[Bioperl-l] Newbie: Format GenBank

[adlai burman]

I have finally got past two major hurdles (for me) only to get stumped:
1. I have written a perl script that can take a genbank formated text  
file as a filehandle and do all sorts of nifty (for me) things with it.
2. I have gotten my BioPerl installation working on a web hosting  
service so my advisor can use this through a browser.

BUT the code I have to fetch GB record can print it as a single HTML  
line, and what I need is for it to assign the retrieved file to a  
scaler variable. I am going blind trying to figure out how access  
(not write) the gb file from an SeqIO object and assign it to a  
variable.

Here's an example of the code I have going on the server:

#!/usr/bin/perl
print "Content-type: text/html\n\n";
use Bio::SeqIO;
use Bio::DB::GenBank;

$genBank = new Bio::DB::GenBank;  # This object knows how to talk to  
GenBank

my $seq = $genBank->get_Seq_by_acc('DQ897681');  # get a record by  
accession

my $seqOut = new Bio::SeqIO(-format => 'genbank');

$seqOut->write_seq($seq);


exit;

where 'DQ897861' will be replaced by a CGI post.

I know that write_seq is not what I need, and I assume that this is a  
simple problem but can anyone tell me how to assign the retrieved gb  
file to a scaler?

Thanks,
Adlai