my %ranges_by_seq;

while (<>) {
    my ($seq, $p1, $p2) = (split)[0, 2, 3];
    ($p2, $p1) = ($p1, $p2) if $p2 < $p1;
    push @{ $ranges_by_seq{$seq} }, [ $p1, $p2 ];
}

for my $seq (keys(%ranges_by_seq)) {
    my $ranges = $ranges_by_seq{$seq};

    system(extractseq =>
        "-sequence=$seq.seq",
        "-auto",
        "-stdout",
        "-separate",
        "-reg=" . join(',', map { "$_->[0]..$_->[1]" } @$ranges),
    )
        and die("system: $?/$!\n");
}