def fromovl(args):
    """
    %prog graph nucmer2ovl.ovl fastafile

    Build overlap graph from ovl file which is converted using NUCMER2OVL.
    """
    p = OptionParser(fromovl.__doc__)
    opts, args = p.parse_args(args)

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

    ovlfile, fastafile = args
    ovl = OVL(ovlfile)
    g = ovl.graph

    fw = open("contained.ids", "w")
    print("\n".join(sorted(ovl.contained)), file=fw)

    graph_to_agp(g, ovlfile, fastafile, exclude=ovl.contained, verbose=False)
def fromovl ( args ) : p = OptionParser ( fromovl . __doc__ ) opts , args = p . parse_args ( args ) if len ( args ) != 2 : sys . exit ( not p . print_help ( ) ) ovlfile , fastafile = args ovl = OVL ( ovlfile ) g = ovl . graph fw = open ( "contained.ids" , "w" ) print ( "\n" . join ( sorted ( ovl . contained ) ) , file = fw ) graph_to_agp ( g , ovlfile , fastafile , exclude = ovl . contained , verbose = False )
%prog graph nucmer2ovl.ovl fastafile

    Build overlap graph from ovl file which is converted using NUCMER2OVL.