open GRAPHIN, '>', 'data-in'
    or die "Can't open data-in: $!\n";
open GRAPHOUT, '>', data-out'
    or die "Can't open data-out: $!\n";
while (<>)    # You can pass the input file name on the command line
{
    my @f = split /\s/;    # Like awk: split at white space

    print GRAPHIN  $f[0], ' ', $f[3], "\n";
    print GRAPHOUT $f[0], ' ', $f[4], "\n";
}
close GRAPHIN;            # Could live without these
close GRAPHOUT;
system './graph';         # Execute your graph program