$gene_seq_id = $1;
$gene_seq_status = $2;
$gene_seq_CDS_number = $3;
...
$gene_seq_endopen = $9;
$gene_seq_complement = $10;

Is there a specific reason you're not using a hash here? Then you can access the data more easily, and pass it around more easily.

my %gene_seq = (    id => $1,
                status => $2,
            CDS_number => $3,
                  ...     # the yaddah yaddah yaddah operator
);

return \%gene_seq; # return a reference to the hash, to be dereffed at
+ the other end
[download]

Apologies for not helping with your specific problem more, but once the code is down to a reasonable size, I'm sure it'll be much easier to debug. :)

Jasper

ps do '='s need to be escaped in a regex? (rhetorical question) Also, using different regex delimiters (# instead of /) might make it more readable again when you are escaping a load of characters. Well, unless you're using a lot of comments in a //x regex! Then you could use a pipe, or whatever.