[Bioperl-l] Newbie: Format GenBank

[Roy Chaudhuri]

Hi Adlai,

In Perl you can open a string as if it was a file:

my $string;
open my $fh, '>', \$string or die $!;
my $seqOut=Bio::SeqIO->new(-fh=>$fh, -format=>'genbank';

$seqOut->write_seq($seq) should now write to the string.

However, are you sure this is your problem? Printing to STDOUT (which is 
what SeqIO does if you don't specify a file) should work fine with a CGI 
script. Your sequence is being displayed as one line because HTML 
ignores newline characters, but you can get around that by using a <pre> 
tag to specify pre-formatted text:

my $seqOut = new Bio::SeqIO(-format => 'genbank');
print "<pre>\n";
$seqOut->write_seq($seq);

Hope this helps.
Roy.

adlai burman wrote:
> 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
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