[Bioperl-l] Parsing sequence records in memory

[Ewan Birney]

On Sun, 15 Dec 2002, Peter Schattner wrote:

> Hi folks
> 
> A question.
> 
> If I have, say, a fasta sequence or Genbank record stored in a perl variable
> in memory (either the complete record in a scalar or each line as an entry in
> an array), is it possible to have SeqIO parse that record and create a Seq
> object directly?  That is, without printing the record to a file first and
> then reading it back in with SeqIO.  (I guess writing records to a file is
> not such a big deal, but I would prefer not to be creating and destroying
> lots of temporary files)
> 

use  IO::String, the syntax is in the Bio::SeqIO documentation

my $stringio = IO::String->new($string);      
my $out =bBio::SeqIO->new('-fh' => $stringio,
                          '-format' => 'fasta');






> TIA
> 
> Peter
> 
> 
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