Bioperl: Creating a SeqIO object

[Aaron J Mackey]

I think you might want to do something like this, using IO::Scalar to turn
your string into a pseudo-filehandle:

$seqs = param('seqs'); # grab your CGI form variable.

$fh = new IO::Scalar \$seqs;

$in = new Bio::SeqIO -fh => $fh, -format => 'Fasta';

while($seq = $in->next_seq()) {

	# do stuff with each $seq.

}


-Aaron

On Fri, 26 May 2000, gert thijs wrote:

> Hello,
> 
> I hope this is not a stupid question, but I still haven't captured all the
> gory details of perl yet.
> I am developping a web interface where one can enter some DNA sequences that
> will be processed. Those DNA sequences should be in Fasta format. When I read
> the inputs of the web interface the sequences are stored as one long string in
> a variable $dnaseq. Now I am first writing this string to a file and then I
> use the filehandle to read the sequences into a new SeqIO object. 
> But I was wondering if I can do this without writing $dnaseq to a file. 
> 
> tnx,
> Gert Thijs
> 
> 

-- 
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