Rather than writing a subroutine to do the job, you could use Perl's quoting constructs. They also avoid the need to escape the double quotes you are wrapping around the string.

$ perl -le '
> $seq_num = 1234;
> $quoted_seq_num = qq{"$seq_num"};
> print qq{$seq_num - $quoted_seq_num};'
1234 - "1234"
$
[download]

The code would become

$return_val = system($grph_gen_multi_seq,
    $data_source_contents[2],
    qq{"$data_source_contents[2]"},
    $seq_num,
    qq{"$seq_num"},
    $data_source_contents[1]);
[download]

Cheers,

JohnGG