The typical Perl way to interact with a RDBMS is to use a DBI and the DBD for you RDBMS which I assume is Sybase. You might have to google around to find the correct DBD package. Another way deal with this would be to treat the output from isql just as you would any other program.

my $cmd="isql $connect-string";
open ISQL, "|$cmd" or die "couldn't open $cmd:$!\n";
print ISQL <<end;
select * from whatever;
...
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... that code snippet would query the database. You would need a second script that would execute and read the output. Something like this ...

my $cmd="exec_isql.pl";
open OUT, "$cmd|" or die "couldn't open $cmd:$!\n";
my @results = <OUT>;
print "First row is " . $results[0] ."\n";
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