OptionParser(bed.__doc__)
    opts, args = p.parse_args(args)

    if len(args) < 2:
        sys.exit(not p.print_help())

    bedfile = args[0]
    bamfiles = args[1:]
    for bamfile in bamfiles:
        cmd = "bamToBed -i {0}".format(bamfile)
        sh(cmd, outfile=bedfile, append=True)
def bed ( args ) : p = OptionParser ( bed . __doc__ ) opts , args = p . parse_args ( args ) if len ( args ) < 2 : sys . exit ( not p . print_help ( ) ) bedfile = args [ 0 ] bamfiles = args [ 1 : ] for bamfile in bamfiles : cmd = "bamToBed -i {0}" . format ( bamfile ) sh ( cmd , outfile = bedfile , append = True )
%prog bed bedfile bamfiles

    Convert bam files to bed.