open(TMP, ">/tmp/t$$.sql") || die "can't open temp file: $!";
# Set nocount to avoid the "xxx rows affected" message in isql
print TMP "set nocount on\ngo\nselect * from the_table\ngo\n";
close(TMP);
# Note: -b flag suppresses column headers.
open(ISQL, "isql -Ujoe -Pjoespwd -Smyserver -s'%%^^%%' -w 1024 -b -i /tmp/t$$.sql") || die "Can't run isql: $!";
while(<ISQL>) {
    chomp;
    my @row = split(/%%^^%%/, $_);
    .... do something with the @row of data....
}
close(ISQL);